OS name is: Windows 7 arch: amd64

Executing:
win64\progressiveMauve --output=C:\Users\Melissa-Jad\Desktop\Strains\Comparing t
he 31 S.aureus Strains\31 strains 05 05 2012 --output-guide-tree=C:\Users\Meliss
a-Jad\Desktop\Strains\Comparing the 31 S.aureus Strains\31 strains 05 05 2012.gu
ide_tree --backbone-output=C:\Users\Melissa-Jad\Desktop\Strains\Comparing the 31
S.aureus Strains\31 strains 05 05 2012.backbone C:\Users\Melissa-Jad\Desktop\St
rains\1 Staphylococcus aureus 04-02981.gb C:\Users\Melissa-Jad\Desktop\Strains\2
nd Staphylococcus aureus RF122.gb C:\Users\Melissa-Jad\Desktop\Strains\3rd Staph
ylococcus aureus subsp. aureus 11819-97.gb C:\Users\Melissa-Jad\Desktop\Strains\
4th Staphylococcus aureus subsp. aureus COL.gb C:\Users\Melissa-Jad\Desktop\Stra
ins\5th Staphylococcus aureus subsp. aureus ECT-R 2.gb C:\Users\Melissa-Jad\Desk
top\Strains\6th Staphylococcus aureus subsp. aureus ED133.gb C:\Users\Melissa-Ja
d\Desktop\Strains\7th Staphylococcus aureus subsp. aureus ED98.gb C:\Users\Melis
sa-Jad\Desktop\Strains\8th Staphylococcus aureus subsp. aureus JH1.gb C:\Users\M
elissa-Jad\Desktop\Strains\9th Staphylococcus aureus subsp. aureus JH9.gb C:\Use
rs\Melissa-Jad\Desktop\Strains\10th Staphylococcus aureus subsp. aureus JKD6159.
gb C:\Users\Melissa-Jad\Desktop\Strains\11th Staphylococcus aureus subsp. aureus
LGA251.gb C:\Users\Melissa-Jad\Desktop\Strains\12th Staphylococcus aureus subsp
. aureus M013.gb C:\Users\Melissa-Jad\Desktop\Strains\13th Staphylococcus aureus
subsp. aureus strain MRSA252.gb C:\Users\Melissa-Jad\Desktop\Strains\14th Staph
ylococcus aureus strain MSSA476.gb C:\Users\Melissa-Jad\Desktop\Strains\15th Sta
phylococcus aureus subsp. aureus MW2 DNA.gb C:\Users\Melissa-Jad\Desktop\Strains
\16th Staphylococcus aureus subsp. aureus Mu3 DNA.gb C:\Users\Melissa-Jad\Deskto
p\Strains\17th Staphylococcus aureus subsp. aureus Mu50 DNA.gb C:\Users\MelissaJad\Desktop\Strains\18th Staphylococcus aureus subsp. aureus N315 DNA.gb C:\User
s\Melissa-Jad\Desktop\Strains\19th Staphylococcus aureus subsp. aureus NCTC 8325
.gb C:\Users\Melissa-Jad\Desktop\Strains\20th Staphylococcus aureus subsp. aureu
s ST398 complete genome, isolate SO385.gb C:\Users\Melissa-Jad\Desktop\Strains\2
1st Staphylococcus aureus subsp. aureus T0131, complete genome.gb C:\Users\Melis
sa-Jad\Desktop\Strains\22nd Staphylococcus aureus subsp. aureus TCH60, complete
genome.gb C:\Users\Melissa-Jad\Desktop\Strains\23rd Staphylococcus aureus subsp.
aureus TW20, complete genome.gb C:\Users\Melissa-Jad\Desktop\Strains\24th Staph
ylococcus aureus subsp. aureus USA300_FPR3757, complete genome.gb C:\Users\Melis
sa-Jad\Desktop\Strains\25th Staphylococcus aureus subsp. aureus USA300_TCH1516,
complete genome.gb C:\Users\Melissa-Jad\Desktop\Strains\26th Staphylococcus aure
us subsp. aureus str. JKD6008, complete genome.gb C:\Users\Melissa-Jad\Desktop\S
trains\27th Staphylococcus aureus subsp. aureus str. Newman DNA, complete genome
.gb C:\Users\Melissa-Jad\Desktop\Strains\28th Staphylococcus aureus subsp. aureu
s MSHR1132.gb C:\Users\Melissa-Jad\Desktop\Strains\29th Staphylococcus aureus su
bsp. aureus VC40.gb C:\Users\Melissa-Jad\Desktop\Strains\30th Staphylococcus aur
eus subsp. aureus HO 5096 0412.gb C:\Users\Melissa-Jad\Desktop\Strains\31st Stap
hylococcus aureus subsp. aureus 71193.gb
Storing raw sequence at C:\Users\MELISS~1\AppData\Local\Temp\raw619.tmp
Sequence loaded successfully.
C:\Users\Melissa-Jad\Desktop\Strains\1 Staphylococcus aureus 04-02981.gb 2821452
base pairs.
Storing raw sequence at C:\Users\MELISS~1\AppData\Local\Temp\raw658.tmp
Sequence loaded successfully.
C:\Users\Melissa-Jad\Desktop\Strains\2nd Staphylococcus aureus RF122.gb 2742531
base pairs.
Storing raw sequence at C:\Users\MELISS~1\AppData\Local\Temp\raw698.tmp
Sequence loaded successfully.
C:\Users\Melissa-Jad\Desktop\Strains\3rd Staphylococcus aureus subsp. aureus 118
19-97.gb 2846546 base pairs.
Storing raw sequence at C:\Users\MELISS~1\AppData\Local\Temp\raw6C8.tmp
Sequence loaded successfully.
C:\Users\Melissa-Jad\Desktop\Strains\4th Staphylococcus aureus subsp. aureus COL
.gb 2809422 base pairs.
Storing raw sequence at C:\Users\MELISS~1\AppData\Local\Temp\raw707.tmp

Sequence loaded successfully.

C:\Users\Melissa-Jad\Desktop\Strains\5th Staphylococcus aureus subsp. aureus ECT
-R 2.gb 2729540 base pairs.
Storing raw sequence at C:\Users\MELISS~1\AppData\Local\Temp\raw737.tmp
Sequence loaded successfully.
C:\Users\Melissa-Jad\Desktop\Strains\6th Staphylococcus aureus subsp. aureus ED1
33.gb 2832478 base pairs.
Storing raw sequence at C:\Users\MELISS~1\AppData\Local\Temp\raw767.tmp
Sequence loaded successfully.
C:\Users\Melissa-Jad\Desktop\Strains\7th Staphylococcus aureus subsp. aureus ED9
8.gb 2824404 base pairs.
Storing raw sequence at C:\Users\MELISS~1\AppData\Local\Temp\raw7A6.tmp
Sequence loaded successfully.
C:\Users\Melissa-Jad\Desktop\Strains\8th Staphylococcus aureus subsp. aureus JH1
.gb 2906507 base pairs.
Storing raw sequence at C:\Users\MELISS~1\AppData\Local\Temp\raw7E5.tmp
Sequence loaded successfully.
C:\Users\Melissa-Jad\Desktop\Strains\9th Staphylococcus aureus subsp. aureus JH9
.gb 2906700 base pairs.
Storing raw sequence at C:\Users\MELISS~1\AppData\Local\Temp\raw815.tmp
Sequence loaded successfully.
C:\Users\Melissa-Jad\Desktop\Strains\10th Staphylococcus aureus subsp. aureus JK
D6159.gb 2811435 base pairs.
Storing raw sequence at C:\Users\MELISS~1\AppData\Local\Temp\raw855.tmp
Sequence loaded successfully.
C:\Users\Melissa-Jad\Desktop\Strains\11th Staphylococcus aureus subsp. aureus LG
A251.gb 2750834 base pairs.
Storing raw sequence at C:\Users\MELISS~1\AppData\Local\Temp\raw884.tmp
Sequence loaded successfully.
C:\Users\Melissa-Jad\Desktop\Strains\12th Staphylococcus aureus subsp. aureus M0
13.gb 2788636 base pairs.
Storing raw sequence at C:\Users\MELISS~1\AppData\Local\Temp\raw8C4.tmp
Sequence loaded successfully.
C:\Users\Melissa-Jad\Desktop\Strains\13th Staphylococcus aureus subsp. aureus st
rain MRSA252.gb 2902619 base pairs.
Storing raw sequence at C:\Users\MELISS~1\AppData\Local\Temp\raw903.tmp
Sequence loaded successfully.
C:\Users\Melissa-Jad\Desktop\Strains\14th Staphylococcus aureus strain MSSA476.g
b 2799802 base pairs.
Storing raw sequence at C:\Users\MELISS~1\AppData\Local\Temp\raw933.tmp
Sequence loaded successfully.
C:\Users\Melissa-Jad\Desktop\Strains\15th Staphylococcus aureus subsp. aureus MW
2 DNA.gb 2820462 base pairs.
Storing raw sequence at C:\Users\MELISS~1\AppData\Local\Temp\raw972.tmp
Sequence loaded successfully.
C:\Users\Melissa-Jad\Desktop\Strains\16th Staphylococcus aureus subsp. aureus Mu
3 DNA.gb 2880168 base pairs.
Storing raw sequence at C:\Users\MELISS~1\AppData\Local\Temp\raw9A2.tmp
Sequence loaded successfully.
C:\Users\Melissa-Jad\Desktop\Strains\17th Staphylococcus aureus subsp. aureus Mu
50 DNA.gb 2878529 base pairs.
Storing raw sequence at C:\Users\MELISS~1\AppData\Local\Temp\raw9D2.tmp
Sequence loaded successfully.
C:\Users\Melissa-Jad\Desktop\Strains\18th Staphylococcus aureus subsp. aureus N3
15 DNA.gb 2814816 base pairs.
Storing raw sequence at C:\Users\MELISS~1\AppData\Local\Temp\rawA11.tmp
Sequence loaded successfully.
C:\Users\Melissa-Jad\Desktop\Strains\19th Staphylococcus aureus subsp. aureus NC
TC 8325.gb 2821361 base pairs.
Storing raw sequence at C:\Users\MELISS~1\AppData\Local\Temp\rawA51.tmp

Sequence loaded successfully.

C:\Users\Melissa-Jad\Desktop\Strains\20th Staphylococcus aureus subsp. aureus
398 complete genome, isolate SO385.gb 2872582 base pairs.
Storing raw sequence at C:\Users\MELISS~1\AppData\Local\Temp\rawA81.tmp
Sequence loaded successfully.
C:\Users\Melissa-Jad\Desktop\Strains\21st Staphylococcus aureus subsp. aureus
131, complete genome.gb 2913900 base pairs.
Storing raw sequence at C:\Users\MELISS~1\AppData\Local\Temp\rawAB0.tmp
Sequence loaded successfully.
C:\Users\Melissa-Jad\Desktop\Strains\22nd Staphylococcus aureus subsp. aureus
H60, complete genome.gb 2802675 base pairs.
Storing raw sequence at C:\Users\MELISS~1\AppData\Local\Temp\rawAF0.tmp
Sequence loaded successfully.
C:\Users\Melissa-Jad\Desktop\Strains\23rd Staphylococcus aureus subsp. aureus
20, complete genome.gb 3043210 base pairs.
Storing raw sequence at C:\Users\MELISS~1\AppData\Local\Temp\rawB2F.tmp
Sequence loaded successfully.
C:\Users\Melissa-Jad\Desktop\Strains\24th Staphylococcus aureus subsp. aureus
A300_FPR3757, complete genome.gb 2872769 base pairs.
Storing raw sequence at C:\Users\MELISS~1\AppData\Local\Temp\rawB5F.tmp
Sequence loaded successfully.
C:\Users\Melissa-Jad\Desktop\Strains\25th Staphylococcus aureus subsp. aureus
A300_TCH1516, complete genome.gb 2872915 base pairs.
Storing raw sequence at C:\Users\MELISS~1\AppData\Local\Temp\rawB9E.tmp
Sequence loaded successfully.
C:\Users\Melissa-Jad\Desktop\Strains\26th Staphylococcus aureus subsp. aureus
r. JKD6008, complete genome.gb 2924344 base pairs.
Storing raw sequence at C:\Users\MELISS~1\AppData\Local\Temp\rawBCE.tmp
Sequence loaded successfully.
C:\Users\Melissa-Jad\Desktop\Strains\27th Staphylococcus aureus subsp. aureus
r. Newman DNA, complete genome.gb 2878897 base pairs.
Storing raw sequence at C:\Users\MELISS~1\AppData\Local\Temp\rawC0E.tmp
Sequence loaded successfully.
C:\Users\Melissa-Jad\Desktop\Strains\28th Staphylococcus aureus subsp. aureus
HR1132.gb 2762785 base pairs.
Storing raw sequence at C:\Users\MELISS~1\AppData\Local\Temp\rawC2E.tmp
Sequence loaded successfully.
C:\Users\Melissa-Jad\Desktop\Strains\29th Staphylococcus aureus subsp. aureus
40.gb 2692570 base pairs.
Storing raw sequence at C:\Users\MELISS~1\AppData\Local\Temp\rawC6D.tmp
Sequence loaded successfully.
C:\Users\Melissa-Jad\Desktop\Strains\30th Staphylococcus aureus subsp. aureus
5096 0412.gb 2832299 base pairs.
Storing raw sequence at C:\Users\MELISS~1\AppData\Local\Temp\rawC9D.tmp
Sequence loaded successfully.
C:\Users\Melissa-Jad\Desktop\Strains\31st Staphylococcus aureus subsp. aureus
193.gb 2715000 base pairs.
Using weight 15 mers for initial seeds
Creating sorted mer list
Create time was: 0 seconds.
Creating sorted mer list
Create time was: 1 seconds.
Creating sorted mer list
Create time was: 1 seconds.
Creating sorted mer list
Create time was: 1 seconds.
Creating sorted mer list
Create time was: 1 seconds.
Creating sorted mer list
Create time was: 1 seconds.

ST

T0

TC

TW

US

US

st

st

MS

VC

HO

71

Creating sorted mer list

Create time was: 0 seconds.
Creating sorted mer list
Create time was: 1 seconds.
Creating sorted mer list
Create time was: 1 seconds.
Creating sorted mer list
Create time was: 1 seconds.
Creating sorted mer list
Create time was: 1 seconds.
Creating sorted mer list
Create time was: 1 seconds.
Creating sorted mer list
Create time was: 0 seconds.
Creating sorted mer list
Create time was: 1 seconds.
Creating sorted mer list
Create time was: 1 seconds.
Creating sorted mer list
Create time was: 1 seconds.
Creating sorted mer list
Create time was: 1 seconds.
Creating sorted mer list
Create time was: 1 seconds.
Creating sorted mer list
Create time was: 0 seconds.
Creating sorted mer list
Create time was: 1 seconds.
Creating sorted mer list
Create time was: 1 seconds.
Creating sorted mer list
Create time was: 1 seconds.
Creating sorted mer list
Create time was: 1 seconds.
Creating sorted mer list
Create time was: 1 seconds.
Creating sorted mer list
Create time was: 1 seconds.
Creating sorted mer list
Create time was: 0 seconds.
Creating sorted mer list
Create time was: 1 seconds.
Creating sorted mer list
Create time was: 1 seconds.
Creating sorted mer list
Create time was: 1 seconds.
Creating sorted mer list
Create time was: 1 seconds.
Creating sorted mer list
Create time was: 1 seconds.
0%..1%..2%..3%..4%..5%..6%..7%..8%..9%..10%..
11%..12%..13%..14%..15%..16%..17%..18%..19%..20%..
21%..22%..23%..24%..25%..26%..27%..28%..29%..30%..
31%..32%..33%..34%..35%..36%..37%..38%..39%..40%..
41%..42%..43%..44%..45%..46%..47%..48%..49%..50%..
51%..52%..53%..54%..55%..56%..57%..58%..59%..60%..
61%..62%..63%..64%..65%..66%..67%..68%..69%..70%..
71%..72%..73%..74%..75%..76%..77%..78%..79%..80%..
81%..82%..83%..84%..85%..86%..87%..88%..89%..90%..
91%..92%..93%..94%..95%..96%..97%..98%..99%..done.

using default bp penalty: 150043

using default bp estimate min score: 450129
Starting with 633960 multi-matches
Computing genome content distance matrix...
Genome conservation distance matrix:
0
0.0877608
0.0725771
0.0711681
0.0183331
0.092809
8
0.0456404
0.0208364
0.0209105
0.0923713
0.085607
6
0.0860071
0.0870396
0.0717535
0.0704131
0.017995
0.018287
0.0147867
0.0649757
0.116667
0.0849381
0.0897507
0.0958171
0.0674732
0.0682136
0.0845789
0.068293
0.208912
0.0613001
0.0838756
0.0847359
0.0877608
0
0.0919648
0.0874218
0.0821319
0.084016
8
0.0893187
0.0958969
0.096647
0.097461
0.079477
6
0.0889019
0.107388
0.0858967
0.0869083
0.090135
6
0.0901022
0.0906945
0.0859643
0.11446 0.108511
0.094341
0.11925 0.0960438
0.0957886
0.111424
0.09739
0.218912
0.078916
0.106509
0.0946115
0.0725771
0.0919648
0
0.0676085
0.0712704
0.084419
0.0740223
0.0729611
0.074643
0.0849803
0.0892142
0.0908548
0.0922173
0.0539122
0.0498369
0.0785591
0.0787805
0.0791768
0.0572564
0.117177
0.0937648
0.0814833
0.104619
0.0651843
0.0662154
0.0957328
0.0773313
0.21042 0.0690823
0.0829517
0.0918824
0.0711681
0.0874218
0.0676085
0
0.0631265
0.081780
7
0.0617734
0.0724488
0.074441
0.0895244
0.079004
8
0.0848315
0.095474
0.0550686
0.0533717
0.076254
4
0.0756607
0.0701853
0.0353167
0.104971
0.068515
3
0.0829028
0.0811188
0.0291887
0.0311237
0.074439
9
0.0485045
0.210706
0.027596
0.0781697
0.087644
7
0.0183331
0.0821319
0.0712704
0.0631265
0
0.080788
2
0.0355654
0.0367226
0.036876
0.0842998
0.075488
3
0.0767015
0.0868568
0.0595847
0.0607617
0.029332
4
0.0296424
0.0171856
0.0619378
0.105835
0.075301
3
0.0819164
0.092308
0.0593501
0.0602955
0.079368
5
0.0630374
0.204423
0.0484393
0.0751431
0.072537
4
0.0928098
0.0840168
0.084419
0.0817807
0.0807882
0
0.0836282
0.0943953
0.0950708
0.0925116
0.070861
3
0.0861026
0.0989504
0.0798986
0.0784669
0.096758
9
0.0969789
0.0925139
0.077914
0.112542
0.103687
0.0849337
0.11517 0.0814209
0.0829029
0.104292
0.095398
4
0.220993
0.0790345
0.0928351
0.0922735
0.0456404
0.0893187
0.0740223
0.0617734
0.0355654
0.0836282
0
0.0507314
0.0508449
0.0949548
0.083861
2
0.0881852
0.0978867
0.0622261
0.0630628
0.052450
9
0.0525393
0.0447991
0.0640255
0.110383
0.090961
1
0.0866425
0.104964
0.0671347
0.0670573
0.094933
4
0.0819288
0.211523
0.0618732
0.0827252
0.089834
7
0.0208364
0.0958969
0.0729611
0.0724488
0.0367226
0.0943953
0.0507314
0
0.000186299
0.0950338
0.091397
2
0.0970206
0.091687
0.0713539
0.0702865
0.033997
8
0.0342923
0.0344632
0.0650803
0.123097
0.10043
0.0902899
0.102874
0.0716504
0.0713634
0.0941867
0.0783984
0.217683
0.0747733
0.0846801
0.09628
0.0209105
0.096647
0.074643
0.074441
0.036876
0.0950708
0.0508449
0.000186299
0
0.0950436
0.094065

1
0.0973544
0.0919313
0.0733101
0.0724639
0.034115
8
0.0344104
0.0345329
0.0652913
0.123985
0.100602
0.0905321
0.103756
0.0725526
0.0722656
0.0950836
0.0793076
0.217746
0.0750174
0.0850126
0.0973955
0.0923713
0.097461
0.0849803
0.0895244
0.0842998
0.0925116
0.0949548
0.0950338
0.0950436
0
0.095373
5
0.0906053
0.0945604
0.0812594
0.0770087
0.098213
0.0983914
0.0921694
0.0888407
0.113291
0.104075
0.0837625
0.118185
0.0794664
0.0792547
0.104177
0.102329
0.205179
0.088317
0.0862361
0.0846678
0.0856076
0.0794776
0.0892142
0.0790048
0.0754883
0.0708613
0.0838612
0.0913972
0.0940651
0.0953735
0
0.0769267
0.100781
0.0824367
0.0839898
0.091122
9
0.0913077
0.087128
0.0841536
0.105547
0.098376
0.0862605
0.108144
0.0890572
0.0900769
0.0986491
0.0883452
0.220597
0.0709197
0.0915094
0.0835203
0.0860071
0.0889019
0.0908548
0.0848315
0.0767015
0.0861026
0.0881852
0.0970206
0.0973544
0.0906053
0.0769267
0
0.0962354
0.0836369
0.0829345
0.090902
2
0.0905788
0.0850173
0.0883791
0.104308
0.091550
5
0.0802696
0.105201
0.0857448
0.0859581
0.094890
1
0.0957532
0.215442
0.0774124
0.0876522
0.082926
0.0870396
0.107388
0.0922173
0.095474
0.0868568
0.0989504
0.0978867
0.091687
0.0919313
0.0945604
0.100781
0.0962354
0
0.0924478
0.0905392
0.091491
1
0.0914776
0.0851524
0.0980504
0.105794
0.093743
9
0.0365896
0.10664 0.0884578
0.0889674
0.0917209
0.110921
0.215562
0.0979779
0.0781088
0.0813018
0.0717535
0.0858967
0.0539122
0.0550686
0.0595847
0.0798986
0.0622261
0.0713539
0.0733101
0.0812594
0.0824367
0.0836369
0.0924478
0
0.014212
0.077530
5
0.0777033
0.0709831
0.0531335
0.111262
0.086372
7
0.0820491
0.0988593
0.0561525
0.0564365
0.091898
0.0723802
0.208876
0.0560014
0.0775097
0.0835397
0.0704131
0.0869083
0.0498369
0.0533717
0.0607617
0.0784669
0.0630628
0.0702865
0.0724639
0.0770087
0.0839898
0.0829345
0.0905392
0.014212
0
0.075168
4
0.075347
0.0685347
0.0538098
0.109597
0.084298
1
0.0778284
0.0977835
0.0489132
0.0491944
0.090176
9
0.0734437
0.207869
0.0568492
0.074238
0.085596
9
0.017995
0.0901356
0.0785591
0.0762544
0.0293324
0.0967589
0.0524509
0.0339978
0.0341158
0.098213
0.0911229
0.0909022
0.0914911
0.0775305
0.0751684
0
0.00113751
0.0222047
0.0729946
0.12062 0.0786561
0.0940886
0.0933584
0.0734024
0.0743775
0.0803839
0.0728713
0.212248
0.0688717
0.089806
0.0922209
0.018287
0.0901022
0.0787805
0.0756607
0.0296424
0.0969789
0.0525393
0.0342923
0.0344104
0.0983914
0.0913077
0.0905788
0.0914776
0.0777033
0.075347
0.00113751
0
0.0217143
0.0731761
0.120639
0.07885
0.0940719
0.0933141
0.0737297
0.074705
0.0805646
0.0730548
0.212265
0.0690649
0.0897393
0.0922576
0.0147867
0.0906945
0.0791768
0.0701853
0.0171856
0.0925139
0.0447991
0.0344632
0.0345329
0.0921694
0.087128
0.0850173
0.0851524
0.0709831
0.0685347
0.0222047
0.0217143
0
0.0732597
0.115725
0.080740
3
0.0878706
0.0971978
0.0666916
0.06746 0.0833109
0.0755153
0.209334
0.0600868
0.0834596
0.0848423
0.0649757
0.0859643
0.0572564
0.0353167
0.0619378

0.077914
0.0640255
0.0650803
0.0652913
0.0888407
0.0841536
0.0883791
0.0980504
0.0531335
0.0538098
0.0729946
0.0731761
0.0732597
0
0.112299
0.078583
2
0.0853317
0.0861736
0.0370941
0.0374669
0.080353
3
0.0396506
0.214328
0.0248825
0.0806593
0.089810
8
0.116667
0.11446 0.117177
0.104971
0.105835
0.112542
0.110383
0.123097
0.123985
0.113291
0.105547
0.104308
0.105794
0.111262
0.109597
0.12062 0.120639
0.115725
0.112299
0
0.118799
0.0957466
0.128618
0.110196
0.111165
0.12035 0.122783
0.228646
0.100428
0.10184 0.0528278
0.0849381
0.108511
0.0937648
0.0685153
0.0753013
0.103687
0.0909611
0.10043 0.100602
0.104075
0.098376
0.0915505
0.0937439
0.0863727
0.0842981
0.0786561
0.07885 0.0807403
0.0785832
0.118799
0
0.093455
0.0523941
0.0658616
0.0657754
0.0400735
0.0778114
0.219419
0.0645797
0.0946893
0.0962708
0.0897507
0.094341
0.0814833
0.0829028
0.0819164
0.0849337
0.0866425
0.0902899
0.0905321
0.0837625
0.0862605
0.0802696
0.0365896
0.0820491
0.0778284
0.0940886
0.0940719
0.0878706
0.0853317
0.0957466
0.093455
0
0.106846
0.0817822
0.0822248
0.095364
1
0.102196
0.211976
0.0834132
0.0716975
0.073936
4
0.0958171
0.11925 0.104619
0.0811188
0.092308
0.11517
0.104964
0.102874
0.103756
0.118185
0.108144
0.105201
0.10664 0.0988593
0.0977835
0.0933584
0.093314
1
0.0971978
0.0861736
0.128618
0.0523941
0.106846
0
0.0809056
0.0810625
0.0544181
0.0854778
0.224429
0.0774707
0.109025
0.109212
0.0674732
0.0960438
0.0651843
0.0291887
0.0593501
0.0814209
0.0671347
0.0716504
0.0725526
0.0794664
0.0890572
0.0857448
0.0884578
0.0561525
0.0489132
0.0734024
0.0737297
0.0666916
0.0370941
0.110196
0.0658616
0.0817822
0.0809056
0
0.00037193
0.072940
2
0.045915
0.20562 0.0353942
0.0728839
0.0866611
0.0682136
0.0957886
0.0662154
0.0311237
0.0602955
0.0829029
0.0670573
0.0713634
0.0722656
0.0792547
0.0900769
0.0859581
0.0889674
0.0564365
0.0491944
0.0743775
0.074705
0.06746 0.0374669
0.111165
0.065775
4
0.0822248
0.0810625
0.00037193
0
0.0729207
0.0465789
0.205443
0.0359626
0.0734292
0.0880644
0.0845789
0.111424
0.0957328
0.0744399
0.0793685
0.104292
0.0949334
0.0941867
0.0950836
0.104177
0.0986491
0.0948901
0.0917209
0.091898
0.0901769
0.0803839
0.0805646
0.0833109
0.0803533
0.12035 0.040073
5
0.0953641
0.0544181
0.0729402
0.0729207
0
0.0792185
0.220067
0.0720507
0.0953667
0.0960072
0.068293
0.09739 0.0773313
0.0485045
0.0630374
0.095398
4
0.0819288
0.0783984
0.0793076
0.102329
0.088345
2
0.0957532
0.110921
0.0723802
0.0734437
0.072871
3
0.0730548
0.0755153
0.0396506
0.122783
0.077811
4
0.102196
0.0854778
0.045915
0.0465789
0.079218
5
0
0.221401
0.0360575
0.0951004
0.0923052
0.208912
0.218912
0.21042 0.210706
0.204423
0.220993
0.211523
0.217683
0.217746
0.205179
0.220597
0.215442
0.215562
0.208876
0.207869
0.212248
0.212265
0.209334
0.214328
0.228646
0.219419
0.211976
0.224429
0.20562 0.205443
0.220067
0.221401

0
0.210748
0.209466
0.209714
0.0613001
0.078916
0.0690823
0.027596
0.0484393
0.0790345
0.0618732
0.0747733
0.0750174
0.088317
0.0709197
0.0774124
0.0979779
0.0560014
0.0568492
0.0688717
0.0690649
0.0600868
0.0248825
0.100428
0.0645797
0.0834132
0.0774707
0.0353942
0.0359626
0.0720507
0.0360575
0.210748
0
0.080101
0.077886
8
0.0838756
0.106509
0.0829517
0.0781697
0.0751431
0.0928351
0.0827252
0.0846801
0.0850126
0.0862361
0.0915094
0.0876522
0.0781088
0.0775097
0.074238
0.089806
0.0897393
0.0834596
0.0806593
0.10184 0.094689
3
0.0716975
0.109025
0.0728839
0.0734292
0.095366
7
0.0951004
0.209466
0.080101
0
0.0779986
0.0847359
0.0946115
0.0918824
0.0876447
0.0725374
0.0922735
0.0898347
0.09628 0.0973955
0.0846678
0.083520
3
0.082926
0.0813018
0.0835397
0.0855969
0.092220
9
0.0922576
0.0848423
0.0898108
0.0528278
0.096270
8
0.0739364
0.109212
0.0866611
0.0880644
0.096007
2
0.0923052
0.209714
0.0778868
0.0779986
0
Writing guide tree to C:\Users\Melissa-Jad\Desktop\Strains\Comparing the 31 S.au
reus Strains\31 strains 05 05 2012.guide_tree
reading tree...
initializing alignment tree...
Constructing seed occurrence lists for repeat detection
Calculating pairwise breakpoint distances
Pair 0, 1 has 4252 initial LCBs
Pair 11, 28 has 3313 initial LCBs
Pair 19, 28 has 4733 initial LCBs
Pair 15, 20 has 2151 initial LCBs
Pair 2, 3 has 1732 initial LCBs
Pair 8, 30 has 5156 initial LCBs
Pair 6, 17 has 232 initial LCBs
Pair 4, 8 has 72 initial LCBs
Using scaled bp penalty: 311725
Using scaled bp penalty: 340197
Pair (0,1) has 4 well-supported breakpoints
Using scaled bp penalty: 326112
Pair (2,3) has 4 well-supported breakpoints
Using scaled bp penalty: 324357
Pair (15,20) has 1 well-supported breakpoints
Pair (11,28) has 1 well-supported breakpoints
Using scaled bp penalty: 294768
Using scaled bp penalty: 298763
Using scaled bp penalty: 374728
Pair (19,28) has 1 well-supported breakpoints
Pair (6,17) has 1 well-supported breakpoints
Pair (8,30) has 1 well-supported breakpoints
Using scaled bp penalty: 387316
Pair (4,8) has 1 well-supported breakpoints
Pair 0, 2 has 1753 initial LCBs
Pair 2, 4 has 1755 initial LCBs
Pair 11, 29 has 4286 initial LCBs
Pair 19, 29 has 4251 initial LCBs
Pair 9, 10 has 4399 initial LCBs
Pair 4, 9 has 4327 initial LCBs
Pair 6, 18 has 1688 initial LCBs
Pair 15, 21 has 9836 initial LCBs
Using scaled bp penalty: 333003

Pair (0,2) has 4 well-supported breakpoints

Using scaled bp penalty: 334884
Pair (2,4) has 1 well-supported breakpoints
Using scaled bp penalty: 301449
Using scaled bp penalty: 311874
Using scaled bp penalty: 292922
Using scaled bp penalty: 345456
Pair (6,18) has 6 well-supported breakpoints
Pair (11,29) has 4 well-supported breakpoints
Pair (9,10) has 1 well-supported breakpoints
Pair (19,29) has 1 well-supported breakpoints
Using scaled bp penalty: 316483
Pair (4,9) has 1 well-supported breakpoints
Using scaled bp penalty: 303165
Pair (15,21) has 2 well-supported breakpoints
Pair 0, 3 has 1803 initial LCBs
Pair 2, 5 has 3732 initial LCBs
Pair 6, 19 has 5508 initial LCBs
Using scaled bp penalty: 335031
Pair 11, 30 has 4358 initial LCBs
Pair (0,3) has 4 well-supported breakpoints
Pair 4, 10 has 3219 initial LCBs
Pair 19, 30 has 140 initial LCBs
Pair 9, 11 has 4313 initial LCBs
Using scaled bp penalty: 316318
Pair (2,5) has 7 well-supported breakpoints
Using scaled bp penalty: 281935
Using scaled bp penalty: 318386
Pair (6,19) has 4 well-supported breakpoints
Using scaled bp penalty: 328841
Pair 15, 22 has 2819 initial LCBs
Pair (11,30) has 4 well-supported breakpoints
Using scaled bp penalty: 362287
Pair (4,10) has 1 well-supported breakpoints
Pair (19,30) has 1 well-supported breakpoints
Using scaled bp penalty: 307855
Pair (9,11) has 4 well-supported breakpoints
Using scaled bp penalty: 304144
Pair (15,22) has 4 well-supported breakpoints
Pair 0, 4 has 22 initial LCBs
Pair 2, 6 has 1997 initial LCBs
Pair 12, 13 has 5623 initial LCBs
Using scaled bp penalty: 418016
Pair (0,4) has 1 well-supported breakpoints
Pair 4, 11 has 3185 initial LCBs
Pair 6, 20 has 2577 initial LCBs
Pair 9, 12 has 5893 initial LCBs
Pair 20, 21 has 7675 initial LCBs
Using scaled bp penalty: 330932
Pair (2,6) has 6 well-supported breakpoints
Using scaled bp penalty: 307374
Using scaled bp penalty: 327119
Using scaled bp penalty: 305368
Pair (6,20) has 4 well-supported breakpoints
Pair (4,11) has 4 well-supported breakpoints
Pair (12,13) has 4 well-supported breakpoints
Pair 15, 23 has 1894 initial LCBs
Using scaled bp penalty: 302534
Using scaled bp penalty: 304015
Pair (9,12) has 1 well-supported breakpoints

Using scaled bp penalty: 331819

Pair 0, 5 has 3818 initial LCBs
Pair (15,23) has 1 well-supported breakpoints
Pair (20,21) has 2 well-supported breakpoints
Using scaled bp penalty: 304881
Pair (0,5) has 4 well-supported breakpoints
Pair 2, 7 has 1865 initial LCBs
Pair 4, 12 has 4631 initial LCBs
Pair 12, 14 has 5475 initial LCBs
Pair 6, 21 has 9614 initial LCBs
Using scaled bp penalty: 332452
Pair (2,7) has 7 well-supported breakpoints
Pair 9, 13 has 4773 initial LCBs
Using scaled bp penalty: 312963
Using scaled bp penalty: 307945
Pair (4,12) has 1 well-supported breakpoints
Pair 15, 24 has 1890 initial LCBs
Pair (12,14) has 1 well-supported breakpoints
Using scaled bp penalty: 313256
Pair 20, 22 has 195 initial LCBs
Using scaled bp penalty: 320707
Using scaled bp penalty: 330425
Pair (6,21) has 5 well-supported breakpoints
Pair (15,24) has 1 well-supported breakpoints
Pair (9,13) has 4 well-supported breakpoints
Pair 0, 6 has 288 initial LCBs
Using scaled bp penalty: 362951
Pair (20,22) has 4 well-supported breakpoints
Using scaled bp penalty: 373409
Pair (0,6) has 1 well-supported breakpoints
Pair 2, 8 has 1869 initial LCBs
Pair 12, 15 has 5064 initial LCBs
Pair 4, 13 has 1445 initial LCBs
Using scaled bp penalty: 330046
Pair (2,8) has 7 well-supported breakpoints
Pair 6, 22 has 3171 initial LCBs
Using scaled bp penalty: 306658
Using scaled bp penalty: 352059
Pair 15, 25 has 2373 initial LCBs
Pair (4,13) has 1 well-supported breakpoints
Pair 9, 14 has 4362 initial LCBs
Pair (12,15) has 1 well-supported breakpoints
Pair 20, 23 has 893 initial LCBs
Using scaled bp penalty: 288868
Pair 0, 7 has 70 initial LCBs
Using scaled bp penalty: 321931
Pair (15,25) has 6 well-supported breakpoints
Pair (6,22) has 4 well-supported breakpoints
Using scaled bp penalty: 326684
Pair (9,14) has 1 well-supported breakpoints
Using scaled bp penalty: 342753
Pair (20,23) has 4 well-supported breakpoints
Using scaled bp penalty: 413769
Pair (0,7) has 1 well-supported breakpoints
Pair 2, 9 has 4718 initial LCBs
Pair 4, 14 has 1481 initial LCBs
Pair 12, 16 has 5061 initial LCBs
Using scaled bp penalty: 315543
Pair (2,9) has 1 well-supported breakpoints
Using scaled bp penalty: 350300

Pair 6, 23 has 1873 initial LCBs

Pair (4,14) has 1 well-supported breakpoints
Pair 15, 26 has 1574 initial LCBs
Using scaled bp penalty: 306676
Pair 9, 15 has 5011 initial LCBs
Pair (12,16) has 1 well-supported breakpoints
Pair 20, 24 has 888 initial LCBs
Using scaled bp penalty: 340889
Pair 0, 8 has 70 initial LCBs
Using scaled bp penalty: 332581
Pair (6,23) has 7 well-supported breakpoints
Pair (15,26) has 1 well-supported breakpoints
Using scaled bp penalty: 297682
Pair (9,15) has 1 well-supported breakpoints
Using scaled bp penalty: 413644
Pair (0,8) has 1 well-supported breakpoints
Pair 2, 10 has 3924 initial LCBs
Using scaled bp penalty: 342880
Pair (20,24) has 4 well-supported breakpoints
Using scaled bp penalty: 309743
Pair (2,10) has 4 well-supported breakpoints
Pair 12, 17 has 4652 initial LCBs
Pair 4, 15 has 88 initial LCBs
Pair 15, 27 has 39952 initial LCBs
Pair 6, 24 has 1887 initial LCBs
Using scaled bp penalty: 399594
Pair (4,15) has 1 well-supported breakpoints
Pair 0, 9 has 4742 initial LCBs
Pair 9, 16 has 5000 initial LCBs
Using scaled bp penalty: 315306
Pair (12,17) has 1 well-supported breakpoints
Using scaled bp penalty: 341002
Pair (6,24) has 7 well-supported breakpoints
Pair 20, 25 has 154 initial LCBs
Using scaled bp penalty: 297447
Using scaled bp penalty: 305471
Pair 2, 11 has 3768 initial LCBs
Pair (9,16) has 1 well-supported breakpoints
Pair (0,9) has 1 well-supported breakpoints
Using scaled bp penalty: 382198
Pair (20,25) has 3 well-supported breakpoints
Using scaled bp penalty: 307517
Pair (2,11) has 4 well-supported breakpoints
Pair 12, 18 has 5647 initial LCBs
Using scaled bp penalty: 173338
Pair 4, 16 has 88 initial LCBs
Pair 6, 25 has 2808 initial LCBs
Pair 0, 10 has 3663 initial LCBs
Using scaled bp penalty: 297897
Pair 9, 17 has 4596 initial LCBs
Pair (12,18) has 1 well-supported breakpoints
Using scaled bp penalty: 399084
Pair (4,16) has 1 well-supported breakpoints
Using scaled bp penalty: 302036
Pair (6,25) has 4 well-supported breakpoints
Pair (15,27) has 1 well-supported breakpoints
Using scaled bp penalty: 314679
Pair 20, 26 has 732 initial LCBs
Pair (0,10) has 1 well-supported breakpoints
Using scaled bp penalty: 305743

Pair 2, 12 has 5538 initial LCBs

Pair (9,17) has 1 well-supported breakpoints
Using scaled bp penalty: 325549
Pair (20,26) has 1 well-supported breakpoints
Using scaled bp penalty: 305678
Pair 12, 19 has 3473 initial LCBs
Pair (2,12) has 4 well-supported breakpoints
Pair 0, 11 has 3528 initial LCBs
Pair 6, 26 has 1757 initial LCBs
Pair 15, 28 has 1548 initial LCBs
Pair 4, 17 has 25 initial LCBs
Using scaled bp penalty: 287798
Pair (12,19) has 1 well-supported breakpoints
Pair 9, 18 has 4779 initial LCBs
Using scaled bp penalty: 319773
Pair (6,26) has 1 well-supported breakpoints
Pair 20, 27 has 40368 initial LCBs
Using scaled bp penalty: 314129
Using scaled bp penalty: 338357
Pair (0,11) has 4 well-supported breakpoints
Using scaled bp penalty: 419974
Pair (4,17) has 1 well-supported breakpoints
Pair (15,28) has 1 well-supported breakpoints
Using scaled bp penalty: 310252
Pair (9,18) has 1 well-supported breakpoints
Pair 2, 13 has 1327 initial LCBs
Using scaled bp penalty: 360631
Pair 12, 20 has 3989 initial LCBs
Pair (2,13) has 4 well-supported breakpoints
Pair 6, 27 has 40147 initial LCBs
Pair 0, 12 has 4758 initial LCBs
Pair 15, 29 has 3333 initial LCBs
Pair 4, 18 has 1381 initial LCBs
Using scaled bp penalty: 167113
Using scaled bp penalty: 303627
Pair (12,20) has 6 well-supported breakpoints
Using scaled bp penalty: 312712
Pair 9, 19 has 5956 initial LCBs
Using scaled bp penalty: 348549
Pair (4,18) has 1 well-supported breakpoints
Using scaled bp penalty: 308939
Pair (0,12) has 1 well-supported breakpoints
Pair (15,29) has 1 well-supported breakpoints
Using scaled bp penalty: 278267
Pair (20,27) has 4 well-supported breakpoints
Pair 2, 14 has 1178 initial LCBs
Pair (9,19) has 1 well-supported breakpoints
Using scaled bp penalty: 173977
Using scaled bp penalty: 366885
Pair (2,14) has 1 well-supported breakpoints
Pair 4, 19 has 5117 initial LCBs
Pair 0, 13 has 1699 initial LCBs
Pair 15, 30 has 5172 initial LCBs
Pair (6,27) has 4 well-supported breakpoints
Using scaled bp penalty: 334187
Pair (0,13) has 1 well-supported breakpoints
Pair 12, 21 has 355 initial LCBs
Using scaled bp penalty: 287745
Using scaled bp penalty: 305673
Pair 9, 20 has 5283 initial LCBs

Pair (4,19) has 1 well-supported breakpoints

Pair (15,30) has 1 well-supported breakpoints
Pair 20, 28 has 662 initial LCBs
Using scaled bp penalty: 387777
Pair 2, 15 has 1953 initial LCBs
Using scaled bp penalty: 344639
Pair (20,28) has 1 well-supported breakpoints
Using scaled bp penalty: 290017
Pair (12,21) has 2 well-supported breakpoints
Pair (9,20) has 1 well-supported breakpoints
Using scaled bp penalty: 324494
Pair (2,15) has 4 well-supported breakpoints
Pair 0, 14 has 1692 initial LCBs
Pair 6, 28 has 1429 initial LCBs
Pair 4, 20 has 1979 initial LCBs
Using scaled bp penalty: 336122
Using scaled bp penalty: 348645
Pair (0,14) has 1 well-supported breakpoints
Pair (6,28) has 1 well-supported breakpoints
Pair 16, 17 has 68 initial LCBs
Pair 20, 29 has 3582 initial LCBs
Using scaled bp penalty: 329107
Pair (4,20) has 1 well-supported breakpoints
Pair 12, 22 has 5058 initial LCBs
Using scaled bp penalty: 412287
Pair (16,17) has 1 well-supported breakpoints
Pair 2, 16 has 1964 initial LCBs
Using scaled bp penalty: 302362
Pair (20,29) has 4 well-supported breakpoints
Pair 9, 21 has 9743 initial LCBs
Using scaled bp penalty: 286710
Using scaled bp penalty: 324182
Pair 6, 29 has 3309 initial LCBs
Pair (12,22) has 6 well-supported breakpoints
Pair (2,16) has 4 well-supported breakpoints
Pair 0, 15 has 84 initial LCBs
Using scaled bp penalty: 318665
Using scaled bp penalty: 317226
Pair (6,29) has 7 well-supported breakpoints
Using scaled bp penalty: 418593
Pair (0,15) has 1 well-supported breakpoints
Pair 4, 21 has 8982 initial LCBs
Pair 16, 18 has 1832 initial LCBs
Pair (9,21) has 2 well-supported breakpoints
Pair 20, 30 has 4710 initial LCBs
Using scaled bp penalty: 332144
Pair (16,18) has 4 well-supported breakpoints
Pair 12, 23 has 5414 initial LCBs
Pair 2, 17 has 1840 initial LCBs
Using scaled bp penalty: 319791
Using scaled bp penalty: 300255
Pair (20,30) has 1 well-supported breakpoints
Pair (4,21) has 2 well-supported breakpoints
Pair 6, 30 has 5322 initial LCBs
Using scaled bp penalty: 310774
Using scaled bp penalty: 323625
Pair (12,23) has 4 well-supported breakpoints
Pair (2,17) has 1 well-supported breakpoints
Pair 9, 22 has 6441 initial LCBs
Pair 0, 16 has 85 initial LCBs

Using scaled bp penalty: 308900

Pair (6,30) has 1 well-supported breakpoints
Pair 16, 19 has 5879 initial LCBs
Using scaled bp penalty: 418095
Pair (0,16) has 1 well-supported breakpoints
Using scaled bp penalty: 272174
Pair (9,22) has 1 well-supported breakpoints
Using scaled bp penalty: 269157
Pair 4, 22 has 2413 initial LCBs
Pair 21, 22 has 8543 initial LCBs
Pair (16,19) has 1 well-supported breakpoints
Pair 2, 18 has 1498 initial LCBs
Using scaled bp penalty: 305556
Pair (4,22) has 1 well-supported breakpoints
Using scaled bp penalty: 355559
Using scaled bp penalty: 286446
Pair (2,18) has 4 well-supported breakpoints
Pair 7, 8 has 2 initial LCBs
Pair (21,22) has 2 well-supported breakpoints
Pair 0, 17 has 25 initial LCBs
Pair 9, 23 has 4473 initial LCBs
Pair 12, 24 has 5409 initial LCBs
Using scaled bp penalty: 449794
Pair (7,8) has 1 well-supported breakpoints
Pair 16, 20 has 2171 initial LCBs
Using scaled bp penalty: 424090
Pair (0,17) has 1 well-supported breakpoints
Using scaled bp penalty: 310079
Using scaled bp penalty: 323218
Pair (12,24) has 4 well-supported breakpoints
Using scaled bp penalty: 324085
Pair (9,23) has 1 well-supported breakpoints
Pair (16,20) has 1 well-supported breakpoints
Pair 2, 19 has 5640 initial LCBs
Pair 4, 23 has 1438 initial LCBs
Using scaled bp penalty: 352411
Pair 7, 9 has 4657 initial LCBs
Pair (4,23) has 1 well-supported breakpoints
Pair 21, 23 has 9702 initial LCBs
Using scaled bp penalty: 273421
Pair (2,19) has 1 well-supported breakpoints
Pair 0, 18 has 1595 initial LCBs
Using scaled bp penalty: 301902
Pair (7,9) has 4 well-supported breakpoints
Pair 12, 25 has 4059 initial LCBs
Using scaled bp penalty: 344055
Pair 9, 24 has 4461 initial LCBs
Pair (0,18) has 4 well-supported breakpoints
Using scaled bp penalty: 319978
Pair 16, 21 has 9799 initial LCBs
Using scaled bp penalty: 306347
Pair (21,23) has 2 well-supported breakpoints
Pair (12,25) has 8 well-supported breakpoints
Using scaled bp penalty: 323515
Pair 4, 24 has 1432 initial LCBs
Pair (9,24) has 1 well-supported breakpoints
Pair 2, 20 has 2320 initial LCBs
Using scaled bp penalty: 303188
Pair 7, 10 has 3988 initial LCBs
Using scaled bp penalty: 350996

Pair (4,24) has 1 well-supported breakpoints

Pair 0, 19 has 5542 initial LCBs
Pair (16,21) has 2 well-supported breakpoints
Using scaled bp penalty: 303599
Pair (2,20) has 4 well-supported breakpoints
Using scaled bp penalty: 306784
Pair (7,10) has 4 well-supported breakpoints
Using scaled bp penalty: 274052
Pair 12, 26 has 5457 initial LCBs
Pair (0,19) has 1 well-supported breakpoints
Pair 21, 24 has 9684 initial LCBs
Pair 9, 25 has 5408 initial LCBs
Using scaled bp penalty: 281254
Pair (12,26) has 1 well-supported breakpoints
Pair 4, 25 has 2125 initial LCBs
Pair 16, 22 has 2832 initial LCBs
Using scaled bp penalty: 289885
Using scaled bp penalty: 319361
Pair (9,25) has 3 well-supported breakpoints
Pair 7, 11 has 3756 initial LCBs
Pair 2, 21 has 9401 initial LCBs
Using scaled bp penalty: 323355
Pair (21,24) has 2 well-supported breakpoints
Pair (4,25) has 3 well-supported breakpoints
Pair 0, 20 has 2272 initial LCBs
Using scaled bp penalty: 304204
Pair (16,22) has 4 well-supported breakpoints
Using scaled bp penalty: 299260
Pair (7,11) has 4 well-supported breakpoints
Using scaled bp penalty: 315601
Pair (0,20) has 1 well-supported breakpoints
Pair 12, 27 has 40431 initial LCBs
Using scaled bp penalty: 320395
Pair (2,21) has 2 well-supported breakpoints
Pair 9, 26 has 4742 initial LCBs
Pair 4, 26 has 1158 initial LCBs
Pair 7, 12 has 4951 initial LCBs
Pair 21, 25 has 7509 initial LCBs
Using scaled bp penalty: 292285
Pair 16, 23 has 1914 initial LCBs
Pair (9,26) has 1 well-supported breakpoints
Using scaled bp penalty: 346917
Pair (4,26) has 1 well-supported breakpoints
Pair 0, 21 has 9420 initial LCBs
Using scaled bp penalty: 331351
Using scaled bp penalty: 306393
Pair (16,23) has 1 well-supported breakpoints
Pair (7,12) has 4 well-supported breakpoints
Pair 2, 22 has 2922 initial LCBs
Using scaled bp penalty: 170440
Using scaled bp penalty: 301462
Pair (21,25) has 4 well-supported breakpoints
Using scaled bp penalty: 289313
Using scaled bp penalty: 309014
Pair (2,22) has 7 well-supported breakpoints
Pair 9, 27 has 38656 initial LCBs
Pair (0,21) has 2 well-supported breakpoints
Pair 4, 27 has 38768 initial LCBs
Pair (12,27) has 4 well-supported breakpoints
Pair 7, 13 has 1724 initial LCBs

Pair 16, 24 has 1921 initial LCBs

Using scaled bp penalty: 334763
Pair (7,13) has 1 well-supported breakpoints
Using scaled bp penalty: 329957
Pair (16,24) has 1 well-supported breakpoints
Pair 21, 26 has 9652 initial LCBs
Pair 2, 23 has 1772 initial LCBs
Pair 0, 22 has 2739 initial LCBs
Pair 12, 28 has 5483 initial LCBs
Using scaled bp penalty: 179645
Using scaled bp penalty: 180329
Using scaled bp penalty: 343749
Pair (2,23) has 1 well-supported breakpoints
Using scaled bp penalty: 300858
Pair (0,22) has 4 well-supported breakpoints
Using scaled bp penalty: 292458
Using scaled bp penalty: 297993
Pair (12,28) has 1 well-supported breakpoints
Pair (21,26) has 2 well-supported breakpoints
Pair 7, 14 has 1761 initial LCBs
Pair (9,27) has 1 well-supported breakpoints
Pair (4,27) has 1 well-supported breakpoints
Pair 16, 25 has 2380 initial LCBs
Using scaled bp penalty: 336305
Pair (7,14) has 4 well-supported breakpoints
Using scaled bp penalty: 321678
Pair 2, 24 has 1767 initial LCBs
Pair (16,25) has 6 well-supported breakpoints
Pair 0, 23 has 1700 initial LCBs
Pair 12, 29 has 4263 initial LCBs
Pair 21, 27 has 42163 initial LCBs
Using scaled bp penalty: 342234
Pair (2,24) has 1 well-supported breakpoints
Using scaled bp penalty: 340394
Pair (0,23) has 1 well-supported breakpoints
Pair 9, 28 has 4672 initial LCBs
Pair 4, 28 has 1181 initial LCBs
Using scaled bp penalty: 325129
Pair (12,29) has 4 well-supported breakpoints
Using scaled bp penalty: 369048
Pair (4,28) has 1 well-supported breakpoints
Using scaled bp penalty: 310966
Pair (9,28) has 1 well-supported breakpoints
Pair 7, 15 has 186 initial LCBs
Pair 16, 26 has 1568 initial LCBs
Using scaled bp penalty: 391967
Pair (7,15) has 1 well-supported breakpoints
Pair 2, 25 has 2677 initial LCBs
Using scaled bp penalty: 332317
Pair 0, 24 has 1687 initial LCBs
Pair (16,26) has 1 well-supported breakpoints
Using scaled bp penalty: 173578
Pair 12, 30 has 2932 initial LCBs
Using scaled bp penalty: 339314
Using scaled bp penalty: 300970
Pair (0,24) has 1 well-supported breakpoints
Pair (2,25) has 9 well-supported breakpoints
Pair 4, 29 has 2738 initial LCBs
Pair 9, 29 has 5013 initial LCBs
Using scaled bp penalty: 320648

Pair (12,30) has 1 well-supported breakpoints

Using scaled bp penalty: 329333
Using scaled bp penalty: 313814
Pair (21,27) has 2 well-supported breakpoints
Pair (4,29) has 1 well-supported breakpoints
Pair (9,29) has 1 well-supported breakpoints
Pair 16, 27 has 39927 initial LCBs
Pair 7, 16 has 188 initial LCBs
Pair 2, 26 has 1702 initial LCBs
Pair 0, 25 has 2403 initial LCBs
Using scaled bp penalty: 391489
Pair (7,16) has 1 well-supported breakpoints
Using scaled bp penalty: 326227
Pair (2,26) has 1 well-supported breakpoints
Using scaled bp penalty: 316097
Pair (0,25) has 6 well-supported breakpoints
Pair 13, 14 has 81 initial LCBs
Pair 9, 30 has 5370 initial LCBs
Pair 4, 30 has 4330 initial LCBs
Pair 21, 28 has 9340 initial LCBs
Using scaled bp penalty: 425080
Pair (13,14) has 4 well-supported breakpoints
Using scaled bp penalty: 173323
Using scaled bp penalty: 315974
Pair (9,30) has 1 well-supported breakpoints
Using scaled bp penalty: 333060
Pair (4,30) has 1 well-supported breakpoints
Using scaled bp penalty: 317710
Pair 2, 27 has 39889 initial LCBs
Pair 0, 26 has 1371 initial LCBs
Pair (21,28) has 2 well-supported breakpoints
Pair (16,27) has 1 well-supported breakpoints
Pair 7, 17 has 94 initial LCBs
Using scaled bp penalty: 339199
Pair (0,26) has 1 well-supported breakpoints
Pair 13, 15 has 1875 initial LCBs
Pair 10, 11 has 2444 initial LCBs
Using scaled bp penalty: 391212
Pair (7,17) has 1 well-supported breakpoints
Pair 5, 6 has 3851 initial LCBs
Using scaled bp penalty: 325945
Pair (13,15) has 1 well-supported breakpoints
Using scaled bp penalty: 326800
Pair (10,11) has 1 well-supported breakpoints
Using scaled bp penalty: 317412
Pair (5,6) has 7 well-supported breakpoints
Using scaled bp penalty: 174953
Pair 16, 28 has 1556 initial LCBs
Pair 21, 29 has 8316 initial LCBs
Pair 0, 27 has 39495 initial LCBs
Using scaled bp penalty: 338076
Pair (16,28) has 1 well-supported breakpoints
Pair 7, 18 has 1648 initial LCBs
Pair 10, 12 has 4938 initial LCBs
Pair (2,27) has 1 well-supported breakpoints
Using scaled bp penalty: 334268
Using scaled bp penalty: 343902
Pair (7,18) has 7 well-supported breakpoints
Pair 5, 7 has 3766 initial LCBs
Pair 13, 16 has 1871 initial LCBs

Pair (21,29) has 2 well-supported breakpoints

Using scaled bp penalty: 325701
Using scaled bp penalty: 294305
Pair (13,16) has 1 well-supported breakpoints
Pair (10,12) has 1 well-supported breakpoints
Using scaled bp penalty: 302755
Pair (5,7) has 7 well-supported breakpoints
Using scaled bp penalty: 176293
Pair 16, 29 has 3326 initial LCBs
Pair 7, 19 has 5616 initial LCBs
Pair 2, 28 has 1528 initial LCBs
Using scaled bp penalty: 309030
Pair (16,29) has 1 well-supported breakpoints
Pair (0,27) has 1 well-supported breakpoints
Using scaled bp penalty: 338051
Pair (2,28) has 1 well-supported breakpoints
Using scaled bp penalty: 266160
Pair 13, 17 has 1697 initial LCBs
Pair 21, 30 has 5847 initial LCBs
Pair 5, 8 has 3766 initial LCBs
Pair 10, 13 has 3681 initial LCBs
Pair (7,19) has 1 well-supported breakpoints
Using scaled bp penalty: 335298
Pair (13,17) has 1 well-supported breakpoints
Using scaled bp penalty: 301853
Using scaled bp penalty: 319066
Pair (5,8) has 7 well-supported breakpoints
Using scaled bp penalty: 331055
Pair (10,13) has 1 well-supported breakpoints
Pair 16, 30 has 5166 initial LCBs
Pair (21,30) has 2 well-supported breakpoints
Pair 0, 28 has 1381 initial LCBs
Pair 2, 29 has 3240 initial LCBs
Using scaled bp penalty: 349497
Using scaled bp penalty: 305624
Pair 7, 20 has 2538 initial LCBs
Pair (0,28) has 1 well-supported breakpoints
Pair (16,30) has 1 well-supported breakpoints
Using scaled bp penalty: 318351
Pair 5, 9 has 4289 initial LCBs
Pair (2,29) has 1 well-supported breakpoints
Pair 13, 18 has 1118 initial LCBs
Using scaled bp penalty: 294765
Pair 10, 14 has 3849 initial LCBs
Pair (7,20) has 1 well-supported breakpoints
Using scaled bp penalty: 361819
Using scaled bp penalty: 305282
Pair (13,18) has 4 well-supported breakpoints
Pair 22, 23 has 1344 initial LCBs
Pair (5,9) has 7 well-supported breakpoints
Using scaled bp penalty: 316912
Pair (10,14) has 1 well-supported breakpoints
Pair 0, 29 has 3080 initial LCBs
Using scaled bp penalty: 321201
Pair (22,23) has 4 well-supported breakpoints
Pair 17, 18 has 1588 initial LCBs
Pair 2, 30 has 5244 initial LCBs
Using scaled bp penalty: 317070
Pair (0,29) has 1 well-supported breakpoints
Using scaled bp penalty: 332024

Pair (17,18) has 1 well-supported breakpoints

Pair 13, 19 has 5327 initial LCBs
Pair 7, 21 has 9154 initial LCBs
Using scaled bp penalty: 306129
Pair 5, 10 has 1498 initial LCBs
Pair (2,30) has 1 well-supported breakpoints
Pair 10, 15 has 3798 initial LCBs
Using scaled bp penalty: 280823
Using scaled bp penalty: 335474
Pair (5,10) has 1 well-supported breakpoints
Pair (13,19) has 1 well-supported breakpoints
Pair 22, 24 has 1343 initial LCBs
Pair 0, 30 has 4802 initial LCBs
Using scaled bp penalty: 308283
Using scaled bp penalty: 307155
Pair (10,15) has 1 well-supported breakpoints
Pair 17, 19 has 5397 initial LCBs
Pair (7,21) has 5 well-supported breakpoints
Using scaled bp penalty: 320982
Pair (22,24) has 4 well-supported breakpoints
Using scaled bp penalty: 315880
Pair 3, 4 has 1559 initial LCBs
Pair (0,30) has 1 well-supported breakpoints
Using scaled bp penalty: 275224
Pair (17,19) has 1 well-supported breakpoints
Using scaled bp penalty: 346785
Pair 5, 11 has 2608 initial LCBs
Pair (3,4) has 1 well-supported breakpoints
Pair 13, 20 has 1943 initial LCBs
Pair 10, 16 has 3816 initial LCBs
Using scaled bp penalty: 313998
Pair (5,11) has 4 well-supported breakpoints
Pair 7, 22 has 3035 initial LCBs
Using scaled bp penalty: 313627
Pair (13,20) has 1 well-supported breakpoints
Pair 1, 2 has 4555 initial LCBs
Pair 22, 25 has 318 initial LCBs
Using scaled bp penalty: 306905
Pair (10,16) has 1 well-supported breakpoints
Using scaled bp penalty: 291575
Pair (7,22) has 4 well-supported breakpoints
Pair 17, 20 has 2105 initial LCBs
Pair 3, 5 has 3783 initial LCBs
Using scaled bp penalty: 306018
Using scaled bp penalty: 359860
Pair (22,25) has 6 well-supported breakpoints
Pair (1,2) has 4 well-supported breakpoints
Using scaled bp penalty: 321433
Pair (17,20) has 1 well-supported breakpoints
Using scaled bp penalty: 319980
Pair 5, 12 has 4781 initial LCBs
Pair (3,5) has 1 well-supported breakpoints
Pair 13, 21 has 9555 initial LCBs
Using scaled bp penalty: 296710
Pair 10, 17 has 3384 initial LCBs
Pair (5,12) has 7 well-supported breakpoints
Pair 7, 23 has 1755 initial LCBs
Pair 1, 3 has 4372 initial LCBs
Pair 22, 26 has 1010 initial LCBs
Using scaled bp penalty: 312591

Using scaled bp penalty: 334336

Pair (7,23) has 4 well-supported breakpoints
Using scaled bp penalty: 319606
Pair (10,17) has 1 well-supported breakpoints
Using scaled bp penalty: 312189
Pair (1,3) has 1 well-supported breakpoints
Pair (13,21) has 5 well-supported breakpoints
Using scaled bp penalty: 314857
Pair 3, 6 has 1691 initial LCBs
Pair (22,26) has 1 well-supported breakpoints
Pair 17, 21 has 9171 initial LCBs
Pair 5, 13 has 3562 initial LCBs
Using scaled bp penalty: 348793
Pair (3,6) has 7 well-supported breakpoints
Using scaled bp penalty: 311575
Using scaled bp penalty: 322611
Pair 1, 4 has 3862 initial LCBs
Pair (17,21) has 5 well-supported breakpoints
Pair (5,13) has 7 well-supported breakpoints
Pair 10, 18 has 3552 initial LCBs
Pair 7, 24 has 1760 initial LCBs
Pair 13, 22 has 2474 initial LCBs
Pair 22, 27 has 42625 initial LCBs
Using scaled bp penalty: 319491
Pair (1,4) has 1 well-supported breakpoints
Using scaled bp penalty: 334750
Pair (7,24) has 4 well-supported breakpoints
Using scaled bp penalty: 316685
Pair (10,18) has 1 well-supported breakpoints
Pair 3, 7 has 1697 initial LCBs
Using scaled bp penalty: 296830
Pair (13,22) has 1 well-supported breakpoints
Using scaled bp penalty: 333187
Pair 5, 14 has 3719 initial LCBs
Pair (3,7) has 4 well-supported breakpoints
Pair 17, 22 has 2643 initial LCBs
Pair 1, 5 has 2404 initial LCBs
Using scaled bp penalty: 324624
Using scaled bp penalty: 299025
Pair (5,14) has 7 well-supported breakpoints
Pair (17,22) has 1 well-supported breakpoints
Pair 7, 25 has 2683 initial LCBs
Pair 10, 19 has 4540 initial LCBs
Using scaled bp penalty: 162864
Pair 13, 23 has 1408 initial LCBs
Using scaled bp penalty: 316874
Pair (1,5) has 1 well-supported breakpoints
Using scaled bp penalty: 303034
Pair (7,25) has 6 well-supported breakpoints
Using scaled bp penalty: 288116
Pair 3, 8 has 1709 initial LCBs
Using scaled bp penalty: 357227
Pair (10,19) has 1 well-supported breakpoints
Pair (13,23) has 4 well-supported breakpoints
Pair (22,27) has 4 well-supported breakpoints
Using scaled bp penalty: 330334
Pair (3,8) has 4 well-supported breakpoints
Pair 5, 15 has 4036 initial LCBs
Pair 17, 23 has 1596 initial LCBs
Pair 1, 6 has 4423 initial LCBs

Using scaled bp penalty: 299607

Pair (5,15) has 4 well-supported breakpoints
Using scaled bp penalty: 341537
Pair (17,23) has 1 well-supported breakpoints
Using scaled bp penalty: 309601
Pair 10, 20 has 3845 initial LCBs
Pair 7, 26 has 1572 initial LCBs
Pair (1,6) has 1 well-supported breakpoints
Pair 13, 24 has 1388 initial LCBs
Pair 3, 9 has 5074 initial LCBs
Using scaled bp penalty: 324720
Pair (7,26) has 1 well-supported breakpoints
Using scaled bp penalty: 297467
Pair 22, 28 has 862 initial LCBs
Pair (10,20) has 1 well-supported breakpoints
Using scaled bp penalty: 356797
Pair (13,24) has 4 well-supported breakpoints
Using scaled bp penalty: 326030
Pair (22,28) has 1 well-supported breakpoints
Using scaled bp penalty: 309321
Pair (3,9) has 4 well-supported breakpoints
Pair 5, 16 has 4057 initial LCBs
Pair 1, 7 has 4457 initial LCBs
Pair 17, 24 has 1585 initial LCBs
Using scaled bp penalty: 299315
Using scaled bp penalty: 300752
Pair 7, 27 has 40078 initial LCBs
Pair (5,16) has 4 well-supported breakpoints
Pair (1,7) has 4 well-supported breakpoints
Using scaled bp penalty: 340413
Pair (17,24) has 1 well-supported breakpoints
Pair 13, 25 has 2284 initial LCBs
Pair 10, 21 has 8419 initial LCBs
Pair 22, 29 has 4709 initial LCBs
Pair 3, 10 has 3655 initial LCBs
Using scaled bp penalty: 306108
Pair (13,25) has 3 well-supported breakpoints
Using scaled bp penalty: 283660
Using scaled bp penalty: 323867
Pair (22,29) has 4 well-supported breakpoints
Pair (3,10) has 4 well-supported breakpoints
Pair 1, 8 has 4470 initial LCBs
Pair 5, 17 has 3642 initial LCBs
Using scaled bp penalty: 313781
Using scaled bp penalty: 168604
Pair 17, 25 has 2309 initial LCBs
Pair (10,21) has 2 well-supported breakpoints
Using scaled bp penalty: 299755
Using scaled bp penalty: 305279
Pair (1,8) has 4 well-supported breakpoints
Pair (5,17) has 4 well-supported breakpoints
Using scaled bp penalty: 317852
Pair (17,25) has 3 well-supported breakpoints
Pair 13, 26 has 1235 initial LCBs
Pair (7,27) has 1 well-supported breakpoints
Pair 3, 11 has 3615 initial LCBs
Pair 22, 30 has 5717 initial LCBs
Using scaled bp penalty: 333286
Pair (13,26) has 1 well-supported breakpoints
Pair 10, 22 has 4673 initial LCBs

Pair 1, 9 has 4428 initial LCBs

Using scaled bp penalty: 315748
Pair 5, 18 has 3556 initial LCBs
Pair (3,11) has 1 well-supported breakpoints
Using scaled bp penalty: 283422
Pair (22,30) has 1 well-supported breakpoints
Pair 17, 26 has 1342 initial LCBs
Using scaled bp penalty: 298676
Using scaled bp penalty: 284785
Pair (1,9) has 1 well-supported breakpoints
Using scaled bp penalty: 325404
Pair (10,22) has 4 well-supported breakpoints
Pair 7, 28 has 1531 initial LCBs
Pair (5,18) has 7 well-supported breakpoints
Using scaled bp penalty: 328803
Pair (17,26) has 1 well-supported breakpoints
Pair 13, 27 has 40053 initial LCBs
Using scaled bp penalty: 329860
Pair (7,28) has 1 well-supported breakpoints
Pair 3, 12 has 5676 initial LCBs
Pair 1, 10 has 2359 initial LCBs
Using scaled bp penalty: 301315
Pair 23, 24 has 4 initial LCBs
Pair 5, 19 has 4602 initial LCBs
Pair (3,12) has 7 well-supported breakpoints
Pair 10, 23 has 3933 initial LCBs
Pair 17, 27 has 39194 initial LCBs
Pair 7, 29 has 2944 initial LCBs
Using scaled bp penalty: 323202
Using scaled bp penalty: 449460
Pair (23,24) has 4 well-supported breakpoints
Pair (1,10) has 4 well-supported breakpoints
Using scaled bp penalty: 279208
Using scaled bp penalty: 176326
Using scaled bp penalty: 309957
Pair (10,23) has 1 well-supported breakpoints
Pair (5,19) has 1 well-supported breakpoints
Using scaled bp penalty: 315957
Pair (7,29) has 4 well-supported breakpoints
Pair (13,27) has 1 well-supported breakpoints
Pair 3, 13 has 1222 initial LCBs
Using scaled bp penalty: 175918
Pair 1, 11 has 2880 initial LCBs
Using scaled bp penalty: 358871
Pair (3,13) has 4 well-supported breakpoints
Pair 23, 25 has 1038 initial LCBs
Pair 5, 20 has 4098 initial LCBs
Pair 10, 24 has 3932 initial LCBs
Pair 7, 30 has 5147 initial LCBs
Using scaled bp penalty: 310168
Pair (1,11) has 1 well-supported breakpoints
Using scaled bp penalty: 332482
Pair (23,25) has 6 well-supported breakpoints
Pair (17,27) has 1 well-supported breakpoints
Using scaled bp penalty: 290520
Using scaled bp penalty: 308571
Pair (5,20) has 4 well-supported breakpoints
Pair 13, 28 has 1069 initial LCBs
Using scaled bp penalty: 300243
Pair (10,24) has 1 well-supported breakpoints

Pair (7,30) has 1 well-supported breakpoints

Using scaled bp penalty: 357456
Pair (13,28) has 1 well-supported breakpoints
Pair 3, 14 has 1280 initial LCBs
Pair 1, 12 has 5692 initial LCBs
Using scaled bp penalty: 361456
Pair (3,14) has 4 well-supported breakpoints
Pair 17, 28 has 1328 initial LCBs
Using scaled bp penalty: 285750
Pair 10, 25 has 4154 initial LCBs
Pair 8, 9 has 4672 initial LCBs
Pair 23, 26 has 132 initial LCBs
Pair (1,12) has 1 well-supported breakpoints
Pair 5, 21 has 8229 initial LCBs
Using scaled bp penalty: 351308
Pair (17,28) has 1 well-supported breakpoints
Using scaled bp penalty: 372980
Pair (23,26) has 1 well-supported breakpoints
Pair 13, 29 has 3274 initial LCBs
Using scaled bp penalty: 297107
Using scaled bp penalty: 301889
Pair (10,25) has 4 well-supported breakpoints
Pair (8,9) has 4 well-supported breakpoints
Using scaled bp penalty: 315607
Pair 3, 15 has 1924 initial LCBs
Using scaled bp penalty: 325975
Pair (13,29) has 4 well-supported breakpoints
Pair (5,21) has 5 well-supported breakpoints
Pair 1, 13 has 4046 initial LCBs
Using scaled bp penalty: 327753
Pair (3,15) has 1 well-supported breakpoints
Pair 17, 29 has 2970 initial LCBs
Pair 23, 27 has 39894 initial LCBs
Using scaled bp penalty: 314281
Pair (1,13) has 1 well-supported breakpoints
Pair 8, 10 has 3972 initial LCBs
Pair 10, 26 has 3242 initial LCBs
Using scaled bp penalty: 317646
Pair (17,29) has 1 well-supported breakpoints
Pair 13, 30 has 5025 initial LCBs
Using scaled bp penalty: 303197
Pair (8,10) has 4 well-supported breakpoints
Pair 5, 22 has 4973 initial LCBs
Using scaled bp penalty: 310927
Pair (10,26) has 4 well-supported breakpoints
Using scaled bp penalty: 317535
Pair 3, 16 has 1914 initial LCBs
Pair (13,30) has 1 well-supported breakpoints
Pair 1, 14 has 4172 initial LCBs
Using scaled bp penalty: 275916
Pair (5,22) has 4 well-supported breakpoints
Using scaled bp penalty: 179246
Using scaled bp penalty: 328596
Pair (3,16) has 1 well-supported breakpoints
Using scaled bp penalty: 312892
Pair 17, 30 has 4655 initial LCBs
Pair (1,14) has 1 well-supported breakpoints
Pair 8, 11 has 3778 initial LCBs
Pair 10, 27 has 40410 initial LCBs
Using scaled bp penalty: 315733

Pair (23,27) has 4 well-supported breakpoints

Using scaled bp penalty: 298817
Pair (17,30) has 1 well-supported breakpoints
Pair (8,11) has 4 well-supported breakpoints
Pair 14, 15 has 1863 initial LCBs
Pair 5, 23 has 3939 initial LCBs
Using scaled bp penalty: 329297
Pair (14,15) has 1 well-supported breakpoints
Pair 3, 17 has 1688 initial LCBs
Pair 1, 15 has 4367 initial LCBs
Using scaled bp penalty: 320482
Pair (5,23) has 7 well-supported breakpoints
Using scaled bp penalty: 336451
Pair (3,17) has 1 well-supported breakpoints
Pair 18, 19 has 5253 initial LCBs
Using scaled bp penalty: 166106
Using scaled bp penalty: 308492
Pair 8, 12 has 4925 initial LCBs
Pair (1,15) has 4 well-supported breakpoints
Pair 23, 28 has 82 initial LCBs
Using scaled bp penalty: 279515
Pair (18,19) has 1 well-supported breakpoints
Pair 14, 16 has 1878 initial LCBs
Using scaled bp penalty: 306064
Using scaled bp penalty: 389705
Pair (23,28) has 1 well-supported breakpoints
Pair (8,12) has 4 well-supported breakpoints
Pair (10,27) has 1 well-supported breakpoints
Pair 5, 24 has 3967 initial LCBs
Using scaled bp penalty: 329042
Pair (14,16) has 1 well-supported breakpoints
Pair 1, 16 has 4361 initial LCBs
Pair 3, 18 has 212 initial LCBs
Using scaled bp penalty: 318418
Pair (5,24) has 7 well-supported breakpoints
Using scaled bp penalty: 389831
Pair (3,18) has 4 well-supported breakpoints
Using scaled bp penalty: 308537
Pair (1,16) has 4 well-supported breakpoints
Pair 23, 29 has 2989 initial LCBs
Pair 18, 20 has 946 initial LCBs
Pair 8, 13 has 1731 initial LCBs
Pair 10, 28 has 2992 initial LCBs
Pair 14, 17 has 1675 initial LCBs
Using scaled bp penalty: 324460
Pair (18,20) has 1 well-supported breakpoints
Using scaled bp penalty: 331951
Using scaled bp penalty: 332563
Pair (8,13) has 1 well-supported breakpoints
Pair (23,29) has 4 well-supported breakpoints
Using scaled bp penalty: 335390
Using scaled bp penalty: 338847
Pair (14,17) has 1 well-supported breakpoints
Pair (10,28) has 1 well-supported breakpoints
Pair 5, 25 has 4322 initial LCBs
Pair 3, 19 has 5044 initial LCBs
Pair 1, 17 has 4078 initial LCBs
Using scaled bp penalty: 289736
Pair (5,25) has 5 well-supported breakpoints
Using scaled bp penalty: 307734

Using scaled bp penalty: 288858

Pair (1,17) has 1 well-supported breakpoints
Pair (3,19) has 1 well-supported breakpoints
Pair 23, 30 has 5118 initial LCBs
Pair 8, 14 has 1770 initial LCBs
Pair 18, 21 has 9596 initial LCBs
Pair 10, 29 has 4329 initial LCBs
Pair 14, 18 has 1150 initial LCBs
Using scaled bp penalty: 333166
Pair (8,14) has 4 well-supported breakpoints
Using scaled bp penalty: 313231
Pair (23,30) has 1 well-supported breakpoints
Using scaled bp penalty: 360787
Pair (14,18) has 1 well-supported breakpoints
Pair 5, 26 has 3565 initial LCBs
Using scaled bp penalty: 306633
Pair 1, 18 has 4276 initial LCBs
Using scaled bp penalty: 315059
Pair (10,29) has 1 well-supported breakpoints
Pair (18,21) has 2 well-supported breakpoints
Pair 3, 20 has 820 initial LCBs
Using scaled bp penalty: 301416
Pair (5,26) has 4 well-supported breakpoints
Using scaled bp penalty: 314188
Pair (1,18) has 4 well-supported breakpoints
Using scaled bp penalty: 338875
Pair (3,20) has 4 well-supported breakpoints
Pair 14, 19 has 5279 initial LCBs
Pair 8, 15 has 190 initial LCBs
Pair 24, 25 has 1027 initial LCBs
Pair 10, 30 has 4047 initial LCBs
Using scaled bp penalty: 391775
Pair (8,15) has 1 well-supported breakpoints
Using scaled bp penalty: 282932
Using scaled bp penalty: 332510
Pair 1, 19 has 5282 initial LCBs
Pair (24,25) has 6 well-supported breakpoints
Pair 5, 27 has 40380 initial LCBs
Pair (14,19) has 1 well-supported breakpoints
Pair 18, 22 has 1195 initial LCBs
Using scaled bp penalty: 317562
Pair (10,30) has 1 well-supported breakpoints
Using scaled bp penalty: 313900
Pair (18,22) has 4 well-supported breakpoints
Using scaled bp penalty: 276803
Pair (1,19) has 1 well-supported breakpoints
Pair 3, 21 has 9630 initial LCBs
Pair 14, 20 has 2006 initial LCBs
Using scaled bp penalty: 318418
Pair 8, 16 has 193 initial LCBs
Using scaled bp penalty: 165769
Pair 24, 26 has 126 initial LCBs
Pair 11, 12 has 4841 initial LCBs
Pair 1, 20 has 4856 initial LCBs
Pair (3,21) has 5 well-supported breakpoints
Using scaled bp penalty: 316485
Pair (14,20) has 1 well-supported breakpoints
Using scaled bp penalty: 371943
Pair (24,26) has 1 well-supported breakpoints
Using scaled bp penalty: 391298

Pair (8,16) has 1 well-supported breakpoints

Pair 18, 23 has 211 initial LCBs
Using scaled bp penalty: 300302
Pair (11,12) has 4 well-supported breakpoints
Using scaled bp penalty: 284315
Pair (5,27) has 4 well-supported breakpoints
Pair (1,20) has 1 well-supported breakpoints
Using scaled bp penalty: 386966
Pair (18,23) has 1 well-supported breakpoints
Pair 3, 22 has 1123 initial LCBs
Pair 24, 27 has 39900 initial LCBs
Pair 14, 21 has 9465 initial LCBs
Pair 11, 13 has 3625 initial LCBs
Pair 8, 17 has 99 initial LCBs
Pair 5, 28 has 3303 initial LCBs
Using scaled bp penalty: 320903
Pair (3,22) has 4 well-supported breakpoints
Pair 1, 21 has 9503 initial LCBs
Using scaled bp penalty: 391099
Pair (8,17) has 1 well-supported breakpoints
Pair 18, 24 has 201 initial LCBs
Using scaled bp penalty: 317400
Using scaled bp penalty: 325525
Using scaled bp penalty: 323825
Pair (5,28) has 1 well-supported breakpoints
Pair (14,21) has 2 well-supported breakpoints
Using scaled bp penalty: 386367
Using scaled bp penalty: 302828
Pair (18,24) has 1 well-supported breakpoints
Pair (1,21) has 2 well-supported breakpoints
Using scaled bp penalty: 179406
Pair 11, 14 has 3630 initial LCBs
Pair 8, 18 has 1649 initial LCBs
Pair 3, 23 has 186 initial LCBs
Pair 5, 29 has 4527 initial LCBs
Pair (24,27) has 4 well-supported breakpoints
Pair 14, 22 has 2569 initial LCBs
Using scaled bp penalty: 343591
Using scaled bp penalty: 399831
Pair (3,23) has 4 well-supported breakpoints
Pair (8,18) has 7 well-supported breakpoints
Using scaled bp penalty: 318374
Pair 1, 22 has 5792 initial LCBs
Pair 18, 25 has 1093 initial LCBs
Pair (11,14) has 4 well-supported breakpoints
Using scaled bp penalty: 304847
Pair (5,29) has 7 well-supported breakpoints
Using scaled bp penalty: 298250
Pair (14,22) has 1 well-supported breakpoints
Using scaled bp penalty: 321974
Pair (18,25) has 3 well-supported breakpoints
Using scaled bp penalty: 270862
Pair (1,22) has 1 well-supported breakpoints
Pair 11, 15 has 3932 initial LCBs
Pair 8, 19 has 5629 initial LCBs
Pair 24, 28 has 71 initial LCBs
Pair 3, 24 has 189 initial LCBs
Pair 5, 30 has 4346 initial LCBs
Pair 14, 23 has 1158 initial LCBs
Using scaled bp penalty: 388788

Pair (24,28) has 1 well-supported breakpoints

Using scaled bp penalty: 307453
Pair 1, 23 has 4846 initial LCBs
Using scaled bp penalty: 396653
Pair (3,24) has 7 well-supported breakpoints
Pair (11,15) has 4 well-supported breakpoints
Using scaled bp penalty: 265083
Using scaled bp penalty: 305602
Pair 18, 26 has 177 initial LCBs
Pair (5,30) has 4 well-supported breakpoints
Pair (8,19) has 1 well-supported breakpoints
Using scaled bp penalty: 368313
Pair (14,23) has 4 well-supported breakpoints
Using scaled bp penalty: 300557
Using scaled bp penalty: 382872
Pair (18,26) has 1 well-supported breakpoints
Pair (1,23) has 1 well-supported breakpoints
Pair 24, 29 has 2978 initial LCBs
Pair 11, 16 has 3932 initial LCBs
Pair 8, 20 has 2541 initial LCBs
Pair 3, 25 has 1021 initial LCBs
Pair 14, 24 has 1152 initial LCBs
Pair 1, 24 has 4872 initial LCBs
Pair 6, 7 has 350 initial LCBs
Using scaled bp penalty: 331781
Pair 18, 27 has 40069 initial LCBs
Pair (24,29) has 4 well-supported breakpoints
Using scaled bp penalty: 307891
Pair (11,16) has 4 well-supported breakpoints
Using scaled bp penalty: 294540
Using scaled bp penalty: 330336
Pair (8,20) has 1 well-supported breakpoints
Pair (3,25) has 6 well-supported breakpoints
Using scaled bp penalty: 367878
Pair (14,24) has 4 well-supported breakpoints
Using scaled bp penalty: 365505
Pair (6,7) has 4 well-supported breakpoints
Using scaled bp penalty: 300896
Pair (1,24) has 1 well-supported breakpoints
Pair 24, 30 has 5121 initial LCBs
Pair 11, 17 has 3437 initial LCBs
Using scaled bp penalty: 171515
Pair 1, 25 has 5163 initial LCBs
Pair 8, 21 has 9252 initial LCBs
Pair 14, 25 has 2359 initial LCBs
Pair 6, 8 has 344 initial LCBs
Using scaled bp penalty: 311310
Using scaled bp penalty: 315492
Pair 3, 26 has 170 initial LCBs
Pair (24,30) has 1 well-supported breakpoints
Pair (11,17) has 4 well-supported breakpoints
Using scaled bp penalty: 365330
Pair (6,8) has 4 well-supported breakpoints
Using scaled bp penalty: 280618
Using scaled bp penalty: 308436
Pair (14,25) has 3 well-supported breakpoints
Pair (1,25) has 4 well-supported breakpoints
Using scaled bp penalty: 368947
Pair (3,26) has 1 well-supported breakpoints
Pair (18,27) has 1 well-supported breakpoints

Using scaled bp penalty: 307954

Pair (8,21) has 5 well-supported breakpoints
Pair 11, 18 has 3768 initial LCBs
Pair 6, 9 has 5104 initial LCBs
Pair 25, 26 has 846 initial LCBs
Pair 1, 26 has 4116 initial LCBs
Pair 3, 27 has 39827 initial LCBs
Pair 14, 26 has 1288 initial LCBs
Using scaled bp penalty: 310881
Pair (11,18) has 4 well-supported breakpoints
Using scaled bp penalty: 323566
Pair (25,26) has 3 well-supported breakpoints
Using scaled bp penalty: 302008
Pair 18, 28 has 16 initial LCBs
Using scaled bp penalty: 298770
Pair (6,9) has 4 well-supported breakpoints
Pair (1,26) has 1 well-supported breakpoints
Using scaled bp penalty: 331760
Pair (14,26) has 1 well-supported breakpoints
Pair 8, 22 has 3030 initial LCBs
Using scaled bp penalty: 406972
Pair (18,28) has 1 well-supported breakpoints
Using scaled bp penalty: 290430
Pair (8,22) has 4 well-supported breakpoints
Pair 11, 19 has 4635 initial LCBs
Pair 25, 27 has 40596 initial LCBs
Pair 1, 27 has 40300 initial LCBs
Pair 6, 10 has 3740 initial LCBs
Using scaled bp penalty: 174699
Pair 14, 27 has 39710 initial LCBs
Using scaled bp penalty: 289715
Pair (11,19) has 1 well-supported breakpoints
Using scaled bp penalty: 317090
Pair 18, 29 has 3179 initial LCBs
Pair (6,10) has 1 well-supported breakpoints
Pair 8, 23 has 1764 initial LCBs
Pair (3,27) has 4 well-supported breakpoints
Using scaled bp penalty: 321546
Pair (18,29) has 1 well-supported breakpoints
Using scaled bp penalty: 333038
Pair (8,23) has 4 well-supported breakpoints
Using scaled bp penalty: 166558
Using scaled bp penalty: 167547
Using scaled bp penalty: 177225
Pair 11, 20 has 3640 initial LCBs
Pair 6, 11 has 3837 initial LCBs
Using scaled bp penalty: 306577
Pair (25,27) has 6 well-supported breakpoints
Pair (11,20) has 4 well-supported breakpoints
Pair (1,27) has 1 well-supported breakpoints
Using scaled bp penalty: 311145
Pair 18, 30 has 4928 initial LCBs
Pair (6,11) has 4 well-supported breakpoints
Pair (14,27) has 1 well-supported breakpoints
Pair 3, 28 has 36 initial LCBs
Pair 8, 24 has 1757 initial LCBs
Using scaled bp penalty: 402461
Pair (3,28) has 1 well-supported breakpoints
Using scaled bp penalty: 308932
Pair (18,30) has 1 well-supported breakpoints

Using scaled bp penalty: 333451

Pair (8,24) has 4 well-supported breakpoints
Pair 1, 28 has 3751 initial LCBs
Pair 6, 12 has 5598 initial LCBs
Pair 25, 28 has 800 initial LCBs
Pair 11, 21 has 8232 initial LCBs
Pair 14, 28 has 1125 initial LCBs
Using scaled bp penalty: 333760
Pair (25,28) has 1 well-supported breakpoints
Using scaled bp penalty: 323992
Pair 19, 20 has 5122 initial LCBs
Using scaled bp penalty: 298113
Pair (1,28) has 1 well-supported breakpoints
Pair 3, 29 has 3081 initial LCBs
Using scaled bp penalty: 356173
Pair (6,12) has 7 well-supported breakpoints
Pair (14,28) has 1 well-supported breakpoints
Pair 8, 25 has 2678 initial LCBs
Using scaled bp penalty: 322091
Pair (11,21) has 2 well-supported breakpoints
Using scaled bp penalty: 271417
Using scaled bp penalty: 325043
Pair (3,29) has 7 well-supported breakpoints
Pair (19,20) has 4 well-supported breakpoints
Using scaled bp penalty: 301836
Pair (8,25) has 6 well-supported breakpoints
Pair 25, 29 has 3698 initial LCBs
Pair 1, 29 has 5586 initial LCBs
Pair 6, 13 has 1775 initial LCBs
Pair 14, 29 has 3136 initial LCBs
Using scaled bp penalty: 301458
Pair (25,29) has 6 well-supported breakpoints
Using scaled bp penalty: 286878
Pair 3, 30 has 5001 initial LCBs
Using scaled bp penalty: 348120
Pair (1,29) has 1 well-supported breakpoints
Pair (6,13) has 6 well-supported breakpoints
Pair 11, 22 has 4415 initial LCBs
Using scaled bp penalty: 330624
Pair (14,29) has 1 well-supported breakpoints
Pair 8, 26 has 1577 initial LCBs
Pair 19, 21 has 6021 initial LCBs
Using scaled bp penalty: 311884
Using scaled bp penalty: 323441
Using scaled bp penalty: 288562
Pair (3,30) has 1 well-supported breakpoints
Pair (8,26) has 1 well-supported breakpoints
Pair (11,22) has 4 well-supported breakpoints
Using scaled bp penalty: 300952
Pair 1, 30 has 5001 initial LCBs
Pair 25, 30 has 4815 initial LCBs
Pair (19,21) has 5 well-supported breakpoints
Pair 6, 14 has 1814 initial LCBs
Pair 14, 30 has 5084 initial LCBs
Using scaled bp penalty: 302466
Using scaled bp penalty: 300605
Pair (1,30) has 1 well-supported breakpoints
Pair (25,30) has 1 well-supported breakpoints
Using scaled bp penalty: 346880
Pair 4, 5 has 3315 initial LCBs

Pair (6,14) has 6 well-supported breakpoints

Pair 8, 27 has 40051 initial LCBs
Using scaled bp penalty: 314693
Pair 11, 23 has 3904 initial LCBs
Pair (14,30) has 1 well-supported breakpoints
Using scaled bp penalty: 321366
Pair 19, 22 has 5944 initial LCBs
Pair (4,5) has 4 well-supported breakpoints
Using scaled bp penalty: 314490
Pair (11,23) has 4 well-supported breakpoints
Using scaled bp penalty: 259520
Pair 26, 27 has 39454 initial LCBs
Pair (19,22) has 4 well-supported breakpoints
Pair 6, 15 has 385 initial LCBs
Using scaled bp penalty: 168550
Pair 15, 16 has 1 initial LCBs
Using scaled bp penalty: 362864
Pair (6,15) has 1 well-supported breakpoints
Pair 4, 6 has 174 initial LCBs
Pair 11, 24 has 3890 initial LCBs
Using scaled bp penalty: 448084
Pair (15,16) has 1 well-supported breakpoints
Pair (8,27) has 1 well-supported breakpoints
Pair 19, 23 has 5438 initial LCBs
Using scaled bp penalty: 389429
Pair (4,6) has 1 well-supported breakpoints
Using scaled bp penalty: 314196
Using scaled bp penalty: 165422
Pair (11,24) has 4 well-supported breakpoints
Using scaled bp penalty: 282172
Pair (19,23) has 1 well-supported breakpoints
Pair 6, 16 has 386 initial LCBs
Pair (26,27) has 1 well-supported breakpoints
Using scaled bp penalty: 362728
Pair (6,16) has 1 well-supported breakpoints
Pair 8, 28 has 1535 initial LCBs
Pair 15, 17 has 61 initial LCBs
Pair 4, 7 has 74 initial LCBs
Pair 11, 25 has 3884 initial LCBs
Using scaled bp penalty: 329512
Pair (8,28) has 1 well-supported breakpoints
Using scaled bp penalty: 411461
Pair (15,17) has 1 well-supported breakpoints
Pair 19, 24 has 5470 initial LCBs
Using scaled bp penalty: 387563
Pair (4,7) has 1 well-supported breakpoints
Using scaled bp penalty: 302094
Pair (11,25) has 4 well-supported breakpoints
Using scaled bp penalty: 280945
Pair 26, 28 has 32 initial LCBs
Pair (19,24) has 1 well-supported breakpoints
Pair 8, 29 has 2947 initial LCBs
Using scaled bp penalty: 388634
Pair (26,28) has 1 well-supported breakpoints
Pair 15, 18 has 1820 initial LCBs
Pair 11, 26 has 3466 initial LCBs
Using scaled bp penalty: 315498
Pair (8,29) has 4 well-supported breakpoints
Using scaled bp penalty: 332404
Pair (15,18) has 4 well-supported breakpoints

Using scaled bp penalty: 300943

Pair 19, 25 has 5281 initial LCBs
Pair (11,26) has 4 well-supported breakpoints
Pair 26, 29 has 3141 initial LCBs
Using scaled bp penalty: 269511
Pair (19,25) has 4 well-supported breakpoints
Using scaled bp penalty: 301813
Pair 15, 19 has 5915 initial LCBs
Pair (26,29) has 1 well-supported breakpoints
Pair 11, 27 has 39732 initial LCBs
Using scaled bp penalty: 269180
Pair (15,19) has 1 well-supported breakpoints
Pair 19, 26 has 5225 initial LCBs
Pair 26, 30 has 4336 initial LCBs
Using scaled bp penalty: 266541
Pair (19,26) has 1 well-supported breakpoints
Using scaled bp penalty: 170544
Using scaled bp penalty: 305560
Pair (26,30) has 1 well-supported breakpoints
Pair (11,27) has 4 well-supported breakpoints
Pair 19, 27 has 39995 initial LCBs
Pair 27, 28 has 39191 initial LCBs
Using scaled bp penalty: 159350
Using scaled bp penalty: 174662
Pair (19,27) has 1 well-supported breakpoints
Pair (27,28) has 1 well-supported breakpoints
Pair 27, 29 has 39154 initial LCBs
Using scaled bp penalty: 175800
Pair (27,29) has 4 well-supported breakpoints
Pair 27, 30 has 39032 initial LCBs
Using scaled bp penalty: 175579
Pair (27,30) has 1 well-supported breakpoints
Pair 28, 29 has 3009 initial LCBs
Using scaled bp penalty: 322328
Pair (28,29) has 1 well-supported breakpoints
Pair 28, 30 has 4366 initial LCBs
Using scaled bp penalty: 325442
Pair (28,30) has 1 well-supported breakpoints
Pair 29, 30 has 4005 initial LCBs
Using scaled bp penalty: 325284
Pair (29,30) has 1 well-supported breakpoints
genome content distance matrix:
0
0.0877608
0.0725771
0.0711681
0.0183331
0.092809
8
0.0456404
0.0208364
0.0209105
0.0923713
0.085607
6
0.0860071
0.0870396
0.0717535
0.0704131
0.017995
0.018287
0.0147867
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0.0897507
0.0958171
0.0674732
0.0682136
0.0845789
0.068293
0.208912
0.0613001
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0.0847359
0.0877608
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0.0919648
0.0874218
0.0821319
0.084016
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0.0893187
0.0958969
0.096647
0.097461
0.079477
6
0.0889019
0.107388
0.0858967
0.0869083
0.090135
6
0.0901022
0.0906945
0.0859643
0.11446 0.108511
0.094341
0.11925 0.0960438
0.0957886
0.111424
0.09739
0.218912
0.078916
0.106509
0.0946115
0.0725771
0.0919648
0
0.0676085
0.0712704
0.084419
0.0740223
0.0729611
0.074643
0.0849803
0.0892142
0.0908548
0.0922173
0.0539122
0.0498369
0.0785591
0.0787805
0.0791768
0.0572564
0.117177
0.0937648
0.0814833
0.104619
0.0651843
0.0662154
0.0957328
0.0773313
0.21042 0.0690823
0.0829517
0.0918824

0.0711681
0.0874218
0.0676085
0
0.0631265
0.081780
7
0.0617734
0.0724488
0.074441
0.0895244
0.079004
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0.0848315
0.095474
0.0550686
0.0533717
0.076254
4
0.0756607
0.0701853
0.0353167
0.104971
0.068515
3
0.0829028
0.0811188
0.0291887
0.0311237
0.074439
9
0.0485045
0.210706
0.027596
0.0781697
0.087644
7
0.0183331
0.0821319
0.0712704
0.0631265
0
0.080788
2
0.0355654
0.0367226
0.036876
0.0842998
0.075488
3
0.0767015
0.0868568
0.0595847
0.0607617
0.029332
4
0.0296424
0.0171856
0.0619378
0.105835
0.075301
3
0.0819164
0.092308
0.0593501
0.0602955
0.079368
5
0.0630374
0.204423
0.0484393
0.0751431
0.072537
4
0.0928098
0.0840168
0.084419
0.0817807
0.0807882
0
0.0836282
0.0943953
0.0950708
0.0925116
0.070861
3
0.0861026
0.0989504
0.0798986
0.0784669
0.096758
9
0.0969789
0.0925139
0.077914
0.112542
0.103687
0.0849337
0.11517 0.0814209
0.0829029
0.104292
0.095398
4
0.220993
0.0790345
0.0928351
0.0922735
0.0456404
0.0893187
0.0740223
0.0617734
0.0355654
0.0836282
0
0.0507314
0.0508449
0.0949548
0.083861
2
0.0881852
0.0978867
0.0622261
0.0630628
0.052450
9
0.0525393
0.0447991
0.0640255
0.110383
0.090961
1
0.0866425
0.104964
0.0671347
0.0670573
0.094933
4
0.0819288
0.211523
0.0618732
0.0827252
0.089834
7
0.0208364
0.0958969
0.0729611
0.0724488
0.0367226
0.0943953
0.0507314
0
0.000186299
0.0950338
0.091397
2
0.0970206
0.091687
0.0713539
0.0702865
0.033997
8
0.0342923
0.0344632
0.0650803
0.123097
0.10043
0.0902899
0.102874
0.0716504
0.0713634
0.0941867
0.0783984
0.217683
0.0747733
0.0846801
0.09628
0.0209105
0.096647
0.074643
0.074441
0.036876
0.0950708
0.0508449
0.000186299
0
0.0950436
0.094065
1
0.0973544
0.0919313
0.0733101
0.0724639
0.034115
8
0.0344104
0.0345329
0.0652913
0.123985
0.100602
0.0905321
0.103756
0.0725526
0.0722656
0.0950836
0.0793076
0.217746
0.0750174
0.0850126
0.0973955
0.0923713
0.097461
0.0849803
0.0895244
0.0842998
0.0925116
0.0949548
0.0950338
0.0950436
0
0.095373
5
0.0906053
0.0945604
0.0812594
0.0770087
0.098213
0.0983914
0.0921694
0.0888407
0.113291
0.104075
0.0837625
0.118185
0.0794664
0.0792547
0.104177
0.102329
0.205179
0.088317
0.0862361
0.0846678
0.0856076
0.0794776
0.0892142
0.0790048
0.0754883
0.0708613
0.0838612
0.0913972
0.0940651
0.0953735
0
0.0769267
0.100781
0.0824367
0.0839898
0.091122
9
0.0913077
0.087128
0.0841536
0.105547
0.098376
0.0862605
0.108144
0.0890572
0.0900769
0.0986491
0.0883452
0.220597
0.0709197
0.0915094
0.0835203
0.0860071
0.0889019
0.0908548
0.0848315
0.0767015
0.0861026
0.0881852
0.0970206
0.0973544
0.0906053
0.0769267
0
0.0962354
0.0836369
0.0829345
0.090902
2
0.0905788
0.0850173
0.0883791
0.104308
0.091550
5
0.0802696
0.105201
0.0857448
0.0859581
0.094890
1
0.0957532
0.215442
0.0774124
0.0876522
0.082926
0.0870396
0.107388
0.0922173
0.095474
0.0868568
0.0989504
0.0978867
0.091687
0.0919313
0.0945604
0.100781
0.0962354
0
0.0924478
0.0905392
0.091491

1
0.0914776
0.0851524
0.0980504
0.105794
0.093743
9
0.0365896
0.10664 0.0884578
0.0889674
0.0917209
0.110921
0.215562
0.0979779
0.0781088
0.0813018
0.0717535
0.0858967
0.0539122
0.0550686
0.0595847
0.0798986
0.0622261
0.0713539
0.0733101
0.0812594
0.0824367
0.0836369
0.0924478
0
0.014212
0.077530
5
0.0777033
0.0709831
0.0531335
0.111262
0.086372
7
0.0820491
0.0988593
0.0561525
0.0564365
0.091898
0.0723802
0.208876
0.0560014
0.0775097
0.0835397
0.0704131
0.0869083
0.0498369
0.0533717
0.0607617
0.0784669
0.0630628
0.0702865
0.0724639
0.0770087
0.0839898
0.0829345
0.0905392
0.014212
0
0.075168
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0.075347
0.0685347
0.0538098
0.109597
0.084298
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0.0778284
0.0977835
0.0489132
0.0491944
0.090176
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0.207869
0.0568492
0.074238
0.085596
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0.0901356
0.0785591
0.0762544
0.0293324
0.0967589
0.0524509
0.0339978
0.0341158
0.098213
0.0911229
0.0909022
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0.0775305
0.0751684
0
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0.0729946
0.12062 0.0786561
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0.0734024
0.0743775
0.0803839
0.0728713
0.212248
0.0688717
0.089806
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0.0525393
0.0342923
0.0344104
0.0983914
0.0913077
0.0905788
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0.0777033
0.075347
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0.0731761
0.120639
0.07885
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0.0933141
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0.074705
0.0805646
0.0730548
0.212265
0.0690649
0.0897393
0.0922576
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0.0906945
0.0791768
0.0701853
0.0171856
0.0925139
0.0447991
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0.0345329
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0.087128
0.0850173
0.0851524
0.0709831
0.0685347
0.0222047
0.0217143
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0.115725
0.080740
3
0.0878706
0.0971978
0.0666916
0.06746 0.0833109
0.0755153
0.209334
0.0600868
0.0834596
0.0848423
0.0649757
0.0859643
0.0572564
0.0353167
0.0619378
0.077914
0.0640255
0.0650803
0.0652913
0.0888407
0.0841536
0.0883791
0.0980504
0.0531335
0.0538098
0.0729946
0.0731761
0.0732597
0
0.112299
0.078583
2
0.0853317
0.0861736
0.0370941
0.0374669
0.080353
3
0.0396506
0.214328
0.0248825
0.0806593
0.089810
8
0.116667
0.11446 0.117177
0.104971
0.105835
0.112542
0.110383
0.123097
0.123985
0.113291
0.105547
0.104308
0.105794
0.111262
0.109597
0.12062 0.120639
0.115725
0.112299
0
0.118799
0.0957466
0.128618
0.110196
0.111165
0.12035 0.122783
0.228646
0.100428
0.10184 0.0528278
0.0849381
0.108511
0.0937648
0.0685153
0.0753013
0.103687
0.0909611
0.10043 0.100602
0.104075
0.098376
0.0915505
0.0937439
0.0863727
0.0842981
0.0786561
0.07885 0.0807403
0.0785832
0.118799
0
0.093455
0.0523941
0.0658616
0.0657754
0.0400735
0.0778114
0.219419
0.0645797
0.0946893
0.0962708
0.0897507
0.094341
0.0814833
0.0829028
0.0819164
0.0849337
0.0866425
0.0902899
0.0905321
0.0837625
0.0862605
0.0802696
0.0365896
0.0820491
0.0778284
0.0940886
0.0940719
0.0878706
0.0853317
0.0957466
0.093455
0
0.106846
0.0817822
0.0822248
0.095364
1
0.102196
0.211976
0.0834132
0.0716975
0.073936
4

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bp distance matrix:
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0.0214286
0.9
0.0214286
0.021428
6
0.0214286
0.0214286
0.0214286
0.15
0.0214286
0.15
0.15
0.0857143
0.0857143
0.0214286
0.0214286
0.085714
3
0.0857143
0.0857143
0.0214286
0.0214286
0.021428
6
0.0214286
0.0214286
0.0214286
0.0857143
0.042857
1
0.0857143
0.0857143
0.0857143
0.128571
0.021428
6
0.0857143
0.0214286
0.9
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0857143
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0857143
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0428571
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.9
Aligning...
Aligning node 57 to 58 via 56!
Working set size: 1534 Mb
Pagefile usage: 867 Mb
get ancestral matches
Working set size: 1537 Mb
Pagefile usage: 870 Mb
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1537 Mb
Pagefile usage: 870 Mb
construct LCB tracking matches
There are 14 tracking matches
There are 28 / 854 components used
Working set size: 1537 Mb
Pagefile usage: 870 Mb
init tracking match LCB tracking
Working set size: 1537 Mb
Pagefile usage: 870 Mb
pairwise score tracking matches
Working set size: 1540 Mb
Pagefile usage: 873 Mb
get pairwise LCBs
there are 2 pairwise LCBs
Working set size: 1540 Mb
Pagefile usage: 873 Mb
scaling bp penalty by conservation weight:
0.000186299
scaling bp penalty by bp weight:
0.0214286
Greedy BPE
Scoring with scaled breakpoint penalty: 143574
50%..done
Working set size: 1538 Mb
Pagefile usage: 870 Mb
Arrived at 1 intervals
Adding unaligned intervals
addUnalignedIntervals yields 3 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints

descendant 0(57) has 1 intervals

descendant 1(58) has 1 intervals
propagateDescendantBreakpoints yields 1 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 2.11864e+008
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 1 new matches outside LCBs
0,0 has an additional 4 matches
Restoring backed up alignment tree...
8,7 has 4 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1543 Mb
Pagefile usage: 875 Mb
construct LCB tracking matches
There are 17 tracking matches
There are 34 / 1037 components used
Working set size: 1543 Mb
Pagefile usage: 875 Mb
init tracking match LCB tracking
Working set size: 1543 Mb
Pagefile usage: 875 Mb
pairwise score tracking matches
Working set size: 1543 Mb
Pagefile usage: 875 Mb
get pairwise LCBs
there are 2 pairwise LCBs
Working set size: 1543 Mb
Pagefile usage: 875 Mb
scaling bp penalty by conservation weight:
0.000186299
scaling bp penalty by bp weight:
0.0214286
Greedy BPE
Scoring with scaled breakpoint penalty: 143574
50%..done
Working set size: 1543 Mb
Pagefile usage: 875 Mb
Arrived at 1 intervals
Adding unaligned intervals
addUnalignedIntervals yields 3 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(57) has 1 intervals
descendant 1(58) has 1 intervals
propagateDescendantBreakpoints yields 1 intervals
Creating ancestral ordering
Previous anchoring score: 2.11864e+008, new anchor score: 2.11834e+008
Working set size: 1543 Mb
Pagefile usage: 875 Mb
propagating ancestral breakpoints
Working set size: 1543 Mb
Pagefile usage: 875 Mb
performing a gapped alignment

0%..1%..3%..4%..6%..7%..9%..
10%..12%..14%..15%..17%..18%..
20%..21%..23%..25%..26%..28%..29%..
31%..32%..34%..35%..37%..39%..
40%..42%..43%..45%..46%..48%..
50%..51%..53%..54%..56%..57%..59%..
60%..62%..64%..65%..67%..68%..
70%..71%..73%..75%..76%..78%..79%..
81%..82%..84%..85%..87%..89%..
90%..92%..93%..95%..96%..98%..
100%..Working set size: 1523 Mb
Pagefile usage: 857 Mb
Fix left ends
Working set size: 1523 Mb
Pagefile usage: 857 Mb
done.
Working set size: 1523 Mb
Pagefile usage: 857 Mb
Aligning node 27 to 28 via 26!
Working set size: 1521 Mb
Pagefile usage: 854 Mb
get ancestral matches
Working set size: 1525 Mb
Pagefile usage: 859 Mb
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1525 Mb
Pagefile usage: 859 Mb
construct LCB tracking matches
There are 98 tracking matches
There are 196 / 5978 components used
Working set size: 1539 Mb
Pagefile usage: 873 Mb
init tracking match LCB tracking
Working set size: 1539 Mb
Pagefile usage: 873 Mb
pairwise score tracking matches
Working set size: 1546 Mb
Pagefile usage: 879 Mb
get pairwise LCBs
there are 10 pairwise LCBs
Working set size: 1546 Mb
Pagefile usage: 879 Mb
scaling bp penalty by conservation weight:
0.00037193
scaling bp penalty by bp weight:
0.0857143
Greedy BPE
Scoring with scaled breakpoint penalty: 125237
10%..
20%..done
Working set size: 1546 Mb
Pagefile usage: 880 Mb
Arrived at 4 intervals
Adding unaligned intervals

addUnalignedIntervals yields 8 intervals

Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(27) has 1 intervals
descendant 1(28) has 1 intervals
propagateDescendantBreakpoints yields 4 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 2.1299e+008
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 0 new matches outside LCBs
0,0 has an additional 3 matches
Restoring backed up alignment tree...
24,23 has 3 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1547 Mb
Pagefile usage: 881 Mb
construct LCB tracking matches
There are 99 tracking matches
There are 198 / 6039 components used
Working set size: 1547 Mb
Pagefile usage: 881 Mb
init tracking match LCB tracking
Working set size: 1547 Mb
Pagefile usage: 881 Mb
pairwise score tracking matches
Working set size: 1547 Mb
Pagefile usage: 881 Mb
get pairwise LCBs
there are 4 pairwise LCBs
Working set size: 1547 Mb
Pagefile usage: 881 Mb
scaling bp penalty by conservation weight:
0.00037193
scaling bp penalty by bp weight:
0.0857143
Greedy BPE
Scoring with scaled breakpoint penalty: 125237
done
Working set size: 1547 Mb
Pagefile usage: 881 Mb
Arrived at 4 intervals
Adding unaligned intervals
addUnalignedIntervals yields 8 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(27) has 1 intervals
descendant 1(28) has 1 intervals
propagateDescendantBreakpoints yields 4 intervals
Creating ancestral ordering
Previous anchoring score: 2.1299e+008, new anchor score: 2.13806e+008
Working set size: 1547 Mb
Pagefile usage: 881 Mb
propagating ancestral breakpoints

Working set size: 1547 Mb

Pagefile usage: 881 Mb
performing a gapped alignment
0%..1%..2%..4%..5%..7%..8%..
10%..11%..13%..14%..16%..17%..19%..
20%..22%..23%..25%..27%..29%..
31%..33%..35%..38%..
40%..42%..44%..46%..48%..
50%..52%..54%..56%..57%..58%..
60%..62%..64%..65%..66%..67%..68%..69%..
70%..71%..72%..73%..74%..76%..77%..78%..79%..
80%..81%..82%..83%..84%..85%..86%..88%..89%..
90%..91%..92%..93%..94%..95%..96%..97%..98%..
100%..Working set size: 1537 Mb
Pagefile usage: 875 Mb
Fix left ends
Working set size: 1537 Mb
Pagefile usage: 875 Mb
done.
Working set size: 1537 Mb
Pagefile usage: 875 Mb
Aligning node 52 to 53 via 51!
Working set size: 1534 Mb
Pagefile usage: 872 Mb
get ancestral matches
Working set size: 1538 Mb
Pagefile usage: 875 Mb
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1538 Mb
Pagefile usage: 875 Mb
construct LCB tracking matches
There are 43 tracking matches
There are 86 / 2623 components used
Working set size: 1551 Mb
Pagefile usage: 889 Mb
init tracking match LCB tracking
Working set size: 1551 Mb
Pagefile usage: 889 Mb
pairwise score tracking matches
Working set size: 1555 Mb
Pagefile usage: 892 Mb
get pairwise LCBs
there are 1 pairwise LCBs
Working set size: 1555 Mb
Pagefile usage: 892 Mb
scaling bp penalty by conservation weight:
0.00113751
scaling bp penalty by bp weight:
0.0214286
Greedy BPE
Scoring with scaled breakpoint penalty: 143029
done
Working set size: 1555 Mb
Pagefile usage: 892 Mb
Arrived at 1 intervals

Adding unaligned intervals

addUnalignedIntervals yields 1 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(52) has 1 intervals
descendant 1(53) has 1 intervals
propagateDescendantBreakpoints yields 1 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 2.13408e+008
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 0 new matches outside LCBs
0,0 has an additional 2 matches
Restoring backed up alignment tree...
16,15 has 2 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1561 Mb
Pagefile usage: 896 Mb
construct LCB tracking matches
There are 45 tracking matches
There are 90 / 2745 components used
Working set size: 1561 Mb
Pagefile usage: 896 Mb
init tracking match LCB tracking
Working set size: 1561 Mb
Pagefile usage: 896 Mb
pairwise score tracking matches
Working set size: 1561 Mb
Pagefile usage: 896 Mb
get pairwise LCBs
there are 1 pairwise LCBs
Working set size: 1561 Mb
Pagefile usage: 896 Mb
scaling bp penalty by conservation weight:
0.00113751
scaling bp penalty by bp weight:
0.0214286
Greedy BPE
Scoring with scaled breakpoint penalty: 143029
done
Working set size: 1561 Mb
Pagefile usage: 896 Mb
Arrived at 1 intervals
Adding unaligned intervals
addUnalignedIntervals yields 1 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(52) has 1 intervals
descendant 1(53) has 1 intervals
propagateDescendantBreakpoints yields 1 intervals
Creating ancestral ordering
Previous anchoring score: 2.13408e+008, new anchor score: 2.13298e+008
Working set size: 1561 Mb
Pagefile usage: 896 Mb

propagating ancestral breakpoints

Working set size: 1561 Mb
Pagefile usage: 896 Mb
performing a gapped alignment
0%..1%..3%..4%..6%..7%..9%..
10%..12%..14%..15%..17%..18%..
20%..21%..23%..25%..26%..28%..29%..
31%..32%..34%..35%..37%..39%..
40%..42%..43%..45%..46%..48%..
50%..51%..53%..54%..56%..57%..59%..
60%..62%..64%..65%..67%..68%..
70%..71%..73%..75%..76%..78%..79%..
81%..82%..84%..85%..87%..89%..
90%..92%..93%..95%..96%..98%..
100%..Working set size: 1526 Mb
Pagefile usage: 861 Mb
Fix left ends
Working set size: 1526 Mb
Pagefile usage: 861 Mb
done.
Working set size: 1526 Mb
Pagefile usage: 861 Mb
Aligning node 43 to 44 via 42!
Working set size: 1524 Mb
Pagefile usage: 859 Mb
get ancestral matches
Working set size: 1527 Mb
Pagefile usage: 862 Mb
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1527 Mb
Pagefile usage: 862 Mb
construct LCB tracking matches
There are 1443 tracking matches
There are 2886 / 88023 components used
Working set size: 1535 Mb
Pagefile usage: 869 Mb
init tracking match LCB tracking
Working set size: 1535 Mb
Pagefile usage: 869 Mb
pairwise score tracking matches
Working set size: 1538 Mb
Pagefile usage: 873 Mb
get pairwise LCBs
there are 74 pairwise LCBs
Working set size: 1538 Mb
Pagefile usage: 873 Mb
scaling bp penalty by conservation weight:
0.014212
scaling bp penalty by bp weight:
0.0857143
Greedy BPE
Scoring with scaled breakpoint penalty: 118444
1%..2%..4%..5%..6%..8%..9%..
10%..12%..13%..14%..16%..17%..18%..
20%..21%..22%..24%..25%..27%..28%..29%..

31%..32%..33%..35%..36%..37%..39%..
40%..41%..43%..44%..45%..47%..48%..
50%..done
Working set size: 1538 Mb
Pagefile usage: 876 Mb
Arrived at 4 intervals
Adding unaligned intervals
addUnalignedIntervals yields 9 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(43) has 1 intervals
descendant 1(44) has 1 intervals
propagateDescendantBreakpoints yields 4 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 1.9852e+008
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 19 new matches outside LCBs
0,0 has an additional 291 matches
Restoring backed up alignment tree...
14,13 has 291 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1545 Mb
Pagefile usage: 882 Mb
construct LCB tracking matches
There are 1624 tracking matches
There are 3248 / 99064 components used
Working set size: 1545 Mb
Pagefile usage: 882 Mb
init tracking match LCB tracking
Working set size: 1545 Mb
Pagefile usage: 882 Mb
pairwise score tracking matches
Working set size: 1545 Mb
Pagefile usage: 882 Mb
get pairwise LCBs
there are 260 pairwise LCBs
Working set size: 1545 Mb
Pagefile usage: 882 Mb
scaling bp penalty by conservation weight:
0.014212
scaling bp penalty by bp weight:
0.0857143
Greedy BPE
Scoring with scaled breakpoint penalty: 118444
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..47%..48%..49%..
50%..51%..52%..53%..54%..55%..56%..57%..58%..59%..
60%..61%..62%..63%..64%..65%..66%..67%..68%..69%..
70%..71%..72%..73%..74%..75%..76%..77%..78%..79%..
80%..done
Working set size: 1545 Mb

Pagefile usage: 881 Mb

Arrived at 4 intervals
Adding unaligned intervals
addUnalignedIntervals yields 8 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(43) has 1 intervals
descendant 1(44) has 1 intervals
propagateDescendantBreakpoints yields 4 intervals
Creating ancestral ordering
Previous anchoring score: 1.9852e+008, new anchor score: 2.07278e+008
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 5 new matches outside LCBs
0,0 has an additional 222 matches
Restoring backed up alignment tree...
14,13 has 222 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1546 Mb
Pagefile usage: 883 Mb
construct LCB tracking matches
There are 1622 tracking matches
There are 3244 / 98942 components used
Working set size: 1546 Mb
Pagefile usage: 883 Mb
init tracking match LCB tracking
Working set size: 1546 Mb
Pagefile usage: 883 Mb
pairwise score tracking matches
Working set size: 1546 Mb
Pagefile usage: 883 Mb
get pairwise LCBs
there are 230 pairwise LCBs
Working set size: 1546 Mb
Pagefile usage: 883 Mb
scaling bp penalty by conservation weight:
0.014212
scaling bp penalty by bp weight:
0.0857143
Greedy BPE
Scoring with scaled breakpoint penalty: 118444
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..47%..48%..49%..
50%..51%..52%..53%..54%..55%..56%..57%..58%..59%..
60%..61%..62%..63%..64%..65%..66%..67%..68%..69%..
70%..71%..72%..73%..74%..75%..76%..77%..78%..79%..
80%..done
Working set size: 1546 Mb
Pagefile usage: 882 Mb
Arrived at 4 intervals
Adding unaligned intervals
addUnalignedIntervals yields 8 intervals

Merging unaligned intervals

Marbling gaps
Propagating descendant breakpoints
descendant 0(43) has 1 intervals
descendant 1(44) has 1 intervals
propagateDescendantBreakpoints yields 4 intervals
Creating ancestral ordering
Previous anchoring score: 2.07278e+008, new anchor score: 2.07288e+008
Working set size: 1546 Mb
Pagefile usage: 882 Mb
propagating ancestral breakpoints
Working set size: 1546 Mb
Pagefile usage: 882 Mb
performing a gapped alignment
0%..1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..13%..14%..15%..16%..17%..18%..19%..
21%..22%..23%..24%..26%..27%..28%..
30%..31%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..45%..46%..47%..48%..49%..
50%..52%..53%..54%..55%..56%..58%..59%..
60%..62%..63%..64%..66%..67%..68%..
70%..71%..72%..74%..75%..76%..78%..79%..
81%..82%..83%..85%..86%..87%..89%..
90%..91%..93%..94%..95%..97%..98%..
100%..Working set size: 1537 Mb
Pagefile usage: 880 Mb
Fix left ends
Working set size: 1537 Mb
Pagefile usage: 880 Mb
done.
Working set size: 1537 Mb
Pagefile usage: 880 Mb
Aligning node 51 to 54 via 50!
Working set size: 1533 Mb
Pagefile usage: 876 Mb
get ancestral matches
Working set size: 1692 Mb
Pagefile usage: 1047 Mb
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1692 Mb
Pagefile usage: 1047 Mb
construct LCB tracking matches
There are 608 tracking matches
There are 2431 / 37088 components used
Working set size: 1692 Mb
Pagefile usage: 1047 Mb
init tracking match LCB tracking
Working set size: 1692 Mb
Pagefile usage: 1047 Mb
pairwise score tracking matches
Working set size: 1691 Mb
Pagefile usage: 1046 Mb
get pairwise LCBs
there are 170 pairwise LCBs
Working set size: 1691 Mb
Pagefile usage: 1046 Mb
scaling bp penalty by conservation weight:
0.017995

0.018287
scaling bp penalty by bp weight:
0.0214286
0.0214286
Greedy BPE
Scoring with scaled breakpoint penalty: 133615
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..done
Working set size: 1691 Mb
Pagefile usage: 1046 Mb
Arrived at 1 intervals
Adding unaligned intervals
addUnalignedIntervals yields 1 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(51) has 1 intervals
descendant 1(54) has 1 intervals
propagateDescendantBreakpoints yields 1 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 4.03348e+008
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 0 new matches outside LCBs
1,0 have 0 new matches outside LCBs
0,0 has an additional 390 matches
1,0 has an additional 390 matches
Restoring backed up alignment tree...
15,0 has 390 pairwise matches
16,0 has 390 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1691 Mb
Pagefile usage: 1046 Mb
construct LCB tracking matches
There are 873 tracking matches
There are 3491 / 53253 components used
Working set size: 1691 Mb
Pagefile usage: 1046 Mb
init tracking match LCB tracking
Working set size: 1691 Mb
Pagefile usage: 1046 Mb
pairwise score tracking matches
Working set size: 1692 Mb
Pagefile usage: 1046 Mb
get pairwise LCBs
there are 716 pairwise LCBs
Working set size: 1692 Mb
Pagefile usage: 1046 Mb
scaling bp penalty by conservation weight:
0.017995
0.018287
scaling bp penalty by bp weight:
0.0214286

0.0214286
Greedy BPE
Scoring with scaled breakpoint penalty: 133615
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..done
Working set size: 1692 Mb
Pagefile usage: 1046 Mb
Arrived at 3 intervals
Adding unaligned intervals
addUnalignedIntervals yields 7 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(51) has 1 intervals
descendant 1(54) has 1 intervals
propagateDescendantBreakpoints yields 3 intervals
Creating ancestral ordering
Previous anchoring score: 4.03348e+008, new anchor score: 4.16903e+008
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 11 new matches outside LCBs
1,0 have 11 new matches outside LCBs
0,0 has an additional 145 matches
1,0 has an additional 145 matches
Restoring backed up alignment tree...
15,0 has 145 pairwise matches
16,0 has 145 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1649 Mb
Pagefile usage: 1018 Mb
construct LCB tracking matches
There are 731 tracking matches
There are 2923 / 44591 components used
Working set size: 1656 Mb
Pagefile usage: 1024 Mb
init tracking match LCB tracking
Working set size: 1656 Mb
Pagefile usage: 1024 Mb
pairwise score tracking matches
Working set size: 1660 Mb
Pagefile usage: 1028 Mb
get pairwise LCBs
there are 304 pairwise LCBs
Working set size: 1660 Mb
Pagefile usage: 1028 Mb
scaling bp penalty by conservation weight:
0.017995
0.018287
scaling bp penalty by bp weight:
0.0214286
0.0214286
Greedy BPE
Scoring with scaled breakpoint penalty: 133615

1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..done
Working set size: 1660 Mb
Pagefile usage: 1028 Mb
Arrived at 3 intervals
Adding unaligned intervals
addUnalignedIntervals yields 7 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(51) has 1 intervals
descendant 1(54) has 1 intervals
propagateDescendantBreakpoints yields 3 intervals
Creating ancestral ordering
Previous anchoring score: 4.16903e+008, new anchor score: 4.16914e+008
Working set size: 1660 Mb
Pagefile usage: 1028 Mb
propagating ancestral breakpoints
Working set size: 1660 Mb
Pagefile usage: 1028 Mb
performing a gapped alignment
0%..1%..3%..5%..7%..9%..
11%..13%..15%..17%..19%..
21%..22%..24%..26%..28%..29%..
30%..31%..32%..33%..35%..36%..37%..39%..
40%..41%..42%..44%..45%..46%..48%..49%..
50%..52%..53%..54%..55%..57%..58%..59%..
61%..62%..63%..65%..66%..67%..69%..
70%..71%..72%..73%..74%..76%..77%..79%..
81%..82%..84%..85%..87%..88%..
90%..92%..93%..95%..96%..98%..
100%..Working set size: 1645 Mb
Pagefile usage: 1015 Mb
Fix left ends
Working set size: 1645 Mb
Pagefile usage: 1015 Mb
done.
Working set size: 1645 Mb
Pagefile usage: 1015 Mb
Aligning node 50 to 55 via 49!
Working set size: 1639 Mb
Pagefile usage: 1011 Mb
get ancestral matches
Working set size: 1697 Mb
Pagefile usage: 1050 Mb
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1697 Mb
Pagefile usage: 1050 Mb
construct LCB tracking matches
There are 776 tracking matches
There are 4426 / 47336 components used
Working set size: 1697 Mb
Pagefile usage: 1050 Mb
init tracking match LCB tracking
Working set size: 1697 Mb
Pagefile usage: 1050 Mb

pairwise score tracking matches

Working set size: 1698 Mb
Pagefile usage: 1051 Mb
get pairwise LCBs
there are 103 pairwise LCBs
Working set size: 1698 Mb
Pagefile usage: 1051 Mb
scaling bp penalty by conservation weight:
0.0147867
0.0222047
0.0217143
scaling bp penalty by bp weight:
0.0214286
0.0214286
0.0214286
Greedy BPE
Scoring with scaled breakpoint penalty: 135370
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..done
Working set size: 1698 Mb
Pagefile usage: 1051 Mb
Arrived at 4 intervals
Adding unaligned intervals
addUnalignedIntervals yields 10 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(50) has 3 intervals
descendant 1(55) has 1 intervals
propagateDescendantBreakpoints yields 6 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 6.02079e+008
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 264 new matches outside LCBs
1,0 have 11 new matches outside LCBs
2,0 have 12 new matches outside LCBs
0,0 has an additional 480 matches
1,0 has an additional 256 matches
2,0 has an additional 258 matches
Restoring backed up alignment tree...
0,17 has 480 pairwise matches
15,17 has 256 pairwise matches
16,17 has 258 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1700 Mb
Pagefile usage: 1053 Mb
construct LCB tracking matches
There are 753 tracking matches
There are 4295 / 45933 components used
Working set size: 1700 Mb
Pagefile usage: 1053 Mb
init tracking match LCB tracking
Working set size: 1700 Mb
Pagefile usage: 1053 Mb
pairwise score tracking matches

Working set size: 1700 Mb

Pagefile usage: 1053 Mb
get pairwise LCBs
there are 75 pairwise LCBs
Working set size: 1700 Mb
Pagefile usage: 1053 Mb
scaling bp penalty by conservation weight:
0.0147867
0.0222047
0.0217143
scaling bp penalty by bp weight:
0.0214286
0.0214286
0.0214286
Greedy BPE
Scoring with scaled breakpoint penalty: 135370
1%..2%..4%..5%..6%..8%..9%..
10%..12%..13%..14%..16%..done
Working set size: 1700 Mb
Pagefile usage: 1053 Mb
Arrived at 6 intervals
Adding unaligned intervals
addUnalignedIntervals yields 11 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(50) has 3 intervals
descendant 1(55) has 1 intervals
propagateDescendantBreakpoints yields 8 intervals
Creating ancestral ordering
Previous anchoring score: 6.02079e+008, new anchor score: 6.20606e+008
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 263 new matches outside LCBs
1,0 have 0 new matches outside LCBs
2,0 have 0 new matches outside LCBs
0,0 has an additional 263 matches
1,0 has an additional 1 matches
2,0 has an additional 1 matches
Restoring backed up alignment tree...
0,17 has 263 pairwise matches
15,17 has 1 pairwise matches
16,17 has 1 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1658 Mb
Pagefile usage: 1026 Mb
construct LCB tracking matches
There are 753 tracking matches
There are 4294 / 45933 components used
Working set size: 1664 Mb
Pagefile usage: 1031 Mb
init tracking match LCB tracking
Working set size: 1664 Mb
Pagefile usage: 1031 Mb
pairwise score tracking matches
Working set size: 1668 Mb

Pagefile usage: 1034 Mb

get pairwise LCBs
there are 72 pairwise LCBs
Working set size: 1668 Mb
Pagefile usage: 1034 Mb
scaling bp penalty by conservation weight:
0.0147867
0.0222047
0.0217143
scaling bp penalty by bp weight:
0.0214286
0.0214286
0.0214286
Greedy BPE
Scoring with scaled breakpoint penalty: 135370
1%..2%..4%..5%..6%..8%..9%..
11%..12%..13%..15%..16%..done
Working set size: 1668 Mb
Pagefile usage: 1035 Mb
Arrived at 6 intervals
Adding unaligned intervals
addUnalignedIntervals yields 11 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(50) has 3 intervals
descendant 1(55) has 1 intervals
propagateDescendantBreakpoints yields 8 intervals
Creating ancestral ordering
Previous anchoring score: 6.20606e+008, new anchor score: 6.20641e+008
Working set size: 1668 Mb
Pagefile usage: 1035 Mb
propagating ancestral breakpoints
Working set size: 1668 Mb
Pagefile usage: 1035 Mb
performing a gapped alignment
0%..2%..3%..5%..7%..9%..
11%..13%..15%..16%..17%..19%..
21%..23%..24%..26%..28%..
30%..31%..33%..34%..35%..37%..38%..39%..
40%..42%..43%..44%..45%..47%..48%..49%..
50%..52%..53%..54%..56%..57%..58%..59%..
61%..62%..63%..64%..66%..67%..68%..69%..
71%..72%..73%..75%..76%..77%..78%..79%..
81%..83%..85%..87%..89%..
91%..93%..95%..96%..97%..98%..
100%..Working set size: 1618 Mb
Pagefile usage: 971 Mb
Fix left ends
Working set size: 1618 Mb
Pagefile usage: 971 Mb
done.
performing iterative refinement
0%..2%..3%..5%..7%..9%..

11%..13%..15%..16%..17%..19%..
21%..23%..24%..26%..28%..
30%..31%..33%..34%..35%..37%..38%..39%..
40%..42%..43%..44%..45%..47%..48%..49%..
50%..52%..53%..54%..56%..57%..58%..59%..
61%..62%..63%..64%..66%..67%..68%..69%..
71%..72%..73%..75%..76%..77%..78%..79%..
81%..83%..85%..87%..89%..
91%..93%..95%..96%..97%..98%..
100%..Working set size: 1618 Mb
Pagefile usage: 971 Mb
Fix left ends
Working set size: 1618 Mb
Pagefile usage: 971 Mb
done.
Working set size: 1618 Mb
Pagefile usage: 971 Mb
Aligning node 49 to 56 via 48!
Working set size: 1615 Mb
Pagefile usage: 978 Mb
get ancestral matches
Working set size: 1697 Mb
Pagefile usage: 1052 Mb
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1697 Mb
Pagefile usage: 1052 Mb
construct LCB tracking matches
There are 1559 tracking matches
There are 14633 / 95099 components used
Working set size: 1697 Mb
Pagefile usage: 1052 Mb
init tracking match LCB tracking
Working set size: 1697 Mb
Pagefile usage: 1052 Mb
pairwise score tracking matches
Working set size: 1697 Mb
Pagefile usage: 1052 Mb
get pairwise LCBs
there are 1542 pairwise LCBs
Working set size: 1697 Mb
Pagefile usage: 1052 Mb
scaling bp penalty by conservation weight:
0.0344632
0.0345329
0.0208364
0.0209105
0.0339978
0.0341158
0.0342923
0.0344104
scaling bp penalty by bp weight:
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
Greedy BPE
Scoring with scaled breakpoint penalty: 124875
1%..2%..3%..4%..5%..6%..7%..8%..9%..done
Working set size: 1697 Mb
Pagefile usage: 1052 Mb

Arrived at 9 intervals
Adding unaligned intervals
addUnalignedIntervals yields 26 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(49) has 8 intervals
descendant 1(56) has 1 intervals
propagateDescendantBreakpoints yields 15 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 1.5821e+009
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 416 new matches outside LCBs
0,1 have 416 new matches outside LCBs
1,0 have 13 new matches outside LCBs
1,1 have 13 new matches outside LCBs
2,0 have 250 new matches outside LCBs
2,1 have 250 new matches outside LCBs
3,0 have 249 new matches outside LCBs
3,1 have 249 new matches outside LCBs
0,0 has an additional 543 matches
0,1 has an additional 543 matches
1,0 has an additional 139 matches
1,1 has an additional 139 matches
2,0 has an additional 556 matches
2,1 has an additional 556 matches
3,0 has an additional 557 matches
3,1 has an additional 557 matches
Restoring backed up alignment tree...
17,7 has 543 pairwise matches
17,8 has 543 pairwise matches
0,7 has 139 pairwise matches
0,8 has 139 pairwise matches
15,7 has 556 pairwise matches
15,8 has 556 pairwise matches
16,7 has 557 pairwise matches
16,8 has 557 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1704 Mb
Pagefile usage: 1058 Mb
construct LCB tracking matches
There are 1953 tracking matches
There are 18066 / 119133 components used
Working set size: 1704 Mb
Pagefile usage: 1058 Mb
init tracking match LCB tracking
Working set size: 1704 Mb
Pagefile usage: 1058 Mb
pairwise score tracking matches
Working set size: 1704 Mb
Pagefile usage: 1058 Mb
get pairwise LCBs
there are 3658 pairwise LCBs
Working set size: 1704 Mb
Pagefile usage: 1058 Mb
scaling bp penalty by conservation weight:
0.0344632
0.0345329
0.0208364
0.0209105

0.0339978
0.0342923

0.0341158
0.0344104

scaling bp penalty by bp weight:

0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
Greedy BPE
Scoring with scaled breakpoint penalty: 124875
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..done
Working set size: 1704 Mb
Pagefile usage: 1058 Mb
Arrived at 9 intervals
Adding unaligned intervals
addUnalignedIntervals yields 22 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(49) has 8 intervals
descendant 1(56) has 1 intervals
propagateDescendantBreakpoints yields 15 intervals
Creating ancestral ordering
Previous anchoring score: 1.5821e+009, new anchor score: 1.65308e+009
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 416 new matches outside LCBs
0,1 have 416 new matches outside LCBs
1,0 have 4 new matches outside LCBs
1,1 have 4 new matches outside LCBs
2,0 have 223 new matches outside LCBs
2,1 have 223 new matches outside LCBs
3,0 have 221 new matches outside LCBs
3,1 have 221 new matches outside LCBs
0,0 has an additional 447 matches
0,1 has an additional 447 matches
1,0 has an additional 37 matches
1,1 has an additional 37 matches
2,0 has an additional 428 matches
2,1 has an additional 428 matches
3,0 has an additional 426 matches
3,1 has an additional 426 matches
Restoring backed up alignment tree...
17,7 has 447 pairwise matches
17,8 has 447 pairwise matches
0,7 has 37 pairwise matches
0,8 has 37 pairwise matches
15,7 has 428 pairwise matches
15,8 has 428 pairwise matches
16,7 has 426 pairwise matches
16,8 has 426 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1668 Mb
Pagefile usage: 1028 Mb
construct LCB tracking matches
There are 1943 tracking matches

There are 17925 / 118523 components used

Working set size: 1672 Mb
Pagefile usage: 1031 Mb
init tracking match LCB tracking
Working set size: 1672 Mb
Pagefile usage: 1031 Mb
pairwise score tracking matches
Working set size: 1673 Mb
Pagefile usage: 1032 Mb
get pairwise LCBs
there are 3310 pairwise LCBs
Working set size: 1674 Mb
Pagefile usage: 1032 Mb
scaling bp penalty by conservation weight:
0.0344632
0.0345329
0.0208364
0.0209105
0.0339978
0.0341158
0.0342923
0.0344104
scaling bp penalty by bp weight:
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
Greedy BPE
Scoring with scaled breakpoint penalty: 124875
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..done
Working set size: 1674 Mb
Pagefile usage: 1033 Mb
Arrived at 9 intervals
Adding unaligned intervals
addUnalignedIntervals yields 22 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(49) has 8 intervals
descendant 1(56) has 1 intervals
propagateDescendantBreakpoints yields 15 intervals
Creating ancestral ordering
Previous anchoring score: 1.65308e+009, new anchor score: 1.65308e+009
Working set size: 1674 Mb
Pagefile usage: 1034 Mb
propagating ancestral breakpoints
Working set size: 1674 Mb
Pagefile usage: 1034 Mb
performing a gapped alignment
0%..1%..3%..4%..5%..7%..8%..9%..
11%..12%..13%..15%..16%..18%..
20%..21%..22%..23%..25%..26%..27%..28%..
30%..31%..32%..33%..35%..37%..38%..39%..
40%..41%..42%..44%..45%..46%..47%..48%..49%..
50%..51%..52%..54%..55%..56%..57%..58%..59%..
60%..61%..62%..63%..65%..66%..67%..68%..69%..
70%..71%..72%..73%..74%..75%..76%..77%..78%..79%..
81%..83%..85%..87%..89%..
91%..93%..95%..96%..97%..98%..

100%..Working set size: 1628 Mb

Pagefile usage: 981 Mb
Fix left ends
Working set size: 1628 Mb
Pagefile usage: 981 Mb
done.
Working set size: 1628 Mb
Pagefile usage: 981 Mb
Aligning node 48 to 59 via 47!
Working set size: 1625 Mb
Pagefile usage: 991 Mb
get ancestral matches
Working set size: 1702 Mb
Pagefile usage: 1057 Mb
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1702 Mb
Pagefile usage: 1057 Mb
construct LCB tracking matches
There are 960 tracking matches
There are 11068 / 58560 components used
Working set size: 1702 Mb
Pagefile usage: 1057 Mb
init tracking match LCB tracking
Working set size: 1702 Mb
Pagefile usage: 1057 Mb
pairwise score tracking matches
Working set size: 1703 Mb
Pagefile usage: 1057 Mb
get pairwise LCBs
there are 381 pairwise LCBs
Working set size: 1703 Mb
Pagefile usage: 1057 Mb
scaling bp penalty by conservation weight:
0.0367226
0.036876
0.0171856
0.0183331
0.0293324
0.0296424
scaling bp penalty by bp weight:
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
Greedy BPE
Scoring with scaled breakpoint penalty: 123710
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..done
Working set size: 1702 Mb
Pagefile usage: 1057 Mb
Arrived at 4 intervals
Adding unaligned intervals
addUnalignedIntervals yields 13 intervals
Merging unaligned intervals

Marbling gaps
Propagating descendant breakpoints
descendant 0(48) has 15 intervals
descendant 1(59) has 1 intervals
propagateDescendantBreakpoints yields 18 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 1.02505e+009
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 121 new matches outside LCBs
1,0 have 122 new matches outside LCBs
2,0 have 9 new matches outside LCBs
3,0 have 9 new matches outside LCBs
4,0 have 109 new matches outside LCBs
5,0 have 105 new matches outside LCBs
0,0 has an additional 435 matches
1,0 has an additional 436 matches
2,0 has an additional 70 matches
3,0 has an additional 68 matches
4,0 has an additional 323 matches
5,0 has an additional 320 matches
Restoring backed up alignment tree...
7,4 has 435 pairwise matches
8,4 has 436 pairwise matches
17,4 has 70 pairwise matches
0,4 has 68 pairwise matches
15,4 has 323 pairwise matches
16,4 has 320 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1710 Mb
Pagefile usage: 1065 Mb
construct LCB tracking matches
There are 787 tracking matches
There are 9238 / 48007 components used
Working set size: 1710 Mb
Pagefile usage: 1065 Mb
init tracking match LCB tracking
Working set size: 1710 Mb
Pagefile usage: 1065 Mb
pairwise score tracking matches
Working set size: 1710 Mb
Pagefile usage: 1065 Mb
get pairwise LCBs
there are 138 pairwise LCBs
Working set size: 1710 Mb
Pagefile usage: 1065 Mb
scaling bp penalty by conservation weight:
0.0367226
0.036876
0.0171856
0.0183331
0.0293324
0.0296424
scaling bp penalty by bp weight:
0.0214286
0.0214286
0.0214286

0.0214286
0.0214286
0.0214286
Greedy BPE
Scoring with scaled breakpoint penalty: 123710
1%..2%..3%..4%..5%..6%..7%..8%..done
Working set size: 1710 Mb
Pagefile usage: 1066 Mb
Arrived at 1 intervals
Adding unaligned intervals
addUnalignedIntervals yields 2 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(48) has 15 intervals
descendant 1(59) has 1 intervals
propagateDescendantBreakpoints yields 15 intervals
Creating ancestral ordering
Previous anchoring score: 1.02505e+009, new anchor score: 1.23025e+009
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 1 new matches outside LCBs
1,0 have 1 new matches outside LCBs
2,0 have 1 new matches outside LCBs
3,0 have 0 new matches outside LCBs
4,0 have 0 new matches outside LCBs
5,0 have 0 new matches outside LCBs
0,0 has an additional 165 matches
1,0 has an additional 165 matches
2,0 has an additional 50 matches
3,0 has an additional 49 matches
4,0 has an additional 50 matches
5,0 has an additional 50 matches
Restoring backed up alignment tree...
7,4 has 165 pairwise matches
8,4 has 165 pairwise matches
17,4 has 50 pairwise matches
0,4 has 49 pairwise matches
15,4 has 50 pairwise matches
16,4 has 50 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1663 Mb
Pagefile usage: 1026 Mb
construct LCB tracking matches
There are 818 tracking matches
There are 9610 / 49898 components used
Working set size: 1667 Mb
Pagefile usage: 1029 Mb
init tracking match LCB tracking
Working set size: 1667 Mb
Pagefile usage: 1029 Mb
pairwise score tracking matches
Working set size: 1669 Mb
Pagefile usage: 1031 Mb
get pairwise LCBs
there are 312 pairwise LCBs
Working set size: 1669 Mb
Pagefile usage: 1031 Mb

scaling bp penalty by conservation weight:

0.0367226
0.036876
0.0171856
0.0183331
0.0293324
0.0296424
scaling bp penalty by bp weight:
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
Greedy BPE
Scoring with scaled breakpoint penalty: 123710
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..done
Working set size: 1669 Mb
Pagefile usage: 1031 Mb
Arrived at 1 intervals
Adding unaligned intervals
addUnalignedIntervals yields 2 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(48) has 15 intervals
descendant 1(59) has 1 intervals
propagateDescendantBreakpoints yields 15 intervals
Creating ancestral ordering
Previous anchoring score: 1.23025e+009, new anchor score: 1.23026e+009
Working set size: 1669 Mb
Pagefile usage: 1032 Mb
propagating ancestral breakpoints
Working set size: 1669 Mb
Pagefile usage: 1032 Mb
performing a gapped alignment
0%..4%..5%..6%..8%..9%..
11%..12%..14%..15%..17%..18%..19%..
21%..23%..25%..26%..27%..28%..29%..
31%..32%..33%..34%..35%..37%..39%..
41%..42%..43%..45%..46%..48%..49%..
51%..52%..53%..55%..56%..58%..59%..
60%..62%..64%..65%..67%..68%..
70%..71%..73%..75%..76%..77%..78%..79%..
81%..83%..85%..87%..89%..
91%..93%..95%..96%..97%..98%..
100%..Working set size: 1630 Mb
Pagefile usage: 983 Mb
Fix left ends
Working set size: 1630 Mb
Pagefile usage: 983 Mb
done.
performing iterative refinement

0%..4%..5%..6%..7%..9%..
11%..12%..14%..15%..17%..18%..19%..
21%..23%..25%..26%..27%..28%..29%..
31%..32%..33%..34%..35%..37%..39%..
41%..42%..43%..45%..46%..48%..49%..
51%..52%..53%..55%..56%..58%..59%..
61%..62%..64%..65%..67%..68%..
70%..71%..73%..74%..75%..76%..77%..78%..79%..
81%..83%..85%..87%..89%..
91%..93%..95%..96%..97%..98%..
100%..Working set size: 1632 Mb
Pagefile usage: 985 Mb
Fix left ends
Working set size: 1632 Mb
Pagefile usage: 985 Mb
done.
Working set size: 1632 Mb
Pagefile usage: 985 Mb
Aligning node 47 to 60 via 46!
Working set size: 1629 Mb
Pagefile usage: 996 Mb
get ancestral matches
Working set size: 1704 Mb
Pagefile usage: 1062 Mb
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1704 Mb
Pagefile usage: 1062 Mb
construct LCB tracking matches
There are 2823 tracking matches
There are 32451 / 172203 components used
Working set size: 1704 Mb
Pagefile usage: 1062 Mb
init tracking match LCB tracking
Working set size: 1704 Mb
Pagefile usage: 1062 Mb
pairwise score tracking matches
Working set size: 1704 Mb
Pagefile usage: 1062 Mb
get pairwise LCBs
there are 2894 pairwise LCBs
Working set size: 1704 Mb
Pagefile usage: 1062 Mb
scaling bp penalty by conservation weight:
0.0355654
0.0507314
0.0508449
0.0447991
0.0456404
0.0524509
0.0525393
scaling bp penalty by bp weight:
0.0214286
0.0857143
0.0857143
0.0214286
0.0214286
0.0214286

0.0214286
Greedy BPE
Scoring with scaled breakpoint penalty: 124306
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..done
Working set size: 1704 Mb
Pagefile usage: 1062 Mb
Arrived at 9 intervals
Adding unaligned intervals
addUnalignedIntervals yields 25 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(47) has 15 intervals
descendant 1(60) has 1 intervals
propagateDescendantBreakpoints yields 23 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 1.27171e+009
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 825 new matches outside LCBs
1,0 have 805 new matches outside LCBs
2,0 have 804 new matches outside LCBs
3,0 have 974 new matches outside LCBs
4,0 have 1150 new matches outside LCBs
5,0 have 803 new matches outside LCBs
6,0 have 807 new matches outside LCBs
0,0 has an additional 1046 matches
1,0 has an additional 1449 matches
2,0 has an additional 1448 matches
3,0 has an additional 1197 matches
4,0 has an additional 1641 matches
5,0 has an additional 1403 matches
6,0 has an additional 1410 matches
Restoring backed up alignment tree...
4,6 has 1046 pairwise matches
7,6 has 1449 pairwise matches
8,6 has 1448 pairwise matches
17,6 has 1197 pairwise matches
0,6 has 1641 pairwise matches
15,6 has 1403 pairwise matches
16,6 has 1410 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1714 Mb
Pagefile usage: 1069 Mb
construct LCB tracking matches
There are 3603 tracking matches
There are 41253 / 219783 components used
Working set size: 1714 Mb
Pagefile usage: 1069 Mb
init tracking match LCB tracking
Working set size: 1714 Mb
Pagefile usage: 1069 Mb
pairwise score tracking matches
Working set size: 1714 Mb
Pagefile usage: 1069 Mb
get pairwise LCBs
there are 9733 pairwise LCBs

Working set size: 1714 Mb

Pagefile usage: 1069 Mb
scaling bp penalty by conservation weight:
0.0355654
0.0507314
0.0508449
0.0447991
0.0456404
0.0524509
0.0525393
scaling bp penalty by bp weight:
0.0214286
0.0857143
0.0857143
0.0214286
0.0214286
0.0214286
0.0214286
Greedy BPE
Scoring with scaled breakpoint penalty: 124306
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..done
Working set size: 1714 Mb
Pagefile usage: 1069 Mb
Arrived at 14 intervals
Adding unaligned intervals
addUnalignedIntervals yields 39 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(47) has 15 intervals
descendant 1(60) has 1 intervals
propagateDescendantBreakpoints yields 28 intervals
Creating ancestral ordering
Previous anchoring score: 1.27171e+009, new anchor score: 1.41249e+009
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 791 new matches outside LCBs
1,0 have 619 new matches outside LCBs
2,0 have 618 new matches outside LCBs
3,0 have 955 new matches outside LCBs
4,0 have 1034 new matches outside LCBs
5,0 have 1434 new matches outside LCBs
6,0 have 1427 new matches outside LCBs
0,0 has an additional 1006 matches
1,0 has an additional 1267 matches
2,0 has an additional 1266 matches
3,0 has an additional 1176 matches
4,0 has an additional 1428 matches
5,0 has an additional 2004 matches
6,0 has an additional 1999 matches
Restoring backed up alignment tree...
4,6 has 1006 pairwise matches
7,6 has 1267 pairwise matches
8,6 has 1266 pairwise matches
17,6 has 1176 pairwise matches

0,6 has 1428 pairwise matches

15,6 has 2004 pairwise matches
16,6 has 1999 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1671 Mb
Pagefile usage: 1031 Mb
construct LCB tracking matches
There are 3656 tracking matches
There are 41857 / 223016 components used
Working set size: 1677 Mb
Pagefile usage: 1037 Mb
init tracking match LCB tracking
Working set size: 1677 Mb
Pagefile usage: 1037 Mb
pairwise score tracking matches
Working set size: 1677 Mb
Pagefile usage: 1037 Mb
get pairwise LCBs
there are 10055 pairwise LCBs
Working set size: 1677 Mb
Pagefile usage: 1037 Mb
scaling bp penalty by conservation weight:
0.0355654
0.0507314
0.0508449
0.0447991
0.0456404
0.0524509
0.0525393
scaling bp penalty by bp weight:
0.0214286
0.0857143
0.0857143
0.0214286
0.0214286
0.0214286
0.0214286
Greedy BPE
Scoring with scaled breakpoint penalty: 124306
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..done
Working set size: 1678 Mb
Pagefile usage: 1038 Mb
Arrived at 17 intervals
Adding unaligned intervals
addUnalignedIntervals yields 48 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(47) has 15 intervals
descendant 1(60) has 1 intervals
propagateDescendantBreakpoints yields 31 intervals
Creating ancestral ordering
Previous anchoring score: 1.41249e+009, new anchor score: 1.41335e+009
Working set size: 1678 Mb
Pagefile usage: 1038 Mb
propagating ancestral breakpoints

Working set size: 1678 Mb

Pagefile usage: 1038 Mb
performing a gapped alignment
0%..1%..2%..3%..4%..5%..6%..8%..9%..
11%..12%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..38%..
40%..41%..42%..44%..45%..46%..48%..49%..
51%..52%..53%..55%..56%..58%..59%..
60%..62%..64%..66%..67%..69%..
70%..71%..72%..73%..74%..75%..76%..77%..78%..79%..
80%..82%..84%..86%..87%..89%..
91%..93%..95%..96%..97%..98%..
100%..Working set size: 1638 Mb
Pagefile usage: 991 Mb
Fix left ends
Working set size: 1638 Mb
Pagefile usage: 991 Mb
done.
Working set size: 1638 Mb
Pagefile usage: 991 Mb
Aligning node 26 to 29 via 25!
Working set size: 1636 Mb
Pagefile usage: 1000 Mb
get ancestral matches
Working set size: 1703 Mb
Pagefile usage: 1059 Mb
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1703 Mb
Pagefile usage: 1059 Mb
construct LCB tracking matches
There are 1715 tracking matches
There are 6737 / 104615 components used
Working set size: 1703 Mb
Pagefile usage: 1059 Mb
init tracking match LCB tracking
Working set size: 1703 Mb
Pagefile usage: 1059 Mb
pairwise score tracking matches
Working set size: 1704 Mb
Pagefile usage: 1059 Mb
get pairwise LCBs
there are 399 pairwise LCBs
Working set size: 1704 Mb
Pagefile usage: 1059 Mb
scaling bp penalty by conservation weight:
0.0291887
0.0311237
scaling bp penalty by bp weight:
0.0857143
0.15
Greedy BPE
Scoring with scaled breakpoint penalty: 111409
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..

20%..21%..22%..23%..24%..25%..26%..27%..28%..done
Working set size: 1704 Mb
Pagefile usage: 1059 Mb
Arrived at 4 intervals
Adding unaligned intervals
addUnalignedIntervals yields 9 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(26) has 4 intervals
descendant 1(29) has 1 intervals
propagateDescendantBreakpoints yields 7 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 3.74759e+008
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 4 new matches outside LCBs
1,0 have 4 new matches outside LCBs
0,0 has an additional 985 matches
1,0 has an additional 984 matches
Restoring backed up alignment tree...
23,3 has 985 pairwise matches
24,3 has 984 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1712 Mb
Pagefile usage: 1068 Mb
construct LCB tracking matches
There are 2277 tracking matches
There are 9103 / 138897 components used
Working set size: 1712 Mb
Pagefile usage: 1068 Mb
init tracking match LCB tracking
Working set size: 1712 Mb
Pagefile usage: 1068 Mb
pairwise score tracking matches
Working set size: 1712 Mb
Pagefile usage: 1068 Mb
get pairwise LCBs
there are 1869 pairwise LCBs
Working set size: 1712 Mb
Pagefile usage: 1068 Mb
scaling bp penalty by conservation weight:
0.0291887
0.0311237
scaling bp penalty by bp weight:
0.0857143
0.15
Greedy BPE
Scoring with scaled breakpoint penalty: 111409
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..done
Working set size: 1712 Mb
Pagefile usage: 1068 Mb

Arrived at 4 intervals
Adding unaligned intervals
addUnalignedIntervals yields 8 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(26) has 4 intervals
descendant 1(29) has 1 intervals
propagateDescendantBreakpoints yields 7 intervals
Creating ancestral ordering
Previous anchoring score: 3.74759e+008, new anchor score: 4.08162e+008
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 5 new matches outside LCBs
1,0 have 5 new matches outside LCBs
0,0 has an additional 632 matches
1,0 has an additional 631 matches
Restoring backed up alignment tree...
23,3 has 632 pairwise matches
24,3 has 631 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1668 Mb
Pagefile usage: 1027 Mb
construct LCB tracking matches
There are 2039 tracking matches
There are 8151 / 124379 components used
Working set size: 1671 Mb
Pagefile usage: 1030 Mb
init tracking match LCB tracking
Working set size: 1671 Mb
Pagefile usage: 1030 Mb
pairwise score tracking matches
Working set size: 1673 Mb
Pagefile usage: 1032 Mb
get pairwise LCBs
there are 1295 pairwise LCBs
Working set size: 1674 Mb
Pagefile usage: 1032 Mb
scaling bp penalty by conservation weight:
0.0291887
0.0311237
scaling bp penalty by bp weight:
0.0857143
0.15
Greedy BPE
Scoring with scaled breakpoint penalty: 111409
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..done
Working set size: 1674 Mb
Pagefile usage: 1033 Mb
Arrived at 4 intervals
Adding unaligned intervals
addUnalignedIntervals yields 8 intervals
Merging unaligned intervals

Marbling gaps
Propagating descendant breakpoints
descendant 0(26) has 4 intervals
descendant 1(29) has 1 intervals
propagateDescendantBreakpoints yields 7 intervals
Creating ancestral ordering
Previous anchoring score: 4.08162e+008, new anchor score: 4.08218e+008
Working set size: 1674 Mb
Pagefile usage: 1033 Mb
propagating ancestral breakpoints
Working set size: 1674 Mb
Pagefile usage: 1033 Mb
performing a gapped alignment
0%..1%..2%..3%..4%..5%..6%..7%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..19%..
20%..22%..23%..24%..25%..26%..28%..
30%..32%..33%..35%..37%..39%..
41%..43%..45%..46%..48%..
50%..52%..54%..56%..57%..58%..59%..
61%..63%..64%..65%..67%..69%..
71%..73%..74%..76%..77%..79%..
81%..82%..84%..85%..87%..88%..
90%..92%..93%..95%..96%..98%..
100%..Working set size: 1653 Mb
Pagefile usage: 1017 Mb
Fix left ends
Working set size: 1653 Mb
Pagefile usage: 1017 Mb
done.
Working set size: 1653 Mb
Pagefile usage: 1017 Mb
Aligning node 7 to 8 via 6!
Working set size: 1651 Mb
Pagefile usage: 1018 Mb
get ancestral matches
Working set size: 1654 Mb
Pagefile usage: 1020 Mb
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1655 Mb
Pagefile usage: 1020 Mb
construct LCB tracking matches
There are 70162 tracking matches
There are 140324 / 4279882 components used
Working set size: 2066 Mb
Pagefile usage: 1421 Mb
init tracking match LCB tracking
Working set size: 2067 Mb
Pagefile usage: 1421 Mb
pairwise score tracking matches
Working set size: 2068 Mb
Pagefile usage: 1422 Mb
get pairwise LCBs
there are 318 pairwise LCBs
Working set size: 2074 Mb
Pagefile usage: 1430 Mb
scaling bp penalty by conservation weight:
0.0365896

scaling bp penalty by bp weight:

0.0428571
Greedy BPE
Scoring with scaled breakpoint penalty: 118417
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..47%..48%..49%..
50%..51%..52%..53%..54%..55%..56%..done
Working set size: 1695 Mb
Pagefile usage: 1054 Mb
Arrived at 2 intervals
Adding unaligned intervals
addUnalignedIntervals yields 5 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(7) has 1 intervals
descendant 1(8) has 1 intervals
propagateDescendantBreakpoints yields 2 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 9.28386e+007
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 55 new matches outside LCBs
0,0 has an additional 876 matches
Restoring backed up alignment tree...
21,12 has 876 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1747 Mb
Pagefile usage: 1161 Mb
construct LCB tracking matches
There are 70523 tracking matches
There are 141046 / 4301903 components used
Working set size: 2099 Mb
Pagefile usage: 1509 Mb
init tracking match LCB tracking
Working set size: 2099 Mb
Pagefile usage: 1509 Mb
pairwise score tracking matches
Working set size: 2100 Mb
Pagefile usage: 1510 Mb
get pairwise LCBs
there are 447 pairwise LCBs
Working set size: 2104 Mb
Pagefile usage: 1514 Mb
scaling bp penalty by conservation weight:
0.0365896
scaling bp penalty by bp weight:
0.0428571
Greedy BPE
Scoring with scaled breakpoint penalty: 118417
1%..2%..3%..4%..5%..6%..7%..8%..9%..

10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..47%..48%..49%..
50%..51%..52%..53%..54%..55%..56%..57%..58%..59%..
60%..61%..62%..63%..64%..65%..66%..67%..68%..69%..
70%..71%..72%..73%..74%..75%..76%..77%..78%..79%..
80%..81%..82%..83%..84%..done
Working set size: 1722 Mb
Pagefile usage: 1140 Mb
Arrived at 2 intervals
Adding unaligned intervals
addUnalignedIntervals yields 5 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(7) has 1 intervals
descendant 1(8) has 1 intervals
propagateDescendantBreakpoints yields 2 intervals
Creating ancestral ordering
Previous anchoring score: 9.28386e+007, new anchor score: 9.87278e+007
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 52 new matches outside LCBs
0,0 has an additional 308 matches
Restoring backed up alignment tree...
21,12 has 308 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1772 Mb
Pagefile usage: 1176 Mb
construct LCB tracking matches
There are 70406 tracking matches
There are 140812 / 4294766 components used
Working set size: 2113 Mb
Pagefile usage: 1507 Mb
init tracking match LCB tracking
Working set size: 2113 Mb
Pagefile usage: 1508 Mb
pairwise score tracking matches
Working set size: 2114 Mb
Pagefile usage: 1509 Mb
get pairwise LCBs
there are 293 pairwise LCBs
Working set size: 2118 Mb
Pagefile usage: 1512 Mb
scaling bp penalty by conservation weight:
0.0365896
scaling bp penalty by bp weight:
0.0428571
Greedy BPE
Scoring with scaled breakpoint penalty: 118417
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..47%..48%..49%..

50%..51%..52%..53%..54%..55%..56%..57%..58%..59%..
60%..61%..62%..63%..64%..65%..66%..67%..68%..69%..
70%..71%..72%..73%..74%..75%..76%..77%..78%..79%..
80%..81%..82%..done
Working set size: 1738 Mb
Pagefile usage: 1140 Mb
Arrived at 2 intervals
Adding unaligned intervals
addUnalignedIntervals yields 5 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(7) has 1 intervals
descendant 1(8) has 1 intervals
propagateDescendantBreakpoints yields 2 intervals
Creating ancestral ordering
Previous anchoring score: 9.87278e+007, new anchor score: 9.87202e+007
Working set size: 1741 Mb
Pagefile usage: 1142 Mb
propagating ancestral breakpoints
Working set size: 1741 Mb
Pagefile usage: 1142 Mb
performing a gapped alignment
0%..1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..47%..48%..49%..
50%..51%..52%..53%..54%..55%..56%..57%..58%..59%..
60%..61%..62%..63%..64%..65%..66%..67%..68%..69%..
70%..71%..72%..73%..74%..75%..76%..77%..78%..79%..
80%..81%..82%..83%..84%..85%..86%..87%..88%..89%..
90%..91%..92%..93%..94%..95%..96%..97%..98%..99%..
100%..Working set size: 1780 Mb
Pagefile usage: 1204 Mb
Fix left ends
Working set size: 1780 Mb
Pagefile usage: 1204 Mb
done.
Working set size: 1780 Mb
Pagefile usage: 1204 Mb
Aligning node 32 to 33 via 31!
Working set size: 1713 Mb
Pagefile usage: 1108 Mb
get ancestral matches
Working set size: 1718 Mb
Pagefile usage: 1112 Mb
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1718 Mb
Pagefile usage: 1112 Mb
construct LCB tracking matches
There are 896 tracking matches
There are 1792 / 54656 components used
Working set size: 1727 Mb
Pagefile usage: 1121 Mb
init tracking match LCB tracking
Working set size: 1727 Mb
Pagefile usage: 1121 Mb

pairwise score tracking matches

Working set size: 1731 Mb
Pagefile usage: 1125 Mb
get pairwise LCBs
there are 176 pairwise LCBs
Working set size: 1731 Mb
Pagefile usage: 1125 Mb
scaling bp penalty by conservation weight:
0.0396506
scaling bp penalty by bp weight:
0.0214286
Greedy BPE
Scoring with scaled breakpoint penalty: 122213
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..47%..48%..49%..
50%..51%..52%..53%..54%..55%..56%..57%..58%..59%..
60%..61%..62%..done
Working set size: 1730 Mb
Pagefile usage: 1128 Mb
Arrived at 4 intervals
Adding unaligned intervals
addUnalignedIntervals yields 9 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(32) has 1 intervals
descendant 1(33) has 1 intervals
propagateDescendantBreakpoints yields 4 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 1.98945e+008
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 397 new matches outside LCBs
0,0 has an additional 1455 matches
Restoring backed up alignment tree...
26,18 has 1455 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1749 Mb
Pagefile usage: 1147 Mb
construct LCB tracking matches
There are 1855 tracking matches
There are 3710 / 113155 components used
Working set size: 1753 Mb
Pagefile usage: 1151 Mb
init tracking match LCB tracking
Working set size: 1753 Mb
Pagefile usage: 1151 Mb
pairwise score tracking matches
Working set size: 1754 Mb
Pagefile usage: 1151 Mb
get pairwise LCBs
there are 1238 pairwise LCBs
Working set size: 1754 Mb

Pagefile usage: 1152 Mb

scaling bp penalty by conservation weight:
0.0396506
scaling bp penalty by bp weight:
0.0214286
Greedy BPE
Scoring with scaled breakpoint penalty: 122213
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..47%..48%..49%..
50%..51%..52%..53%..54%..55%..56%..57%..58%..59%..
60%..61%..62%..63%..64%..65%..66%..67%..68%..69%..
70%..71%..72%..73%..74%..75%..76%..77%..78%..79%..
80%..81%..82%..83%..84%..85%..86%..87%..88%..89%..done
Working set size: 1754 Mb
Pagefile usage: 1154 Mb
Arrived at 4 intervals
Adding unaligned intervals
addUnalignedIntervals yields 8 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(32) has 1 intervals
descendant 1(33) has 1 intervals
propagateDescendantBreakpoints yields 4 intervals
Creating ancestral ordering
Previous anchoring score: 1.98945e+008, new anchor score: 2.02635e+008
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 2 new matches outside LCBs
0,0 has an additional 964 matches
Restoring backed up alignment tree...
26,18 has 964 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1757 Mb
Pagefile usage: 1159 Mb
construct LCB tracking matches
There are 1576 tracking matches
There are 3152 / 96136 components used
Working set size: 1758 Mb
Pagefile usage: 1159 Mb
init tracking match LCB tracking
Working set size: 1758 Mb
Pagefile usage: 1159 Mb
pairwise score tracking matches
Working set size: 1758 Mb
Pagefile usage: 1159 Mb
get pairwise LCBs
there are 949 pairwise LCBs
Working set size: 1758 Mb
Pagefile usage: 1159 Mb
scaling bp penalty by conservation weight:
0.0396506

scaling bp penalty by bp weight:

0.0214286
Greedy BPE
Scoring with scaled breakpoint penalty: 122213
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..47%..48%..49%..
50%..51%..52%..53%..54%..55%..56%..57%..58%..59%..
60%..61%..62%..63%..64%..65%..66%..67%..68%..69%..
70%..71%..72%..73%..74%..75%..76%..77%..78%..79%..
80%..81%..82%..83%..84%..85%..done
Working set size: 1758 Mb
Pagefile usage: 1161 Mb
Arrived at 4 intervals
Adding unaligned intervals
addUnalignedIntervals yields 8 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(32) has 1 intervals
descendant 1(33) has 1 intervals
propagateDescendantBreakpoints yields 4 intervals
Creating ancestral ordering
Previous anchoring score: 2.02635e+008, new anchor score: 2.02659e+008
Working set size: 1758 Mb
Pagefile usage: 1161 Mb
propagating ancestral breakpoints
Working set size: 1758 Mb
Pagefile usage: 1161 Mb
performing a gapped alignment
0%..1%..2%..4%..5%..6%..8%..9%..
10%..12%..13%..15%..16%..17%..19%..
20%..21%..23%..24%..25%..27%..28%..29%..
31%..32%..34%..35%..36%..38%..
40%..42%..43%..45%..47%..49%..
50%..51%..52%..53%..55%..57%..59%..
60%..62%..64%..66%..67%..68%..69%..
70%..71%..72%..73%..74%..76%..78%..79%..
81%..82%..84%..85%..87%..89%..
90%..92%..93%..95%..96%..98%..
100%..Working set size: 1734 Mb
Pagefile usage: 1130 Mb
Fix left ends
Working set size: 1734 Mb
Pagefile usage: 1130 Mb
done.
Working set size: 1734 Mb
Pagefile usage: 1130 Mb
Aligning node 31 to 34 via 30!
Working set size: 1730 Mb
Pagefile usage: 1127 Mb
get ancestral matches
Working set size: 1818 Mb
Pagefile usage: 1213 Mb

Performing Sum-of-pairs Greedy Breakpoint Elimination

Working set size: 1818 Mb
Pagefile usage: 1213 Mb
construct LCB tracking matches
There are 340 tracking matches
There are 1346 / 20740 components used
Working set size: 1818 Mb
Pagefile usage: 1213 Mb
init tracking match LCB tracking
Working set size: 1818 Mb
Pagefile usage: 1213 Mb
pairwise score tracking matches
Working set size: 1818 Mb
Pagefile usage: 1213 Mb
get pairwise LCBs
there are 27 pairwise LCBs
Working set size: 1818 Mb
Pagefile usage: 1213 Mb
scaling bp penalty by conservation weight:
0.0248825
0.0360575
scaling bp penalty by bp weight:
0.0214286
0.0214286
Greedy BPE
Scoring with scaled breakpoint penalty: 129906
3%..7%..
11%..14%..18%..
22%..25%..29%..
33%..37%..
40%..44%..done
Working set size: 1818 Mb
Pagefile usage: 1213 Mb
Arrived at 4 intervals
Adding unaligned intervals
addUnalignedIntervals yields 9 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(31) has 4 intervals
descendant 1(34) has 1 intervals
propagateDescendantBreakpoints yields 7 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 3.98317e+008
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 85 new matches outside LCBs
1,0 have 97 new matches outside LCBs
0,0 has an additional 108 matches
1,0 has an additional 203 matches
Restoring backed up alignment tree...
18,28 has 108 pairwise matches
26,28 has 203 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1826 Mb
Pagefile usage: 1222 Mb

construct LCB tracking matches

There are 563 tracking matches
There are 2067 / 34343 components used
Working set size: 1826 Mb
Pagefile usage: 1222 Mb
init tracking match LCB tracking
Working set size: 1826 Mb
Pagefile usage: 1222 Mb
pairwise score tracking matches
Working set size: 1826 Mb
Pagefile usage: 1222 Mb
get pairwise LCBs
there are 276 pairwise LCBs
Working set size: 1826 Mb
Pagefile usage: 1222 Mb
scaling bp penalty by conservation weight:
0.0248825
0.0360575
scaling bp penalty by bp weight:
0.0214286
0.0214286
Greedy BPE
Scoring with scaled breakpoint penalty: 129906
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..47%..48%..49%..
50%..51%..52%..53%..54%..55%..56%..57%..58%..59%..
60%..61%..62%..63%..64%..65%..66%..67%..68%..69%..
70%..71%..72%..73%..done
Working set size: 1826 Mb
Pagefile usage: 1222 Mb
Arrived at 4 intervals
Adding unaligned intervals
addUnalignedIntervals yields 8 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(31) has 4 intervals
descendant 1(34) has 1 intervals
propagateDescendantBreakpoints yields 7 intervals
Creating ancestral ordering
Previous anchoring score: 3.98317e+008, new anchor score: 4.0481e+008
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 82 new matches outside LCBs
1,0 have 44 new matches outside LCBs
0,0 has an additional 119 matches
1,0 has an additional 155 matches
Restoring backed up alignment tree...
18,28 has 119 pairwise matches
26,28 has 155 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1826 Mb
Pagefile usage: 1223 Mb

construct LCB tracking matches

There are 549 tracking matches
There are 2023 / 33489 components used
Working set size: 1826 Mb
Pagefile usage: 1223 Mb
init tracking match LCB tracking
Working set size: 1826 Mb
Pagefile usage: 1223 Mb
pairwise score tracking matches
Working set size: 1826 Mb
Pagefile usage: 1223 Mb
get pairwise LCBs
there are 259 pairwise LCBs
Working set size: 1826 Mb
Pagefile usage: 1223 Mb
scaling bp penalty by conservation weight:
0.0248825
0.0360575
scaling bp penalty by bp weight:
0.0214286
0.0214286
Greedy BPE
Scoring with scaled breakpoint penalty: 129906
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..47%..48%..49%..
50%..51%..52%..53%..54%..55%..56%..57%..58%..59%..
60%..61%..62%..63%..64%..65%..66%..67%..68%..69%..
70%..71%..done
Working set size: 1826 Mb
Pagefile usage: 1225 Mb
Arrived at 4 intervals
Adding unaligned intervals
addUnalignedIntervals yields 8 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(31) has 4 intervals
descendant 1(34) has 1 intervals
propagateDescendantBreakpoints yields 7 intervals
Creating ancestral ordering
Previous anchoring score: 4.0481e+008, new anchor score: 4.04812e+008
Working set size: 1826 Mb
Pagefile usage: 1225 Mb
propagating ancestral breakpoints
Working set size: 1826 Mb
Pagefile usage: 1225 Mb
performing a gapped alignment
0%..2%..3%..4%..6%..7%..8%..
10%..11%..13%..14%..16%..17%..18%..
20%..21%..22%..24%..25%..26%..28%..29%..
31%..32%..33%..35%..36%..37%..39%..
40%..42%..44%..45%..46%..48%..
50%..52%..54%..55%..57%..59%..

61%..62%..64%..66%..68%..69%..
70%..71%..72%..73%..74%..76%..78%..79%..
81%..82%..84%..85%..87%..89%..
90%..92%..93%..95%..96%..98%..
100%..Working set size: 1772 Mb
Pagefile usage: 1181 Mb
Fix left ends
Working set size: 1772 Mb
Pagefile usage: 1181 Mb
done.
Working set size: 1772 Mb
Pagefile usage: 1181 Mb
Aligning node 25 to 30 via 24!
Working set size: 1770 Mb
Pagefile usage: 1181 Mb
get ancestral matches
Working set size: 1830 Mb
Pagefile usage: 1236 Mb
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1830 Mb
Pagefile usage: 1236 Mb
construct LCB tracking matches
There are 3295 tracking matches
There are 27841 / 200995 components used
Working set size: 1830 Mb
Pagefile usage: 1236 Mb
init tracking match LCB tracking
Working set size: 1831 Mb
Pagefile usage: 1237 Mb
pairwise score tracking matches
Working set size: 1831 Mb
Pagefile usage: 1237 Mb
get pairwise LCBs
there are 2107 pairwise LCBs
Working set size: 1831 Mb
Pagefile usage: 1237 Mb
scaling bp penalty by conservation weight:
0.027596
0.0353167
0.0485045
0.0353942
0.0370941
0.045915
0.0359626
0.0374669
0.0465789
scaling bp penalty by bp weight:
0.0214286
0.0857143
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
Greedy BPE
Scoring with scaled breakpoint penalty: 128466
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..done
Working set size: 1831 Mb
Pagefile usage: 1237 Mb
Arrived at 13 intervals
Adding unaligned intervals
addUnalignedIntervals yields 36 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints

descendant 0(25) has 7 intervals

descendant 1(30) has 7 intervals
propagateDescendantBreakpoints yields 23 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 1.61091e+009
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 189 new matches outside LCBs
0,1 have 452 new matches outside LCBs
0,2 have 451 new matches outside LCBs
1,0 have 170 new matches outside LCBs
1,1 have 957 new matches outside LCBs
1,2 have 516 new matches outside LCBs
2,0 have 169 new matches outside LCBs
2,1 have 956 new matches outside LCBs
2,2 have 517 new matches outside LCBs
0,0 has an additional 259 matches
0,1 has an additional 1062 matches
0,2 has an additional 1044 matches
1,0 has an additional 266 matches
1,1 has an additional 1983 matches
1,2 has an additional 1360 matches
2,0 has an additional 268 matches
2,1 has an additional 1987 matches
2,2 has an additional 1364 matches
Restoring backed up alignment tree...
3,28 has 259 pairwise matches
3,18 has 1062 pairwise matches
3,26 has 1044 pairwise matches
23,28 has 266 pairwise matches
23,18 has 1983 pairwise matches
23,26 has 1360 pairwise matches
24,28 has 268 pairwise matches
24,18 has 1987 pairwise matches
24,26 has 1364 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1843 Mb
Pagefile usage: 1243 Mb
construct LCB tracking matches
There are 2876 tracking matches
There are 24082 / 175436 components used
Working set size: 1843 Mb
Pagefile usage: 1243 Mb
init tracking match LCB tracking
Working set size: 1843 Mb
Pagefile usage: 1243 Mb
pairwise score tracking matches
Working set size: 1843 Mb
Pagefile usage: 1243 Mb
get pairwise LCBs
there are 4640 pairwise LCBs
Working set size: 1843 Mb
Pagefile usage: 1243 Mb
scaling bp penalty by conservation weight:
0.027596
0.0353167
0.0485045
0.0353942
0.0370941
0.045915
0.0359626
0.0374669
0.0465789

scaling bp penalty by bp weight:

0.0214286
0.0857143
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
Greedy BPE
Scoring with scaled breakpoint penalty: 128466
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..done
Working set size: 1843 Mb
Pagefile usage: 1243 Mb
Arrived at 15 intervals
Adding unaligned intervals
addUnalignedIntervals yields 40 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(25) has 7 intervals
descendant 1(30) has 7 intervals
propagateDescendantBreakpoints yields 26 intervals
Creating ancestral ordering
Previous anchoring score: 1.61091e+009, new anchor score: 1.81791e+009
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 147 new matches outside LCBs
0,1 have 835 new matches outside LCBs
0,2 have 784 new matches outside LCBs
1,0 have 167 new matches outside LCBs
1,1 have 882 new matches outside LCBs
1,2 have 553 new matches outside LCBs
2,0 have 166 new matches outside LCBs
2,1 have 882 new matches outside LCBs
2,2 have 552 new matches outside LCBs
0,0 has an additional 185 matches
0,1 has an additional 1527 matches
0,2 has an additional 1571 matches
1,0 has an additional 223 matches
1,1 has an additional 1831 matches
1,2 has an additional 1547 matches
2,0 has an additional 222 matches
2,1 has an additional 1832 matches
2,2 has an additional 1547 matches
Restoring backed up alignment tree...
3,28 has 185 pairwise matches
3,18 has 1527 pairwise matches
3,26 has 1571 pairwise matches
23,28 has 223 pairwise matches
23,18 has 1831 pairwise matches
23,26 has 1547 pairwise matches
24,28 has 222 pairwise matches
24,18 has 1832 pairwise matches
24,26 has 1547 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1842 Mb
Pagefile usage: 1242 Mb
construct LCB tracking matches
There are 2702 tracking matches
There are 22930 / 164822 components used

Working set size: 1842 Mb

Pagefile usage: 1242 Mb
init tracking match LCB tracking
Working set size: 1842 Mb
Pagefile usage: 1242 Mb
pairwise score tracking matches
Working set size: 1842 Mb
Pagefile usage: 1242 Mb
get pairwise LCBs
there are 5136 pairwise LCBs
Working set size: 1842 Mb
Pagefile usage: 1242 Mb
scaling bp penalty by conservation weight:
0.027596
0.0353167
0.0485045
0.0353942
0.0370941
0.045915
0.0359626
0.0374669
0.0465789
scaling bp penalty by bp weight:
0.0214286
0.0857143
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
Greedy BPE
Scoring with scaled breakpoint penalty: 128466
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..done
Working set size: 1842 Mb
Pagefile usage: 1242 Mb
Arrived at 19 intervals
Adding unaligned intervals
addUnalignedIntervals yields 50 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(25) has 7 intervals
descendant 1(30) has 7 intervals
propagateDescendantBreakpoints yields 29 intervals
Creating ancestral ordering
Previous anchoring score: 1.81791e+009, new anchor score: 1.82203e+009
Working set size: 1842 Mb
Pagefile usage: 1242 Mb
propagating ancestral breakpoints
Working set size: 1842 Mb
Pagefile usage: 1242 Mb
performing a gapped alignment
0%..1%..2%..4%..5%..7%..8%..9%..
10%..11%..12%..14%..16%..17%..19%..
21%..23%..25%..27%..28%..29%..
31%..32%..34%..35%..36%..37%..38%..39%..
40%..41%..43%..45%..46%..48%..49%..
50%..51%..52%..54%..55%..56%..57%..58%..59%..
61%..62%..63%..64%..66%..67%..68%..
70%..71%..73%..74%..76%..77%..79%..
80%..82%..83%..85%..86%..88%..89%..
90%..91%..92%..93%..94%..95%..96%..97%..98%..99%..Working set size: 1829 Mb
Pagefile usage: 1228 Mb
Fix left ends

Working set size: 1829 Mb

Pagefile usage: 1228 Mb
done.
performing iterative refinement
0%..1%..2%..4%..5%..7%..8%..9%..
10%..11%..12%..14%..15%..17%..19%..
21%..23%..25%..27%..28%..29%..
31%..32%..34%..36%..38%..
40%..41%..43%..45%..46%..48%..49%..
50%..51%..52%..54%..55%..56%..57%..58%..59%..
61%..62%..63%..64%..65%..67%..68%..
70%..71%..73%..74%..76%..77%..79%..
80%..82%..83%..85%..86%..88%..89%..
90%..91%..92%..93%..94%..95%..96%..97%..98%..99%..Working set size: 1781 Mb
Pagefile usage: 1184 Mb
Fix left ends
Working set size: 1781 Mb
Pagefile usage: 1184 Mb
done.
Working set size: 1781 Mb
Pagefile usage: 1184 Mb
Aligning node 37 to 38 via 36!
Working set size: 1779 Mb
Pagefile usage: 1189 Mb
get ancestral matches
Working set size: 1781 Mb
Pagefile usage: 1192 Mb
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1781 Mb
Pagefile usage: 1192 Mb
construct LCB tracking matches
There are 1177 tracking matches
There are 2354 / 71797 components used
Working set size: 1784 Mb
Pagefile usage: 1193 Mb
init tracking match LCB tracking
Working set size: 1784 Mb
Pagefile usage: 1193 Mb
pairwise score tracking matches
Working set size: 1785 Mb
Pagefile usage: 1194 Mb
get pairwise LCBs
there are 167 pairwise LCBs
Working set size: 1785 Mb
Pagefile usage: 1194 Mb
scaling bp penalty by conservation weight:
0.0400735
scaling bp penalty by bp weight:
0.0642857
Greedy BPE
Scoring with scaled breakpoint penalty: 111546
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..

30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..47%..48%..49%..
50%..51%..52%..53%..54%..55%..56%..57%..58%..59%..
60%..61%..62%..63%..64%..done
Working set size: 1785 Mb
Pagefile usage: 1196 Mb
Arrived at 3 intervals
Adding unaligned intervals
addUnalignedIntervals yields 10 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(37) has 1 intervals
descendant 1(38) has 1 intervals
propagateDescendantBreakpoints yields 3 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 2.05284e+008
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 4 new matches outside LCBs
0,0 has an additional 394 matches
Restoring backed up alignment tree...
25,20 has 394 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1794 Mb
Pagefile usage: 1201 Mb
construct LCB tracking matches
There are 1312 tracking matches
There are 2624 / 80032 components used
Working set size: 1794 Mb
Pagefile usage: 1201 Mb
init tracking match LCB tracking
Working set size: 1794 Mb
Pagefile usage: 1201 Mb
pairwise score tracking matches
Working set size: 1794 Mb
Pagefile usage: 1201 Mb
get pairwise LCBs
there are 340 pairwise LCBs
Working set size: 1794 Mb
Pagefile usage: 1201 Mb
scaling bp penalty by conservation weight:
0.0400735
scaling bp penalty by bp weight:
0.0642857
Greedy BPE
Scoring with scaled breakpoint penalty: 111546
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..47%..48%..49%..
50%..51%..52%..53%..54%..55%..56%..57%..58%..59%..
60%..61%..62%..63%..64%..65%..66%..67%..68%..69%..
70%..71%..72%..73%..74%..75%..76%..77%..78%..79%..
80%..81%..82%..83%..done

Working set size: 1794 Mb

Pagefile usage: 1202 Mb
Arrived at 3 intervals
Adding unaligned intervals
addUnalignedIntervals yields 10 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(37) has 1 intervals
descendant 1(38) has 1 intervals
propagateDescendantBreakpoints yields 3 intervals
Creating ancestral ordering
Previous anchoring score: 2.05284e+008, new anchor score: 2.07729e+008
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 1 new matches outside LCBs
0,0 has an additional 312 matches
Restoring backed up alignment tree...
25,20 has 312 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1799 Mb
Pagefile usage: 1209 Mb
construct LCB tracking matches
There are 1285 tracking matches
There are 2570 / 78385 components used
Working set size: 1799 Mb
Pagefile usage: 1209 Mb
init tracking match LCB tracking
Working set size: 1799 Mb
Pagefile usage: 1209 Mb
pairwise score tracking matches
Working set size: 1799 Mb
Pagefile usage: 1209 Mb
get pairwise LCBs
there are 304 pairwise LCBs
Working set size: 1799 Mb
Pagefile usage: 1209 Mb
scaling bp penalty by conservation weight:
0.0400735
scaling bp penalty by bp weight:
0.0642857
Greedy BPE
Scoring with scaled breakpoint penalty: 111546
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..47%..48%..49%..
50%..51%..52%..53%..54%..55%..56%..57%..58%..59%..
60%..61%..62%..63%..64%..65%..66%..67%..68%..69%..
70%..71%..72%..73%..74%..75%..76%..77%..78%..done
Working set size: 1799 Mb
Pagefile usage: 1210 Mb
Arrived at 3 intervals
Adding unaligned intervals
addUnalignedIntervals yields 10 intervals

Merging unaligned intervals

Marbling gaps
Propagating descendant breakpoints
descendant 0(37) has 1 intervals
descendant 1(38) has 1 intervals
propagateDescendantBreakpoints yields 3 intervals
Creating ancestral ordering
Previous anchoring score: 2.07729e+008, new anchor score: 2.07726e+008
Working set size: 1799 Mb
Pagefile usage: 1210 Mb
propagating ancestral breakpoints
Working set size: 1799 Mb
Pagefile usage: 1210 Mb
performing a gapped alignment
0%..1%..2%..4%..5%..7%..8%..
10%..11%..13%..14%..15%..17%..18%..19%..
20%..21%..22%..24%..25%..27%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..47%..48%..
50%..51%..52%..53%..54%..55%..56%..57%..58%..59%..
60%..61%..62%..63%..64%..65%..66%..67%..68%..
70%..71%..72%..73%..74%..75%..76%..78%..79%..
80%..81%..82%..83%..84%..85%..86%..87%..88%..89%..
90%..91%..92%..93%..94%..95%..96%..98%..
100%..Working set size: 1715 Mb
Pagefile usage: 1110 Mb
Fix left ends
Working set size: 1715 Mb
Pagefile usage: 1110 Mb
done.
Working set size: 1715 Mb
Pagefile usage: 1110 Mb
Aligning node 36 to 39 via 35!
Working set size: 1712 Mb
Pagefile usage: 1112 Mb
get ancestral matches
Working set size: 1818 Mb
Pagefile usage: 1215 Mb
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1818 Mb
Pagefile usage: 1215 Mb
construct LCB tracking matches
There are 3471 tracking matches
There are 12134 / 211731 components used
Working set size: 1818 Mb
Pagefile usage: 1215 Mb
init tracking match LCB tracking
Working set size: 1818 Mb
Pagefile usage: 1215 Mb
pairwise score tracking matches
Working set size: 1818 Mb
Pagefile usage: 1215 Mb
get pairwise LCBs
there are 532 pairwise LCBs
Working set size: 1818 Mb
Pagefile usage: 1215 Mb
scaling bp penalty by conservation weight:
0.0523941

0.0544181
scaling bp penalty by bp weight:
0.0857143
0.128571
Greedy BPE
Scoring with scaled breakpoint penalty: 101132
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..47%..48%..49%..
50%..51%..52%..done
Working set size: 1818 Mb
Pagefile usage: 1216 Mb
Arrived at 9 intervals
Adding unaligned intervals
addUnalignedIntervals yields 24 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(36) has 3 intervals
descendant 1(39) has 1 intervals
propagateDescendantBreakpoints yields 11 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 3.99871e+008
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 67 new matches outside LCBs
1,0 have 470 new matches outside LCBs
0,0 has an additional 439 matches
1,0 has an additional 1035 matches
Restoring backed up alignment tree...
20,22 has 439 pairwise matches
25,22 has 1035 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1836 Mb
Pagefile usage: 1233 Mb
construct LCB tracking matches
There are 3861 tracking matches
There are 13359 / 235521 components used
Working set size: 1836 Mb
Pagefile usage: 1233 Mb
init tracking match LCB tracking
Working set size: 1836 Mb
Pagefile usage: 1233 Mb
pairwise score tracking matches
Working set size: 1836 Mb
Pagefile usage: 1233 Mb
get pairwise LCBs
there are 1182 pairwise LCBs
Working set size: 1836 Mb
Pagefile usage: 1233 Mb
scaling bp penalty by conservation weight:
0.0523941
0.0544181

scaling bp penalty by bp weight:

0.0857143
0.128571
Greedy BPE
Scoring with scaled breakpoint penalty: 101132
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..47%..48%..49%..
50%..51%..52%..53%..54%..55%..56%..57%..58%..59%..
60%..61%..62%..63%..64%..65%..66%..67%..68%..69%..
70%..71%..72%..73%..74%..75%..done
Working set size: 1836 Mb
Pagefile usage: 1233 Mb
Arrived at 12 intervals
Adding unaligned intervals
addUnalignedIntervals yields 33 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(36) has 3 intervals
descendant 1(39) has 1 intervals
propagateDescendantBreakpoints yields 14 intervals
Creating ancestral ordering
Previous anchoring score: 3.99871e+008, new anchor score: 4.13905e+008
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 49 new matches outside LCBs
1,0 have 454 new matches outside LCBs
0,0 has an additional 356 matches
1,0 has an additional 767 matches
Restoring backed up alignment tree...
20,22 has 356 pairwise matches
25,22 has 767 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 1837 Mb
Pagefile usage: 1236 Mb
construct LCB tracking matches
There are 3636 tracking matches
There are 12698 / 221796 components used
Working set size: 1837 Mb
Pagefile usage: 1236 Mb
init tracking match LCB tracking
Working set size: 1837 Mb
Pagefile usage: 1236 Mb
pairwise score tracking matches
Working set size: 1837 Mb
Pagefile usage: 1236 Mb
get pairwise LCBs
there are 940 pairwise LCBs
Working set size: 1837 Mb
Pagefile usage: 1236 Mb
scaling bp penalty by conservation weight:
0.0523941
0.0544181

scaling bp penalty by bp weight:

0.0857143
0.128571
Greedy BPE
Scoring with scaled breakpoint penalty: 101132
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..47%..48%..49%..
50%..51%..52%..53%..54%..55%..56%..57%..58%..59%..
60%..61%..62%..63%..64%..65%..66%..67%..68%..done
Working set size: 1837 Mb
Pagefile usage: 1236 Mb
Arrived at 14 intervals
Adding unaligned intervals
addUnalignedIntervals yields 38 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(36) has 3 intervals
descendant 1(39) has 1 intervals
propagateDescendantBreakpoints yields 16 intervals
Creating ancestral ordering
Previous anchoring score: 4.13905e+008, new anchor score: 4.1408e+008
Working set size: 1837 Mb
Pagefile usage: 1236 Mb
propagating ancestral breakpoints
Working set size: 1837 Mb
Pagefile usage: 1236 Mb
performing a gapped alignment
0%..1%..2%..4%..5%..6%..7%..8%..
10%..11%..12%..13%..14%..15%..16%..17%..19%..
20%..22%..23%..25%..26%..28%..29%..
31%..32%..33%..34%..35%..36%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..47%..48%..49%..
50%..52%..53%..54%..55%..56%..57%..58%..59%..
60%..61%..62%..63%..64%..66%..67%..68%..69%..
70%..71%..72%..73%..74%..75%..76%..77%..78%..79%..
80%..81%..83%..84%..85%..86%..88%..89%..
90%..91%..92%..94%..95%..96%..98%..
100%..Working set size: 2039 Mb
Pagefile usage: 1445 Mb
Fix left ends
Working set size: 2039 Mb
Pagefile usage: 1445 Mb
done.
Working set size: 2039 Mb
Pagefile usage: 1445 Mb
Aligning node 24 to 35 via 23!
Working set size: 1940 Mb
Pagefile usage: 1344 Mb
get ancestral matches
Working set size: 2012 Mb
Pagefile usage: 1418 Mb
Performing Sum-of-pairs Greedy Breakpoint Elimination

Working set size: 2012 Mb

Pagefile usage: 1418 Mb
construct LCB tracking matches
There are 10963 tracking matches
There are 152749 / 668743 components used
Working set size: 2027 Mb
Pagefile usage: 1434 Mb
init tracking match LCB tracking
Working set size: 2029 Mb
Pagefile usage: 1435 Mb
pairwise score tracking matches
Working set size: 2031 Mb
Pagefile usage: 1437 Mb
get pairwise LCBs
there are 22023 pairwise LCBs
Working set size: 2033 Mb
Pagefile usage: 1439 Mb
scaling bp penalty by conservation weight:
0.0774707
0.0645797
0.0720507
0.0861736
0.0785832
0.0803533
0.0854778
0.0778114
0.0792185
0.0811188
0.0685153
0.0744399
0.0809056
0.0658616
0.0729402
0.0810625
0.0657754
0.0729207
scaling bp penalty by bp weight:
0.0214286
0.0214286
0.0214286
0.0857143
0.0214286
0.0642857
0.0214286
0.0214286
0.0642857
0.0857143
0.0857143
0.128571
0.0857143
0.0857143
0.128571
0.0857143
0.0857143
0.128571
Greedy BPE
Scoring with scaled breakpoint penalty: 104069
1%..2%..3%..4%..5%..6%..7%..done
Working set size: 2033 Mb
Pagefile usage: 1439 Mb
Arrived at 32 intervals
Adding unaligned intervals
addUnalignedIntervals yields 94 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(24) has 26 intervals
descendant 1(35) has 14 intervals
propagateDescendantBreakpoints yields 69 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 3.12121e+009
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 526 new matches outside LCBs
0,1 have 433 new matches outside LCBs
0,2 have 423 new matches outside LCBs
1,0 have 2166 new matches outside LCBs
1,1 have 1386 new matches outside LCBs
1,2 have 1524 new matches outside LCBs
2,0 have 1286 new matches outside LCBs

2,1 have 885 new matches outside LCBs

2,2 have 928 new matches outside LCBs
3,0 have 1847 new matches outside LCBs
3,1 have 1041 new matches outside LCBs
3,2 have 1297 new matches outside LCBs
4,0 have 1936 new matches outside LCBs
4,1 have 908 new matches outside LCBs
4,2 have 1464 new matches outside LCBs
5,0 have 1936 new matches outside LCBs
5,1 have 907 new matches outside LCBs
5,2 have 1463 new matches outside LCBs
0,0 has an additional 1449 matches
0,1 has an additional 1141 matches
0,2 has an additional 1222 matches
1,0 has an additional 4219 matches
1,1 has an additional 2424 matches
1,2 has an additional 2837 matches
2,0 has an additional 2744 matches
2,1 has an additional 1858 matches
2,2 has an additional 2522 matches
3,0 has an additional 3185 matches
3,1 has an additional 1759 matches
3,2 has an additional 2455 matches
4,0 has an additional 3723 matches
4,1 has an additional 1996 matches
4,2 has an additional 2917 matches
5,0 has an additional 3736 matches
5,1 has an additional 2007 matches
5,2 has an additional 2923 matches
Restoring backed up alignment tree...
28,22 has 1449 pairwise matches
28,20 has 1141 pairwise matches
28,25 has 1222 pairwise matches
18,22 has 4219 pairwise matches
18,20 has 2424 pairwise matches
18,25 has 2837 pairwise matches
26,22 has 2744 pairwise matches
26,20 has 1858 pairwise matches
26,25 has 2522 pairwise matches
3,22 has 3185 pairwise matches
3,20 has 1759 pairwise matches
3,25 has 2455 pairwise matches
23,22 has 3723 pairwise matches
23,20 has 1996 pairwise matches
23,25 has 2917 pairwise matches
24,22 has 3736 pairwise matches
24,20 has 2007 pairwise matches
24,25 has 2923 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 2039 Mb
Pagefile usage: 1444 Mb
construct LCB tracking matches
There are 9757 tracking matches
There are 142228 / 595177 components used
Working set size: 2039 Mb
Pagefile usage: 1444 Mb
init tracking match LCB tracking
Working set size: 2040 Mb
Pagefile usage: 1445 Mb
pairwise score tracking matches

Working set size: 2042 Mb

Pagefile usage: 1446 Mb
get pairwise LCBs
there are 21139 pairwise LCBs
Working set size: 2042 Mb
Pagefile usage: 1446 Mb
scaling bp penalty by conservation weight:
0.0774707
0.0645797
0.0720507
0.0861736
0.0785832
0.0803533
0.0854778
0.0778114
0.0792185
0.0811188
0.0685153
0.0744399
0.0809056
0.0658616
0.0729402
0.0810625
0.0657754
0.0729207
scaling bp penalty by bp weight:
0.0214286
0.0214286
0.0214286
0.0857143
0.0214286
0.0642857
0.0214286
0.0214286
0.0642857
0.0857143
0.0857143
0.128571
0.0857143
0.0857143
0.128571
0.0857143
0.0857143
0.128571
Greedy BPE
Scoring with scaled breakpoint penalty: 104069
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..done
Working set size: 2039 Mb
Pagefile usage: 1444 Mb
Arrived at 24 intervals
Adding unaligned intervals
addUnalignedIntervals yields 63 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(24) has 26 intervals
descendant 1(35) has 14 intervals
propagateDescendantBreakpoints yields 60 intervals
Creating ancestral ordering
Previous anchoring score: 3.12121e+009, new anchor score: 3.45266e+009
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 377 new matches outside LCBs
0,1 have 631 new matches outside LCBs
0,2 have 300 new matches outside LCBs
1,0 have 1822 new matches outside LCBs
1,1 have 1129 new matches outside LCBs
1,2 have 1190 new matches outside LCBs
2,0 have 1118 new matches outside LCBs
2,1 have 812 new matches outside LCBs
2,2 have 761 new matches outside LCBs
3,0 have 1671 new matches outside LCBs
3,1 have 1005 new matches outside LCBs
3,2 have 1119 new matches outside LCBs
4,0 have 2046 new matches outside LCBs
4,1 have 821 new matches outside LCBs
4,2 have 1168 new matches outside LCBs
5,0 have 2042 new matches outside LCBs
5,1 have 819 new matches outside LCBs

5,2 have 1169 new matches outside LCBs

0,0 has an additional 986 matches
0,1 has an additional 879 matches
0,2 has an additional 882 matches
1,0 has an additional 3057 matches
1,1 has an additional 1675 matches
1,2 has an additional 2245 matches
2,0 has an additional 1952 matches
2,1 has an additional 1124 matches
2,2 has an additional 1820 matches
3,0 has an additional 2706 matches
3,1 has an additional 1483 matches
3,2 has an additional 2127 matches
4,0 has an additional 3368 matches
4,1 has an additional 1393 matches
4,2 has an additional 2526 matches
5,0 has an additional 3362 matches
5,1 has an additional 1389 matches
5,2 has an additional 2524 matches
Restoring backed up alignment tree...
28,22 has 986 pairwise matches
28,20 has 879 pairwise matches
28,25 has 882 pairwise matches
18,22 has 3057 pairwise matches
18,20 has 1675 pairwise matches
18,25 has 2245 pairwise matches
26,22 has 1952 pairwise matches
26,20 has 1124 pairwise matches
26,25 has 1820 pairwise matches
3,22 has 2706 pairwise matches
3,20 has 1483 pairwise matches
3,25 has 2127 pairwise matches
23,22 has 3368 pairwise matches
23,20 has 1393 pairwise matches
23,25 has 2526 pairwise matches
24,22 has 3362 pairwise matches
24,20 has 1389 pairwise matches
24,25 has 2524 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 2040 Mb
Pagefile usage: 1443 Mb
construct LCB tracking matches
There are 9869 tracking matches
There are 143014 / 602009 components used
Working set size: 2040 Mb
Pagefile usage: 1443 Mb
init tracking match LCB tracking
Working set size: 2041 Mb
Pagefile usage: 1444 Mb
pairwise score tracking matches
Working set size: 2042 Mb
Pagefile usage: 1446 Mb
get pairwise LCBs
there are 19862 pairwise LCBs
Working set size: 2042 Mb
Pagefile usage: 1446 Mb
scaling bp penalty by conservation weight:
0.0774707
0.0645797
0.0720507
0.0861736
0.0785832
0.0803533
0.0854778
0.0778114
0.0792185

0.0811188
0.0809056
0.0810625

0.0685153
0.0658616
0.0657754

0.0744399
0.0729402
0.0729207

scaling bp penalty by bp weight:

0.0214286
0.0214286
0.0214286
0.0857143
0.0214286
0.0642857
0.0214286
0.0214286
0.0642857
0.0857143
0.0857143
0.128571
0.0857143
0.0857143
0.128571
0.0857143
0.0857143
0.128571
Greedy BPE
Scoring with scaled breakpoint penalty: 104069
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..done
Working set size: 2040 Mb
Pagefile usage: 1443 Mb
Arrived at 19 intervals
Adding unaligned intervals
addUnalignedIntervals yields 51 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(24) has 26 intervals
descendant 1(35) has 14 intervals
propagateDescendantBreakpoints yields 54 intervals
Creating ancestral ordering
Previous anchoring score: 3.45266e+009, new anchor score: 3.45383e+009
Working set size: 2040 Mb
Pagefile usage: 1443 Mb
propagating ancestral breakpoints
Working set size: 2040 Mb
Pagefile usage: 1443 Mb
performing a gapped alignment
0%..1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
21%..22%..24%..25%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..43%..44%..45%..46%..47%..48%..49%..
50%..51%..52%..53%..55%..56%..57%..58%..59%..
60%..61%..62%..63%..65%..66%..67%..68%..69%..
70%..71%..72%..73%..74%..75%..76%..77%..78%..79%..
80%..81%..82%..83%..84%..85%..86%..87%..88%..89%..
90%..91%..92%..93%..94%..95%..96%..97%..98%..
100%..Working set size: 2045 Mb
Pagefile usage: 1448 Mb
Fix left ends
Working set size: 2045 Mb
Pagefile usage: 1448 Mb
done.
performing iterative refinement
0%..1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..15%..16%..17%..18%..19%..
20%..22%..23%..24%..25%..26%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..39%..

40%..41%..43%..44%..45%..46%..47%..48%..49%..
50%..51%..52%..53%..55%..56%..57%..58%..59%..
60%..61%..62%..63%..65%..66%..67%..68%..69%..
70%..71%..72%..73%..74%..75%..76%..77%..78%..79%..
80%..81%..82%..83%..84%..85%..86%..87%..88%..89%..
90%..91%..93%..94%..95%..96%..97%..98%..
100%..Working set size: 2052 Mb
Pagefile usage: 1455 Mb
Fix left ends
Working set size: 2052 Mb
Pagefile usage: 1455 Mb
done.
Working set size: 2052 Mb
Pagefile usage: 1455 Mb
Aligning node 42 to 45 via 41!
Working set size: 2049 Mb
Pagefile usage: 1451 Mb
get ancestral matches
Working set size: 2051 Mb
Pagefile usage: 1454 Mb
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 2051 Mb
Pagefile usage: 1454 Mb
construct LCB tracking matches
There are 9279 tracking matches
There are 36659 / 566019 components used
Working set size: 2051 Mb
Pagefile usage: 1454 Mb
init tracking match LCB tracking
Working set size: 2051 Mb
Pagefile usage: 1454 Mb
pairwise score tracking matches
Working set size: 2051 Mb
Pagefile usage: 1454 Mb
get pairwise LCBs
there are 2753 pairwise LCBs
Working set size: 2051 Mb
Pagefile usage: 1454 Mb
scaling bp penalty by conservation weight:
0.0539122
0.0498369
scaling bp penalty by bp weight:
0.0857143
0.0214286
Greedy BPE
Scoring with scaled breakpoint penalty: 100486
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..done
Working set size: 2051 Mb
Pagefile usage: 1454 Mb
Arrived at 19 intervals
Adding unaligned intervals
addUnalignedIntervals yields 55 intervals
Merging unaligned intervals

Marbling gaps
Propagating descendant breakpoints
descendant 0(42) has 4 intervals
descendant 1(45) has 1 intervals
propagateDescendantBreakpoints yields 22 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 3.20418e+008
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 402 new matches outside LCBs
1,0 have 264 new matches outside LCBs
0,0 has an additional 1981 matches
1,0 has an additional 1597 matches
Restoring backed up alignment tree...
13,2 has 1981 pairwise matches
14,2 has 1597 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 2051 Mb
Pagefile usage: 1454 Mb
construct LCB tracking matches
There are 9650 tracking matches
There are 38052 / 588650 components used
Working set size: 2051 Mb
Pagefile usage: 1454 Mb
init tracking match LCB tracking
Working set size: 2051 Mb
Pagefile usage: 1454 Mb
pairwise score tracking matches
Working set size: 2051 Mb
Pagefile usage: 1454 Mb
get pairwise LCBs
there are 2360 pairwise LCBs
Working set size: 2051 Mb
Pagefile usage: 1454 Mb
scaling bp penalty by conservation weight:
0.0539122
0.0498369
scaling bp penalty by bp weight:
0.0857143
0.0214286
Greedy BPE
Scoring with scaled breakpoint penalty: 100486
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..done
Working set size: 2051 Mb
Pagefile usage: 1454 Mb
Arrived at 11 intervals
Adding unaligned intervals
addUnalignedIntervals yields 28 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(42) has 4 intervals

descendant 1(45) has 1 intervals

propagateDescendantBreakpoints yields 14 intervals
Creating ancestral ordering
Previous anchoring score: 3.20418e+008, new anchor score: 3.90238e+008
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 490 new matches outside LCBs
1,0 have 14 new matches outside LCBs
0,0 has an additional 1096 matches
1,0 has an additional 496 matches
Restoring backed up alignment tree...
13,2 has 1096 pairwise matches
14,2 has 496 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 2051 Mb
Pagefile usage: 1454 Mb
construct LCB tracking matches
There are 9070 tracking matches
There are 35927 / 553270 components used
Working set size: 2051 Mb
Pagefile usage: 1454 Mb
init tracking match LCB tracking
Working set size: 2051 Mb
Pagefile usage: 1454 Mb
pairwise score tracking matches
Working set size: 2051 Mb
Pagefile usage: 1454 Mb
get pairwise LCBs
there are 1126 pairwise LCBs
Working set size: 2051 Mb
Pagefile usage: 1454 Mb
scaling bp penalty by conservation weight:
0.0539122
0.0498369
scaling bp penalty by bp weight:
0.0857143
0.0214286
Greedy BPE
Scoring with scaled breakpoint penalty: 100486
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..47%..done
Working set size: 2051 Mb
Pagefile usage: 1454 Mb
Arrived at 7 intervals
Adding unaligned intervals
addUnalignedIntervals yields 17 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(42) has 4 intervals
descendant 1(45) has 1 intervals
propagateDescendantBreakpoints yields 10 intervals
Creating ancestral ordering

Previous anchoring score: 3.90238e+008, new anchor score: 3.9044e+008

Working set size: 2051 Mb
Pagefile usage: 1454 Mb
propagating ancestral breakpoints
Working set size: 2051 Mb
Pagefile usage: 1454 Mb
performing a gapped alignment
0%..1%..2%..3%..4%..5%..6%..7%..9%..
10%..12%..13%..14%..16%..17%..19%..
20%..22%..24%..25%..27%..29%..
30%..32%..33%..34%..35%..36%..37%..38%..39%..
41%..42%..43%..44%..45%..46%..47%..48%..
50%..51%..52%..53%..54%..55%..56%..57%..59%..
60%..62%..63%..65%..66%..68%..69%..
71%..72%..73%..74%..75%..77%..78%..
80%..82%..83%..84%..85%..86%..87%..88%..
90%..91%..92%..93%..94%..95%..96%..97%..98%..99%..
100%..Working set size: 2066 Mb
Pagefile usage: 1469 Mb
Fix left ends
Working set size: 2066 Mb
Pagefile usage: 1469 Mb
done.
Working set size: 2066 Mb
Pagefile usage: 1469 Mb
Aligning node 41 to 46 via 40!
Working set size: 2064 Mb
Pagefile usage: 1466 Mb
get ancestral matches
Working set size: 2067 Mb
Pagefile usage: 1469 Mb
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 2067 Mb
Pagefile usage: 1469 Mb
construct LCB tracking matches
There are 21591 tracking matches
There are 395293 / 1317051 components used
Working set size: 2106 Mb
Pagefile usage: 1509 Mb
init tracking match LCB tracking
Working set size: 2110 Mb
Pagefile usage: 1513 Mb
pairwise score tracking matches
Working set size: 2114 Mb
Pagefile usage: 1517 Mb
get pairwise LCBs
there are 58384 pairwise LCBs
Working set size: 2121 Mb
Pagefile usage: 1524 Mb
scaling bp penalty by conservation weight:
0.0740223
0.0712704
0.0729611
0.074643
0.0725771
0.0785591
0.0787805
0.0622261
0.0595847
0.0713539
0.0733101
0.0717535
0.0775305
0.0777033
0.0630628
0.0607617
0.0702865
0.0724639
0.0704131
0.0751684
0.075347

0.0791768
0.0709831
0.0685347

scaling bp penalty by bp weight:

0.128571
0.0214286
0.15
0.15
0.0857143
0.0857143
0.128571
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.128571
0.0214286
0.0857143
0.0214286
0.0214286
0.0214286

0.0214286

0.0857143

0.0214286

0.0214286

0.0857143

0.0214286

Greedy BPE
Scoring with scaled breakpoint penalty: 83768.6
1%..2%..3%..4%..done
Working set size: 2104 Mb
Pagefile usage: 1507 Mb
Arrived at 59 intervals
Adding unaligned intervals
addUnalignedIntervals yields 170 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(41) has 14 intervals
descendant 1(46) has 28 intervals
propagateDescendantBreakpoints yields 98 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 3.63146e+009
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 1144 new matches outside LCBs
0,1 have 681 new matches outside LCBs
0,2 have 749 new matches outside LCBs
0,3 have 750 new matches outside LCBs
0,4 have 1066 new matches outside LCBs
0,5 have 987 new matches outside LCBs
0,6 have 1260 new matches outside LCBs
0,7 have 1265 new matches outside LCBs
1,0 have 767 new matches outside LCBs
1,1 have 746 new matches outside LCBs
1,2 have 1103 new matches outside LCBs
1,3 have 1105 new matches outside LCBs
1,4 have 1264 new matches outside LCBs
1,5 have 1459 new matches outside LCBs
1,6 have 1725 new matches outside LCBs
1,7 have 1728 new matches outside LCBs
2,0 have 991 new matches outside LCBs
2,1 have 769 new matches outside LCBs
2,2 have 1141 new matches outside LCBs
2,3 have 1141 new matches outside LCBs
2,4 have 1144 new matches outside LCBs
2,5 have 1421 new matches outside LCBs
2,6 have 1544 new matches outside LCBs
2,7 have 1546 new matches outside LCBs
0,0 has an additional 2995 matches
0,1 has an additional 2422 matches
0,2 has an additional 2877 matches
0,3 has an additional 2879 matches
0,4 has an additional 2941 matches
0,5 has an additional 2995 matches
0,6 has an additional 3392 matches
0,7 has an additional 3396 matches
1,0 has an additional 2364 matches

1,1 has an additional 2424 matches

1,2 has an additional 3136 matches
1,3 has an additional 3140 matches
1,4 has an additional 3278 matches
1,5 has an additional 3444 matches
1,6 has an additional 3928 matches
1,7 has an additional 3934 matches
2,0 has an additional 2713 matches
2,1 has an additional 2302 matches
2,2 has an additional 3165 matches
2,3 has an additional 3168 matches
2,4 has an additional 3068 matches
2,5 has an additional 3315 matches
2,6 has an additional 3824 matches
2,7 has an additional 3828 matches
Restoring backed up alignment tree...
2,6 has 2995 pairwise matches
2,4 has 2422 pairwise matches
2,7 has 2877 pairwise matches
2,8 has 2879 pairwise matches
2,17 has 2941 pairwise matches
2,0 has 2995 pairwise matches
2,15 has 3392 pairwise matches
2,16 has 3396 pairwise matches
13,6 has 2364 pairwise matches
13,4 has 2424 pairwise matches
13,7 has 3136 pairwise matches
13,8 has 3140 pairwise matches
13,17 has 3278 pairwise matches
13,0 has 3444 pairwise matches
13,15 has 3928 pairwise matches
13,16 has 3934 pairwise matches
14,6 has 2713 pairwise matches
14,4 has 2302 pairwise matches
14,7 has 3165 pairwise matches
14,8 has 3168 pairwise matches
14,17 has 3068 pairwise matches
14,0 has 3315 pairwise matches
14,15 has 3824 pairwise matches
14,16 has 3828 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 2053 Mb
Pagefile usage: 1459 Mb
construct LCB tracking matches
There are 19403 tracking matches
There are 365784 / 1183583 components used
Working set size: 2082 Mb
Pagefile usage: 1487 Mb
init tracking match LCB tracking
Working set size: 2086 Mb
Pagefile usage: 1491 Mb
pairwise score tracking matches
Working set size: 2090 Mb
Pagefile usage: 1495 Mb
get pairwise LCBs
there are 35592 pairwise LCBs
Working set size: 2093 Mb
Pagefile usage: 1498 Mb
scaling bp penalty by conservation weight:
0.0740223
0.0712704
0.0729611
0.074643

0.0791768

0.0725771
0.0622261
0.0717535
0.0630628
0.0704131

0.0785591
0.0595847
0.0775305
0.0607617
0.0751684

0.0787805
0.0713539
0.0777033
0.0702865
0.075347

scaling bp penalty by bp weight:

0.128571
0.0214286
0.15
0.15
0.0857143
0.0857143
0.128571
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.128571
0.0214286
0.0857143
0.0214286
0.0214286
0.0214286

0.0733101

0.0709831

0.0724639

0.0685347

0.0214286

0.0857143

0.0214286

0.0214286

0.0857143

0.0214286

Greedy BPE
Scoring with scaled breakpoint penalty: 83768.6
1%..2%..3%..4%..5%..6%..7%..done
Working set size: 2092 Mb
Pagefile usage: 1497 Mb
Arrived at 45 intervals
Adding unaligned intervals
addUnalignedIntervals yields 126 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(41) has 14 intervals
descendant 1(46) has 28 intervals
propagateDescendantBreakpoints yields 84 intervals
Creating ancestral ordering
Previous anchoring score: 3.63146e+009, new anchor score: 4.37786e+009
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 1204 new matches outside LCBs
0,1 have 758 new matches outside LCBs
0,2 have 508 new matches outside LCBs
0,3 have 509 new matches outside LCBs
0,4 have 772 new matches outside LCBs
0,5 have 1125 new matches outside LCBs
0,6 have 962 new matches outside LCBs
0,7 have 963 new matches outside LCBs
1,0 have 1016 new matches outside LCBs
1,1 have 909 new matches outside LCBs
1,2 have 879 new matches outside LCBs
1,3 have 879 new matches outside LCBs
1,4 have 960 new matches outside LCBs
1,5 have 1161 new matches outside LCBs
1,6 have 1442 new matches outside LCBs
1,7 have 1443 new matches outside LCBs
2,0 have 1054 new matches outside LCBs
2,1 have 720 new matches outside LCBs
2,2 have 711 new matches outside LCBs
2,3 have 714 new matches outside LCBs
2,4 have 1095 new matches outside LCBs
2,5 have 913 new matches outside LCBs
2,6 have 1056 new matches outside LCBs
2,7 have 1055 new matches outside LCBs
0,0 has an additional 2189 matches
0,1 has an additional 1805 matches

0,2 has an additional 1682 matches

0,3 has an additional 1683 matches
0,4 has an additional 1770 matches
0,5 has an additional 2328 matches
0,6 has an additional 2216 matches
0,7 has an additional 2217 matches
1,0 has an additional 2164 matches
1,1 has an additional 1949 matches
1,2 has an additional 1855 matches
1,3 has an additional 1858 matches
1,4 has an additional 2112 matches
1,5 has an additional 2194 matches
1,6 has an additional 2653 matches
1,7 has an additional 2659 matches
2,0 has an additional 2106 matches
2,1 has an additional 1734 matches
2,2 has an additional 1628 matches
2,3 has an additional 1634 matches
2,4 has an additional 2072 matches
2,5 has an additional 1800 matches
2,6 has an additional 2155 matches
2,7 has an additional 2158 matches
Restoring backed up alignment tree...
2,6 has 2189 pairwise matches
2,4 has 1805 pairwise matches
2,7 has 1682 pairwise matches
2,8 has 1683 pairwise matches
2,17 has 1770 pairwise matches
2,0 has 2328 pairwise matches
2,15 has 2216 pairwise matches
2,16 has 2217 pairwise matches
13,6 has 2164 pairwise matches
13,4 has 1949 pairwise matches
13,7 has 1855 pairwise matches
13,8 has 1858 pairwise matches
13,17 has 2112 pairwise matches
13,0 has 2194 pairwise matches
13,15 has 2653 pairwise matches
13,16 has 2659 pairwise matches
14,6 has 2106 pairwise matches
14,4 has 1734 pairwise matches
14,7 has 1628 pairwise matches
14,8 has 1634 pairwise matches
14,17 has 2072 pairwise matches
14,0 has 1800 pairwise matches
14,15 has 2155 pairwise matches
14,16 has 2158 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 2084 Mb
Pagefile usage: 1487 Mb
construct LCB tracking matches
There are 18940 tracking matches
There are 358495 / 1155340 components used
Working set size: 2084 Mb
Pagefile usage: 1487 Mb
init tracking match LCB tracking
Working set size: 2087 Mb
Pagefile usage: 1491 Mb
pairwise score tracking matches
Working set size: 2091 Mb

Pagefile usage: 1494 Mb

get pairwise LCBs
there are 27947 pairwise LCBs
Working set size: 2091 Mb
Pagefile usage: 1494 Mb
scaling bp penalty by conservation weight:
0.0740223
0.0712704
0.0729611
0.0725771
0.0785591
0.0787805
0.0622261
0.0595847
0.0713539
0.0717535
0.0775305
0.0777033
0.0630628
0.0607617
0.0702865
0.0704131
0.0751684
0.075347
scaling bp penalty by bp weight:
0.128571
0.0214286
0.15
0.15
0.0857143
0.0857143
0.128571
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.128571
0.0214286
0.0857143
0.0214286
0.0214286
0.0214286

0.074643

0.0791768

0.0733101

0.0709831

0.0724639

0.0685347

0.0214286

0.0857143

0.0214286

0.0214286

0.0857143

0.0214286

Greedy BPE
Scoring with scaled breakpoint penalty: 83768.6
1%..2%..3%..4%..5%..6%..7%..8%..done
Working set size: 2082 Mb
Pagefile usage: 1486 Mb
Arrived at 41 intervals
Adding unaligned intervals
addUnalignedIntervals yields 110 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(41) has 14 intervals
descendant 1(46) has 28 intervals
propagateDescendantBreakpoints yields 80 intervals
Creating ancestral ordering
Previous anchoring score: 4.37786e+009, new anchor score: 4.39259e+009
Working set size: 2081 Mb
Pagefile usage: 1486 Mb
propagating ancestral breakpoints
Working set size: 2081 Mb
Pagefile usage: 1486 Mb
performing a gapped alignment
0%..1%..2%..3%..4%..5%..7%..8%..9%..
10%..11%..12%..13%..15%..16%..17%..18%..
20%..21%..22%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..47%..48%..49%..
51%..52%..53%..54%..55%..56%..57%..58%..59%..
60%..61%..62%..63%..64%..66%..67%..69%..
70%..71%..72%..73%..74%..75%..76%..77%..78%..79%..
80%..81%..82%..83%..84%..85%..86%..87%..88%..89%..
90%..91%..92%..93%..94%..95%..96%..97%..98%..99%..
100%..Working set size: 2101 Mb
Pagefile usage: 1506 Mb
Fix left ends
Working set size: 2101 Mb
Pagefile usage: 1506 Mb

done.
performing iterative refinement
0%..1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..
20%..21%..22%..24%..25%..26%..27%..28%..29%..
30%..31%..33%..34%..35%..36%..37%..38%..39%..
41%..42%..43%..44%..45%..47%..48%..49%..
50%..51%..53%..54%..55%..56%..57%..58%..59%..
60%..61%..62%..63%..64%..66%..67%..69%..
70%..71%..72%..73%..74%..75%..76%..77%..78%..79%..
81%..82%..83%..84%..85%..86%..87%..88%..
90%..92%..93%..94%..95%..96%..97%..98%..99%..
100%..Working set size: 2103 Mb
Pagefile usage: 1508 Mb
Fix left ends
Working set size: 2103 Mb
Pagefile usage: 1508 Mb
done.
Working set size: 2103 Mb
Pagefile usage: 1508 Mb
Aligning node 23 to 40 via 1!
Working set size: 1993 Mb
Pagefile usage: 1414 Mb
get ancestral matches
Working set size: 2061 Mb
Pagefile usage: 1468 Mb
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 2061 Mb
Pagefile usage: 1468 Mb
construct LCB tracking matches
There are 37230 tracking matches
There are 1169920 / 2271030 components used
Working set size: 2268 Mb
Pagefile usage: 1669 Mb
init tracking match LCB tracking
Working set size: 2296 Mb
Pagefile usage: 1697 Mb
pairwise score tracking matches
Working set size: 2325 Mb
Pagefile usage: 1725 Mb
get pairwise LCBs
there are 301336 pairwise LCBs
Working set size: 2359 Mb
Pagefile usage: 1759 Mb
scaling bp penalty by conservation weight:
0.104964
0.092308
0.102874
0.103756
0.0971978
0.0958171
0.0933584
0.0933141
0.104619
0.0988593
0.0977835
0.0909611
0.0753013
0.10043 0.100602
0.0807403
0.084938
1
0.0786561
0.07885 0.0937648
0.0863727
0.0842981
0.0949334
0.0793685
0.0941867
0.0950836
0.0833109
0.0845789
0.0803839
0.0805646
0.0957328
0.091898
0.0901769
0.0618732
0.0484393
0.0747733
0.0750174
0.0600868
0.0613001
0.0688717
0.0690649
0.0690823
0.0560014
0.0568492
0.0640255
0.0619378
0.0650803
0.0652913
0.0732597

0.0649757
0.0729946
0.0731761
0.0572564
0.0531335
0.0538098
0.0819288
0.0630374
0.0783984
0.0793076
0.0755153
0.068293
0.0728713
0.0730548
0.0773313
0.0723802
0.0734437
0.0617734
0.0631265
0.0724488
0.074441
0.0701853
0.0711681
0.0762544
0.0756607
0.0676085
0.0550686
0.0533717
0.0671347
0.0593501
0.0716504
0.0725526
0.0666916
0.0674732
0.0734024
0.0737297
0.0651843
0.0561525
0.0489132
0.0670573
0.0602955
0.0713634
0.0722656
0.06746 0.068213
6
0.0743775
0.074705
0.0662154
0.0564365
0.049194
4
scaling bp penalty by bp weight:
0.0857143
0.0214286
0.0857143
0.0857143
0.0214286
0.0857143
0.0857143
0.0857143
0.15
0.0214286
0.021428
6
0.0857143
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0857143
0.0214286
0.0214286
0.0857143
0.0642857
0.128571
0.128571
0.0642857
0.128571
0.128571
0.128571
0.192857
0.0642857
0.0642857
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.128571
0.0214286
0.15
0.15
0.0214286
0.0857143
0.0857143
0.0857143
0.0857143
0.0857143
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.15
0.0214286
0.0857143
0.0857143
0.0214286
0.085714
3
0.0214286
0.0214286
0.0857143
0.0857143
0.085714
3
0.15
0.0214286
0.0857143
0.0857143
0.0214286
0.021428
6
0.0214286
0.0214286
0.0214286
0.0857143
0.085714
3
0.15
0.0214286
0.0857143
0.0857143
0.0214286
0.021428
6
0.0214286
0.0214286
0.0214286
0.0857143
0.085714
3
Greedy BPE
Scoring with scaled breakpoint penalty: 80489.9
1%..done
Working set size: 2141 Mb
Pagefile usage: 1559 Mb
Arrived at 155 intervals
Adding unaligned intervals
addUnalignedIntervals yields 456 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(23) has 60 intervals
descendant 1(40) has 84 intervals
propagateDescendantBreakpoints yields 296 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 1.35814e+010

Backing up alignment tree...

propagating ancestral breakpoints
recursive anchor search
0,0 have 3507 new matches outside LCBs
0,1 have 1736 new matches outside LCBs
0,2 have 3572 new matches outside LCBs
0,3 have 3571 new matches outside LCBs
0,4 have 2440 new matches outside LCBs
0,5 have 2766 new matches outside LCBs
0,6 have 3112 new matches outside LCBs
0,7 have 3115 new matches outside LCBs
0,8 have 3973 new matches outside LCBs
0,9 have 3079 new matches outside LCBs
0,10 have 3266 new matches outside LCBs
1,0 have 2358 new matches outside LCBs
1,1 have 1359 new matches outside LCBs
1,2 have 2559 new matches outside LCBs
1,3 have 2559 new matches outside LCBs
1,4 have 1639 new matches outside LCBs
1,5 have 2062 new matches outside LCBs
1,6 have 1759 new matches outside LCBs
1,7 have 1767 new matches outside LCBs
1,8 have 2744 new matches outside LCBs
1,9 have 2163 new matches outside LCBs
1,10 have 2080 new matches outside LCBs
2,0 have 2956 new matches outside LCBs
2,1 have 1838 new matches outside LCBs
2,2 have 2827 new matches outside LCBs
2,3 have 2824 new matches outside LCBs
2,4 have 2242 new matches outside LCBs
2,5 have 2440 new matches outside LCBs
2,6 have 2356 new matches outside LCBs
2,7 have 2364 new matches outside LCBs
2,8 have 3318 new matches outside LCBs
2,9 have 2744 new matches outside LCBs
2,10 have 2808 new matches outside LCBs
3,0 have 948 new matches outside LCBs
3,1 have 733 new matches outside LCBs
3,2 have 1079 new matches outside LCBs
3,3 have 1079 new matches outside LCBs
3,4 have 869 new matches outside LCBs
3,5 have 946 new matches outside LCBs
3,6 have 1073 new matches outside LCBs
3,7 have 1089 new matches outside LCBs
3,8 have 1373 new matches outside LCBs
3,9 have 713 new matches outside LCBs
3,10 have 747 new matches outside LCBs
4,0 have 1506 new matches outside LCBs
4,1 have 1189 new matches outside LCBs
4,2 have 1409 new matches outside LCBs
4,3 have 1408 new matches outside LCBs
4,4 have 1733 new matches outside LCBs
4,5 have 1540 new matches outside LCBs
4,6 have 1977 new matches outside LCBs
4,7 have 1991 new matches outside LCBs
4,8 have 1429 new matches outside LCBs
4,9 have 1079 new matches outside LCBs
4,10 have 1112 new matches outside LCBs
5,0 have 1727 new matches outside LCBs
5,1 have 831 new matches outside LCBs

5,2 have 1446 new matches outside LCBs

5,3 have 1446 new matches outside LCBs
5,4 have 1242 new matches outside LCBs
5,5 have 1154 new matches outside LCBs
5,6 have 1422 new matches outside LCBs
5,7 have 1428 new matches outside LCBs
5,8 have 1871 new matches outside LCBs
5,9 have 1377 new matches outside LCBs
5,10 have 1456 new matches outside LCBs
6,0 have 1435 new matches outside LCBs
6,1 have 1451 new matches outside LCBs
6,2 have 1865 new matches outside LCBs
6,3 have 1864 new matches outside LCBs
6,4 have 1796 new matches outside LCBs
6,5 have 2035 new matches outside LCBs
6,6 have 2252 new matches outside LCBs
6,7 have 2265 new matches outside LCBs
6,8 have 2091 new matches outside LCBs
6,9 have 1407 new matches outside LCBs
6,10 have 1445 new matches outside LCBs
7,0 have 1783 new matches outside LCBs
7,1 have 1086 new matches outside LCBs
7,2 have 1925 new matches outside LCBs
7,3 have 1924 new matches outside LCBs
7,4 have 1595 new matches outside LCBs
7,5 have 1904 new matches outside LCBs
7,6 have 2321 new matches outside LCBs
7,7 have 2331 new matches outside LCBs
7,8 have 2089 new matches outside LCBs
7,9 have 1392 new matches outside LCBs
7,10 have 1105 new matches outside LCBs
8,0 have 1779 new matches outside LCBs
8,1 have 1085 new matches outside LCBs
8,2 have 1925 new matches outside LCBs
8,3 have 1925 new matches outside LCBs
8,4 have 1596 new matches outside LCBs
8,5 have 1903 new matches outside LCBs
8,6 have 2322 new matches outside LCBs
8,7 have 2331 new matches outside LCBs
8,8 have 2087 new matches outside LCBs
8,9 have 1392 new matches outside LCBs
8,10 have 1106 new matches outside LCBs
0,0 has an additional 6058 matches
0,1 has an additional 3408 matches
0,2 has an additional 6219 matches
0,3 has an additional 6219 matches
0,4 has an additional 4377 matches
0,5 has an additional 4758 matches
0,6 has an additional 5185 matches
0,7 has an additional 5192 matches
0,8 has an additional 6070 matches
0,9 has an additional 5489 matches
0,10 has an additional 5446 matches
1,0 has an additional 4640 matches
1,1 has an additional 3064 matches
1,2 has an additional 4895 matches
1,3 has an additional 4896 matches
1,4 has an additional 3683 matches
1,5 has an additional 4118 matches
1,6 has an additional 4021 matches

1,7 has an additional 4036 matches

1,8 has an additional 4763 matches
1,9 has an additional 4361 matches
1,10 has an additional 4351 matches
2,0 has an additional 5344 matches
2,1 has an additional 3553 matches
2,2 has an additional 5514 matches
2,3 has an additional 5512 matches
2,4 has an additional 4409 matches
2,5 has an additional 4619 matches
2,6 has an additional 4547 matches
2,7 has an additional 4561 matches
2,8 has an additional 5547 matches
2,9 has an additional 5109 matches
2,10 has an additional 5076 matches
3,0 has an additional 2283 matches
3,1 has an additional 2033 matches
3,2 has an additional 2550 matches
3,3 has an additional 2547 matches
3,4 has an additional 2273 matches
3,5 has an additional 2347 matches
3,6 has an additional 2533 matches
3,7 has an additional 2556 matches
3,8 has an additional 2826 matches
3,9 has an additional 1898 matches
3,10 has an additional 1923 matches
4,0 has an additional 3268 matches
4,1 has an additional 2889 matches
4,2 has an additional 3849 matches
4,3 has an additional 3845 matches
4,4 has an additional 3613 matches
4,5 has an additional 3419 matches
4,6 has an additional 3977 matches
4,7 has an additional 3998 matches
4,8 has an additional 3507 matches
4,9 has an additional 2701 matches
4,10 has an additional 2784 matches
5,0 has an additional 3475 matches
5,1 has an additional 2463 matches
5,2 has an additional 3771 matches
5,3 has an additional 3772 matches
5,4 has an additional 3396 matches
5,5 has an additional 3292 matches
5,6 has an additional 3686 matches
5,7 has an additional 3699 matches
5,8 has an additional 4127 matches
5,9 has an additional 3161 matches
5,10 has an additional 3304 matches
6,0 has an additional 3154 matches
6,1 has an additional 2885 matches
6,2 has an additional 3890 matches
6,3 has an additional 3894 matches
6,4 has an additional 3530 matches
6,5 has an additional 3775 matches
6,6 has an additional 4067 matches
6,7 has an additional 4099 matches
6,8 has an additional 3963 matches
6,9 has an additional 2992 matches
6,10 has an additional 3079 matches
7,0 has an additional 3886 matches

7,1 has an additional 2814 matches

7,2 has an additional 4379 matches
7,3 has an additional 4379 matches
7,4 has an additional 3628 matches
7,5 has an additional 3964 matches
7,6 has an additional 4567 matches
7,7 has an additional 4581 matches
7,8 has an additional 4156 matches
7,9 has an additional 3273 matches
7,10 has an additional 2925 matches
8,0 has an additional 3885 matches
8,1 has an additional 2813 matches
8,2 has an additional 4380 matches
8,3 has an additional 4381 matches
8,4 has an additional 3631 matches
8,5 has an additional 3965 matches
8,6 has an additional 4571 matches
8,7 has an additional 4584 matches
8,8 has an additional 4154 matches
8,9 has an additional 3276 matches
8,10 has an additional 2929 matches
Restoring backed up alignment tree...
22,6 has 6058 pairwise matches
22,4 has 3408 pairwise matches
22,7 has 6219 pairwise matches
22,8 has 6219 pairwise matches
22,17 has 4377 pairwise matches
22,0 has 4758 pairwise matches
22,15 has 5185 pairwise matches
22,16 has 5192 pairwise matches
22,2 has 6070 pairwise matches
22,13 has 5489 pairwise matches
22,14 has 5446 pairwise matches
20,6 has 4640 pairwise matches
20,4 has 3064 pairwise matches
20,7 has 4895 pairwise matches
20,8 has 4896 pairwise matches
20,17 has 3683 pairwise matches
20,0 has 4118 pairwise matches
20,15 has 4021 pairwise matches
20,16 has 4036 pairwise matches
20,2 has 4763 pairwise matches
20,13 has 4361 pairwise matches
20,14 has 4351 pairwise matches
25,6 has 5344 pairwise matches
25,4 has 3553 pairwise matches
25,7 has 5514 pairwise matches
25,8 has 5512 pairwise matches
25,17 has 4409 pairwise matches
25,0 has 4619 pairwise matches
25,15 has 4547 pairwise matches
25,16 has 4561 pairwise matches
25,2 has 5547 pairwise matches
25,13 has 5109 pairwise matches
25,14 has 5076 pairwise matches
28,6 has 2283 pairwise matches
28,4 has 2033 pairwise matches
28,7 has 2550 pairwise matches
28,8 has 2547 pairwise matches
28,17 has 2273 pairwise matches

28,0 has 2347 pairwise matches

28,15 has 2533 pairwise matches
28,16 has 2556 pairwise matches
28,2 has 2826 pairwise matches
28,13 has 1898 pairwise matches
28,14 has 1923 pairwise matches
18,6 has 3268 pairwise matches
18,4 has 2889 pairwise matches
18,7 has 3849 pairwise matches
18,8 has 3845 pairwise matches
18,17 has 3613 pairwise matches
18,0 has 3419 pairwise matches
18,15 has 3977 pairwise matches
18,16 has 3998 pairwise matches
18,2 has 3507 pairwise matches
18,13 has 2701 pairwise matches
18,14 has 2784 pairwise matches
26,6 has 3475 pairwise matches
26,4 has 2463 pairwise matches
26,7 has 3771 pairwise matches
26,8 has 3772 pairwise matches
26,17 has 3396 pairwise matches
26,0 has 3292 pairwise matches
26,15 has 3686 pairwise matches
26,16 has 3699 pairwise matches
26,2 has 4127 pairwise matches
26,13 has 3161 pairwise matches
26,14 has 3304 pairwise matches
3,6 has 3154 pairwise matches
3,4 has 2885 pairwise matches
3,7 has 3890 pairwise matches
3,8 has 3894 pairwise matches
3,17 has 3530 pairwise matches
3,0 has 3775 pairwise matches
3,15 has 4067 pairwise matches
3,16 has 4099 pairwise matches
3,2 has 3963 pairwise matches
3,13 has 2992 pairwise matches
3,14 has 3079 pairwise matches
23,6 has 3886 pairwise matches
23,4 has 2814 pairwise matches
23,7 has 4379 pairwise matches
23,8 has 4379 pairwise matches
23,17 has 3628 pairwise matches
23,0 has 3964 pairwise matches
23,15 has 4567 pairwise matches
23,16 has 4581 pairwise matches
23,2 has 4156 pairwise matches
23,13 has 3273 pairwise matches
23,14 has 2925 pairwise matches
24,6 has 3885 pairwise matches
24,4 has 2813 pairwise matches
24,7 has 4380 pairwise matches
24,8 has 4381 pairwise matches
24,17 has 3631 pairwise matches
24,0 has 3965 pairwise matches
24,15 has 4571 pairwise matches
24,16 has 4584 pairwise matches
24,2 has 4154 pairwise matches
24,13 has 3276 pairwise matches

24,14 has 2929 pairwise matches

Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 2204 Mb
Pagefile usage: 1652 Mb
construct LCB tracking matches
There are 27671 tracking matches
There are 944424 / 1687931 components used
Working set size: 2281 Mb
Pagefile usage: 1715 Mb
init tracking match LCB tracking
Working set size: 2302 Mb
Pagefile usage: 1736 Mb
pairwise score tracking matches
Working set size: 2323 Mb
Pagefile usage: 1758 Mb
get pairwise LCBs
there are 67825 pairwise LCBs
Working set size: 2333 Mb
Pagefile usage: 1765 Mb
scaling bp penalty by conservation weight:
0.104964
0.092308
0.102874
0.103756
0.0971978
0.0958171
0.0933584
0.0933141
0.104619
0.0988593
0.0977835
0.0909611
0.0753013
0.10043 0.100602
0.0807403
0.084938
1
0.0786561
0.07885 0.0937648
0.0863727
0.0842981
0.0949334
0.0793685
0.0941867
0.0950836
0.0833109
0.0845789
0.0803839
0.0805646
0.0957328
0.091898
0.0901769
0.0618732
0.0484393
0.0747733
0.0750174
0.0600868
0.0613001
0.0688717
0.0690649
0.0690823
0.0560014
0.0568492
0.0640255
0.0619378
0.0650803
0.0652913
0.0732597
0.0649757
0.0729946
0.0731761
0.0572564
0.0531335
0.0538098
0.0819288
0.0630374
0.0783984
0.0793076
0.0755153
0.068293
0.0728713
0.0730548
0.0773313
0.0723802
0.0734437
0.0617734
0.0631265
0.0724488
0.074441
0.0701853
0.0711681
0.0762544
0.0756607
0.0676085
0.0550686
0.0533717
0.0671347
0.0593501
0.0716504
0.0725526
0.0666916
0.0674732
0.0734024
0.0737297
0.0651843
0.0561525
0.0489132
0.0670573
0.0602955
0.0713634
0.0722656
0.06746 0.068213
6
0.0743775
0.074705
0.0662154
0.0564365
0.049194
4
scaling bp penalty by bp weight:
0.0857143
0.0214286
0.0857143
0.0857143
0.0857143
0.0857143
6
0.0857143
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0857143
0.0642857
0.128571
0.128571
0.128571
0.128571
0.0642857
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286

0.0857143
0.0214286
0.15
0.0214286
0.021428
0.0214286
0.0857143

0.0214286
0.0214286

0.128571
0.192857

0.0642857
0.0642857

0.0214286
0.0214286

0.0214286
0.0214286

0.0214286
0.128571
0.0214286
0.15
0.15
0.0214286
0.0857143
0.0857143
0.0857143
0.0857143
0.0857143
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.15
0.0214286
0.0857143
0.0857143
0.0214286
0.085714
3
0.0214286
0.0214286
0.0857143
0.0857143
0.085714
3
0.15
0.0214286
0.0857143
0.0857143
0.0214286
0.021428
6
0.0214286
0.0214286
0.0214286
0.0857143
0.085714
3
0.15
0.0214286
0.0857143
0.0857143
0.0214286
0.021428
6
0.0214286
0.0214286
0.0214286
0.0857143
0.085714
3
Greedy BPE
Scoring with scaled breakpoint penalty: 80489.9
1%..2%..3%..4%..done
Working set size: 2232 Mb
Pagefile usage: 1682 Mb
Arrived at 116 intervals
Adding unaligned intervals
addUnalignedIntervals yields 300 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(23) has 60 intervals
descendant 1(40) has 84 intervals
propagateDescendantBreakpoints yields 254 intervals
Creating ancestral ordering
Previous anchoring score: 1.35814e+010, new anchor score: 1.71816e+010
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 3350 new matches outside LCBs
0,1 have 1521 new matches outside LCBs
0,2 have 3316 new matches outside LCBs
0,3 have 3316 new matches outside LCBs
0,4 have 2149 new matches outside LCBs
0,5 have 2533 new matches outside LCBs
0,6 have 2882 new matches outside LCBs
0,7 have 2880 new matches outside LCBs
0,8 have 3656 new matches outside LCBs
0,9 have 2861 new matches outside LCBs
0,10 have 3036 new matches outside LCBs
1,0 have 2261 new matches outside LCBs
1,1 have 1168 new matches outside LCBs
1,2 have 2361 new matches outside LCBs
1,3 have 2361 new matches outside LCBs
1,4 have 1428 new matches outside LCBs
1,5 have 1862 new matches outside LCBs
1,6 have 1646 new matches outside LCBs
1,7 have 1645 new matches outside LCBs
1,8 have 2458 new matches outside LCBs
1,9 have 1865 new matches outside LCBs
1,10 have 1872 new matches outside LCBs
2,0 have 2680 new matches outside LCBs
2,1 have 1433 new matches outside LCBs
2,2 have 2439 new matches outside LCBs

2,3 have 2439 new matches outside LCBs

2,4 have 1840 new matches outside LCBs
2,5 have 2091 new matches outside LCBs
2,6 have 2049 new matches outside LCBs
2,7 have 2051 new matches outside LCBs
2,8 have 2991 new matches outside LCBs
2,9 have 2542 new matches outside LCBs
2,10 have 2568 new matches outside LCBs
3,0 have 733 new matches outside LCBs
3,1 have 979 new matches outside LCBs
3,2 have 911 new matches outside LCBs
3,3 have 912 new matches outside LCBs
3,4 have 670 new matches outside LCBs
3,5 have 765 new matches outside LCBs
3,6 have 836 new matches outside LCBs
3,7 have 834 new matches outside LCBs
3,8 have 935 new matches outside LCBs
3,9 have 473 new matches outside LCBs
3,10 have 500 new matches outside LCBs
4,0 have 1238 new matches outside LCBs
4,1 have 918 new matches outside LCBs
4,2 have 1132 new matches outside LCBs
4,3 have 1132 new matches outside LCBs
4,4 have 1404 new matches outside LCBs
4,5 have 1262 new matches outside LCBs
4,6 have 1622 new matches outside LCBs
4,7 have 1627 new matches outside LCBs
4,8 have 1036 new matches outside LCBs
4,9 have 763 new matches outside LCBs
4,10 have 800 new matches outside LCBs
5,0 have 1428 new matches outside LCBs
5,1 have 605 new matches outside LCBs
5,2 have 1228 new matches outside LCBs
5,3 have 1227 new matches outside LCBs
5,4 have 985 new matches outside LCBs
5,5 have 918 new matches outside LCBs
5,6 have 1152 new matches outside LCBs
5,7 have 1151 new matches outside LCBs
5,8 have 1474 new matches outside LCBs
5,9 have 1125 new matches outside LCBs
5,10 have 1194 new matches outside LCBs
6,0 have 1405 new matches outside LCBs
6,1 have 1287 new matches outside LCBs
6,2 have 1729 new matches outside LCBs
6,3 have 1729 new matches outside LCBs
6,4 have 1593 new matches outside LCBs
6,5 have 1862 new matches outside LCBs
6,6 have 2061 new matches outside LCBs
6,7 have 2066 new matches outside LCBs
6,8 have 1700 new matches outside LCBs
6,9 have 1129 new matches outside LCBs
6,10 have 1181 new matches outside LCBs
7,0 have 1733 new matches outside LCBs
7,1 have 838 new matches outside LCBs
7,2 have 1690 new matches outside LCBs
7,3 have 1692 new matches outside LCBs
7,4 have 1305 new matches outside LCBs
7,5 have 1635 new matches outside LCBs
7,6 have 2039 new matches outside LCBs
7,7 have 2041 new matches outside LCBs

7,8 have 1715 new matches outside LCBs

7,9 have 1115 new matches outside LCBs
7,10 have 824 new matches outside LCBs
8,0 have 1730 new matches outside LCBs
8,1 have 836 new matches outside LCBs
8,2 have 1689 new matches outside LCBs
8,3 have 1690 new matches outside LCBs
8,4 have 1304 new matches outside LCBs
8,5 have 1632 new matches outside LCBs
8,6 have 2036 new matches outside LCBs
8,7 have 2038 new matches outside LCBs
8,8 have 1713 new matches outside LCBs
8,9 have 1116 new matches outside LCBs
8,10 have 824 new matches outside LCBs
0,0 has an additional 4895 matches
0,1 has an additional 2496 matches
0,2 has an additional 4712 matches
0,3 has an additional 4712 matches
0,4 has an additional 3192 matches
0,5 has an additional 3526 matches
0,6 has an additional 3940 matches
0,7 has an additional 3945 matches
0,8 has an additional 5243 matches
0,9 has an additional 4213 matches
0,10 has an additional 4374 matches
1,0 has an additional 3940 matches
1,1 has an additional 2048 matches
1,2 has an additional 3613 matches
1,3 has an additional 3613 matches
1,4 has an additional 2385 matches
1,5 has an additional 2813 matches
1,6 has an additional 2856 matches
1,7 has an additional 2867 matches
1,8 has an additional 4143 matches
1,9 has an additional 3079 matches
1,10 has an additional 3156 matches
2,0 has an additional 4202 matches
2,1 has an additional 2410 matches
2,2 has an additional 3740 matches
2,3 has an additional 3740 matches
2,4 has an additional 2874 matches
2,5 has an additional 3082 matches
2,6 has an additional 3072 matches
2,7 has an additional 3085 matches
2,8 has an additional 4595 matches
2,9 has an additional 3969 matches
2,10 has an additional 3930 matches
3,0 has an additional 1229 matches
3,1 has an additional 1411 matches
3,2 has an additional 1363 matches
3,3 has an additional 1364 matches
3,4 has an additional 1113 matches
3,5 has an additional 1167 matches
3,6 has an additional 1280 matches
3,7 has an additional 1288 matches
3,8 has an additional 1564 matches
3,9 has an additional 983 matches
3,10 has an additional 1018 matches
4,0 has an additional 1878 matches
4,1 has an additional 1766 matches

4,2 has an additional 2083 matches

4,3 has an additional 2083 matches
4,4 has an additional 2262 matches
4,5 has an additional 2098 matches
4,6 has an additional 2509 matches
4,7 has an additional 2524 matches
4,8 has an additional 2019 matches
4,9 has an additional 1352 matches
4,10 has an additional 1439 matches
5,0 has an additional 2257 matches
5,1 has an additional 1183 matches
5,2 has an additional 1835 matches
5,3 has an additional 1834 matches
5,4 has an additional 1575 matches
5,5 has an additional 1480 matches
5,6 has an additional 1766 matches
5,7 has an additional 1775 matches
5,8 has an additional 2532 matches
5,9 has an additional 1935 matches
5,10 has an additional 2054 matches
6,0 has an additional 2135 matches
6,1 has an additional 1794 matches
6,2 has an additional 2362 matches
6,3 has an additional 2362 matches
6,4 has an additional 2134 matches
6,5 has an additional 2362 matches
6,6 has an additional 2602 matches
6,7 has an additional 2633 matches
6,8 has an additional 2653 matches
6,9 has an additional 1760 matches
6,10 has an additional 1956 matches
7,0 has an additional 2819 matches
7,1 has an additional 1496 matches
7,2 has an additional 2491 matches
7,3 has an additional 2493 matches
7,4 has an additional 1987 matches
7,5 has an additional 2275 matches
7,6 has an additional 2752 matches
7,7 has an additional 2763 matches
7,8 has an additional 2933 matches
7,9 has an additional 1885 matches
7,10 has an additional 1686 matches
8,0 has an additional 2819 matches
8,1 has an additional 1498 matches
8,2 has an additional 2494 matches
8,3 has an additional 2495 matches
8,4 has an additional 1990 matches
8,5 has an additional 2276 matches
8,6 has an additional 2753 matches
8,7 has an additional 2764 matches
8,8 has an additional 2932 matches
8,9 has an additional 1888 matches
8,10 has an additional 1687 matches
Restoring backed up alignment tree...
22,6 has 4895 pairwise matches
22,4 has 2496 pairwise matches
22,7 has 4712 pairwise matches
22,8 has 4712 pairwise matches
22,17 has 3192 pairwise matches
22,0 has 3526 pairwise matches

22,15 has 3940 pairwise matches

22,16 has 3945 pairwise matches
22,2 has 5243 pairwise matches
22,13 has 4213 pairwise matches
22,14 has 4374 pairwise matches
20,6 has 3940 pairwise matches
20,4 has 2048 pairwise matches
20,7 has 3613 pairwise matches
20,8 has 3613 pairwise matches
20,17 has 2385 pairwise matches
20,0 has 2813 pairwise matches
20,15 has 2856 pairwise matches
20,16 has 2867 pairwise matches
20,2 has 4143 pairwise matches
20,13 has 3079 pairwise matches
20,14 has 3156 pairwise matches
25,6 has 4202 pairwise matches
25,4 has 2410 pairwise matches
25,7 has 3740 pairwise matches
25,8 has 3740 pairwise matches
25,17 has 2874 pairwise matches
25,0 has 3082 pairwise matches
25,15 has 3072 pairwise matches
25,16 has 3085 pairwise matches
25,2 has 4595 pairwise matches
25,13 has 3969 pairwise matches
25,14 has 3930 pairwise matches
28,6 has 1229 pairwise matches
28,4 has 1411 pairwise matches
28,7 has 1363 pairwise matches
28,8 has 1364 pairwise matches
28,17 has 1113 pairwise matches
28,0 has 1167 pairwise matches
28,15 has 1280 pairwise matches
28,16 has 1288 pairwise matches
28,2 has 1564 pairwise matches
28,13 has 983 pairwise matches
28,14 has 1018 pairwise matches
18,6 has 1878 pairwise matches
18,4 has 1766 pairwise matches
18,7 has 2083 pairwise matches
18,8 has 2083 pairwise matches
18,17 has 2262 pairwise matches
18,0 has 2098 pairwise matches
18,15 has 2509 pairwise matches
18,16 has 2524 pairwise matches
18,2 has 2019 pairwise matches
18,13 has 1352 pairwise matches
18,14 has 1439 pairwise matches
26,6 has 2257 pairwise matches
26,4 has 1183 pairwise matches
26,7 has 1835 pairwise matches
26,8 has 1834 pairwise matches
26,17 has 1575 pairwise matches
26,0 has 1480 pairwise matches
26,15 has 1766 pairwise matches
26,16 has 1775 pairwise matches
26,2 has 2532 pairwise matches
26,13 has 1935 pairwise matches
26,14 has 2054 pairwise matches

3,6 has 2135 pairwise matches

3,4 has 1794 pairwise matches
3,7 has 2362 pairwise matches
3,8 has 2362 pairwise matches
3,17 has 2134 pairwise matches
3,0 has 2362 pairwise matches
3,15 has 2602 pairwise matches
3,16 has 2633 pairwise matches
3,2 has 2653 pairwise matches
3,13 has 1760 pairwise matches
3,14 has 1956 pairwise matches
23,6 has 2819 pairwise matches
23,4 has 1496 pairwise matches
23,7 has 2491 pairwise matches
23,8 has 2493 pairwise matches
23,17 has 1987 pairwise matches
23,0 has 2275 pairwise matches
23,15 has 2752 pairwise matches
23,16 has 2763 pairwise matches
23,2 has 2933 pairwise matches
23,13 has 1885 pairwise matches
23,14 has 1686 pairwise matches
24,6 has 2819 pairwise matches
24,4 has 1498 pairwise matches
24,7 has 2494 pairwise matches
24,8 has 2495 pairwise matches
24,17 has 1990 pairwise matches
24,0 has 2276 pairwise matches
24,15 has 2753 pairwise matches
24,16 has 2764 pairwise matches
24,2 has 2932 pairwise matches
24,13 has 1888 pairwise matches
24,14 has 1687 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 2189 Mb
Pagefile usage: 1622 Mb
construct LCB tracking matches
There are 25964 tracking matches
There are 915406 / 1583804 components used
Working set size: 2265 Mb
Pagefile usage: 1702 Mb
init tracking match LCB tracking
Working set size: 2285 Mb
Pagefile usage: 1721 Mb
pairwise score tracking matches
Working set size: 2305 Mb
Pagefile usage: 1741 Mb
get pairwise LCBs
there are 49088 pairwise LCBs
Working set size: 2313 Mb
Pagefile usage: 1747 Mb
scaling bp penalty by conservation weight:
0.104964
0.092308
0.102874
0.103756
0.0971978
0.0958171
0.0933584
0.0933141
0.104619
0.0988593
0.0977835
0.0909611
0.0753013
0.10043 0.100602
0.0807403
0.084938
1
0.0786561
0.07885 0.0937648
0.0863727
0.0842981
0.0949334
0.0793685
0.0941867
0.0950836
0.0833109
0.0845789
0.0803839
0.0805646
0.0957328
0.091898
0.0901769

0.0618732
0.0484393
0.0747733
0.0750174
0.0600868
0.0613001
0.0688717
0.0690649
0.0690823
0.0560014
0.0568492
0.0640255
0.0619378
0.0650803
0.0652913
0.0732597
0.0649757
0.0729946
0.0731761
0.0572564
0.0531335
0.0538098
0.0819288
0.0630374
0.0783984
0.0793076
0.0755153
0.068293
0.0728713
0.0730548
0.0773313
0.0723802
0.0734437
0.0617734
0.0631265
0.0724488
0.074441
0.0701853
0.0711681
0.0762544
0.0756607
0.0676085
0.0550686
0.0533717
0.0671347
0.0593501
0.0716504
0.0725526
0.0666916
0.0674732
0.0734024
0.0737297
0.0651843
0.0561525
0.0489132
0.0670573
0.0602955
0.0713634
0.0722656
0.06746 0.068213
6
0.0743775
0.074705
0.0662154
0.0564365
0.049194
4
scaling bp penalty by bp weight:
0.0857143
0.0214286
0.0857143
0.0857143
0.0214286
0.0857143
0.0857143
0.0857143
0.15
0.0214286
0.021428
6
0.0857143
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0857143
0.0214286
0.0214286
0.0857143
0.0642857
0.128571
0.128571
0.0642857
0.128571
0.128571
0.128571
0.192857
0.0642857
0.0642857
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.128571
0.0214286
0.15
0.15
0.0214286
0.0857143
0.0857143
0.0857143
0.0857143
0.0857143
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.15
0.0214286
0.0857143
0.0857143
0.0214286
0.085714
3
0.0214286
0.0214286
0.0857143
0.0857143
0.085714
3
0.15
0.0214286
0.0857143
0.0857143
0.0214286
0.021428
6
0.0214286
0.0214286
0.0214286
0.0857143
0.085714
3
0.15
0.0214286
0.0857143
0.0857143
0.0214286
0.021428
6
0.0214286
0.0214286
0.0214286
0.0857143
0.085714
3
Greedy BPE
Scoring with scaled breakpoint penalty: 80489.9
1%..2%..3%..4%..done
Working set size: 2205 Mb
Pagefile usage: 1659 Mb
Arrived at 88 intervals
Adding unaligned intervals
addUnalignedIntervals yields 224 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(23) has 60 intervals

descendant 1(40) has 84 intervals

propagateDescendantBreakpoints yields 229 intervals
Creating ancestral ordering
Previous anchoring score: 1.71816e+010, new anchor score: 1.72009e+010
Working set size: 2204 Mb
Pagefile usage: 1660 Mb
propagating ancestral breakpoints
Working set size: 2205 Mb
Pagefile usage: 1662 Mb
performing a gapped alignment
0%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..47%..48%..49%..
50%..51%..52%..53%..54%..55%..56%..57%..58%..59%..
60%..61%..62%..63%..64%..65%..66%..67%..68%..69%..
70%..71%..72%..73%..74%..75%..76%..77%..78%..79%..
80%..81%..82%..83%..84%..85%..86%..87%..88%..89%..
90%..91%..92%..93%..94%..95%..96%..97%..98%..99%..
100%..Working set size: 2285 Mb
Pagefile usage: 1721 Mb
Fix left ends
Working set size: 2285 Mb
Pagefile usage: 1721 Mb
done.
Working set size: 2285 Mb
Pagefile usage: 1721 Mb
Aligning node 11 to 12 via 10!
Working set size: 2087 Mb
Pagefile usage: 1571 Mb
get ancestral matches
Working set size: 2091 Mb
Pagefile usage: 1575 Mb
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 2091 Mb
Pagefile usage: 1575 Mb
construct LCB tracking matches
There are 818 tracking matches
There are 1636 / 49898 components used
Working set size: 2091 Mb
Pagefile usage: 1575 Mb
init tracking match LCB tracking
Working set size: 2091 Mb
Pagefile usage: 1575 Mb
pairwise score tracking matches
Working set size: 2098 Mb
Pagefile usage: 1580 Mb
get pairwise LCBs
there are 127 pairwise LCBs
Working set size: 2098 Mb
Pagefile usage: 1580 Mb
scaling bp penalty by conservation weight:
0.0528278
scaling bp penalty by bp weight:
0.0214286

Greedy BPE
Scoring with scaled breakpoint penalty: 115642
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..47%..48%..49%..
50%..51%..52%..53%..54%..55%..56%..57%..58%..59%..
60%..61%..62%..63%..64%..65%..66%..67%..68%..69%..done
Working set size: 2098 Mb
Pagefile usage: 1580 Mb
Arrived at 1 intervals
Adding unaligned intervals
addUnalignedIntervals yields 1 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(11) has 1 intervals
descendant 1(12) has 1 intervals
propagateDescendantBreakpoints yields 1 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 1.91297e+008
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 0 new matches outside LCBs
0,0 has an additional 35 matches
Restoring backed up alignment tree...
30,19 has 35 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 2125 Mb
Pagefile usage: 1595 Mb
construct LCB tracking matches
There are 698 tracking matches
There are 1396 / 42578 components used
Working set size: 2126 Mb
Pagefile usage: 1596 Mb
init tracking match LCB tracking
Working set size: 2126 Mb
Pagefile usage: 1596 Mb
pairwise score tracking matches
Working set size: 2126 Mb
Pagefile usage: 1596 Mb
get pairwise LCBs
there are 9 pairwise LCBs
Working set size: 2126 Mb
Pagefile usage: 1596 Mb
scaling bp penalty by conservation weight:
0.0528278
scaling bp penalty by bp weight:
0.0214286
Greedy BPE
Scoring with scaled breakpoint penalty: 115642
11%..
22%..

33%..done
Working set size: 2126 Mb
Pagefile usage: 1597 Mb
Arrived at 1 intervals
Adding unaligned intervals
addUnalignedIntervals yields 1 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(11) has 1 intervals
descendant 1(12) has 1 intervals
propagateDescendantBreakpoints yields 1 intervals
Creating ancestral ordering
Previous anchoring score: 1.91297e+008, new anchor score: 2.01065e+008
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 0 new matches outside LCBs
0,0 has an additional 1 matches
Restoring backed up alignment tree...
30,19 has 1 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 2129 Mb
Pagefile usage: 1599 Mb
construct LCB tracking matches
There are 695 tracking matches
There are 1390 / 42395 components used
Working set size: 2129 Mb
Pagefile usage: 1599 Mb
init tracking match LCB tracking
Working set size: 2129 Mb
Pagefile usage: 1599 Mb
pairwise score tracking matches
Working set size: 2129 Mb
Pagefile usage: 1599 Mb
get pairwise LCBs
there are 1 pairwise LCBs
Working set size: 2129 Mb
Pagefile usage: 1599 Mb
scaling bp penalty by conservation weight:
0.0528278
scaling bp penalty by bp weight:
0.0214286
Greedy BPE
Scoring with scaled breakpoint penalty: 115642
done
Working set size: 2129 Mb
Pagefile usage: 1600 Mb
Arrived at 1 intervals
Adding unaligned intervals
addUnalignedIntervals yields 1 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(11) has 1 intervals
descendant 1(12) has 1 intervals
propagateDescendantBreakpoints yields 1 intervals

Creating ancestral ordering

Previous anchoring score: 2.01065e+008, new anchor score: 2.01064e+008
Working set size: 2129 Mb
Pagefile usage: 1600 Mb
propagating ancestral breakpoints
Working set size: 2129 Mb
Pagefile usage: 1600 Mb
performing a gapped alignment
0%..1%..3%..4%..5%..6%..7%..9%..
10%..11%..12%..14%..15%..16%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..32%..33%..34%..36%..37%..38%..39%..
41%..42%..43%..44%..45%..47%..48%..49%..
50%..52%..53%..54%..56%..57%..58%..
60%..61%..62%..64%..65%..66%..67%..68%..69%..
70%..71%..72%..73%..74%..76%..77%..79%..
81%..82%..84%..85%..87%..88%..
90%..92%..93%..95%..96%..98%..
100%..Working set size: 2079 Mb
Pagefile usage: 1545 Mb
Fix left ends
Working set size: 2079 Mb
Pagefile usage: 1545 Mb
done.
Working set size: 2079 Mb
Pagefile usage: 1545 Mb
Aligning node 6 to 9 via 5!
Working set size: 2074 Mb
Pagefile usage: 1571 Mb
get ancestral matches
Working set size: 2093 Mb
Pagefile usage: 1592 Mb
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 2093 Mb
Pagefile usage: 1593 Mb
construct LCB tracking matches
There are 57727 tracking matches
There are 229105 / 3521347 components used
Working set size: 2366 Mb
Pagefile usage: 1812 Mb
init tracking match LCB tracking
Working set size: 2367 Mb
Pagefile usage: 1812 Mb
pairwise score tracking matches
Working set size: 2368 Mb
Pagefile usage: 1813 Mb
get pairwise LCBs
there are 17743 pairwise LCBs
Working set size: 2374 Mb
Pagefile usage: 1818 Mb
scaling bp penalty by conservation weight:
0.0781088
0.0716975
scaling bp penalty by bp weight:
0.0857143
0.0428571

Greedy BPE
Scoring with scaled breakpoint penalty: 90593.7
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..done
Working set size: 2093 Mb
Pagefile usage: 1563 Mb
Arrived at 11 intervals
Adding unaligned intervals
addUnalignedIntervals yields 33 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(6) has 2 intervals
descendant 1(9) has 1 intervals
propagateDescendantBreakpoints yields 12 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 1.60044e+008
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 116 new matches outside LCBs
1,0 have 156 new matches outside LCBs
0,0 has an additional 2976 matches
1,0 has an additional 2733 matches
Restoring backed up alignment tree...
12,29 has 2976 pairwise matches
21,29 has 2733 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 2139 Mb
Pagefile usage: 1605 Mb
construct LCB tracking matches
There are 54379 tracking matches
There are 216295 / 3317119 components used
Working set size: 2352 Mb
Pagefile usage: 1787 Mb
init tracking match LCB tracking
Working set size: 2353 Mb
Pagefile usage: 1787 Mb
pairwise score tracking matches
Working set size: 2354 Mb
Pagefile usage: 1789 Mb
get pairwise LCBs
there are 4892 pairwise LCBs
Working set size: 2358 Mb
Pagefile usage: 1792 Mb
scaling bp penalty by conservation weight:
0.0781088
0.0716975
scaling bp penalty by bp weight:
0.0857143
0.0428571
Greedy BPE
Scoring with scaled breakpoint penalty: 90593.7
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..

20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..done
Working set size: 2098 Mb
Pagefile usage: 1540 Mb
Arrived at 8 intervals
Adding unaligned intervals
addUnalignedIntervals yields 24 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(6) has 2 intervals
descendant 1(9) has 1 intervals
propagateDescendantBreakpoints yields 9 intervals
Creating ancestral ordering
Previous anchoring score: 1.60044e+008, new anchor score: 1.89657e+008
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 71 new matches outside LCBs
1,0 have 340 new matches outside LCBs
0,0 has an additional 1130 matches
1,0 has an additional 1671 matches
Restoring backed up alignment tree...
12,29 has 1130 pairwise matches
21,29 has 1671 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 2132 Mb
Pagefile usage: 1582 Mb
construct LCB tracking matches
There are 53742 tracking matches
There are 213899 / 3278262 components used
Working set size: 2338 Mb
Pagefile usage: 1774 Mb
init tracking match LCB tracking
Working set size: 2339 Mb
Pagefile usage: 1774 Mb
pairwise score tracking matches
Working set size: 2340 Mb
Pagefile usage: 1776 Mb
get pairwise LCBs
there are 3639 pairwise LCBs
Working set size: 2343 Mb
Pagefile usage: 1779 Mb
scaling bp penalty by conservation weight:
0.0781088
0.0716975
scaling bp penalty by bp weight:
0.0857143
0.0428571
Greedy BPE
Scoring with scaled breakpoint penalty: 90593.7
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..done

Working set size: 2085 Mb

Pagefile usage: 1530 Mb
Arrived at 15 intervals
Adding unaligned intervals
addUnalignedIntervals yields 45 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(6) has 2 intervals
descendant 1(9) has 1 intervals
propagateDescendantBreakpoints yields 16 intervals
Creating ancestral ordering
Previous anchoring score: 1.89657e+008, new anchor score: 1.90065e+008
Working set size: 2091 Mb
Pagefile usage: 1536 Mb
propagating ancestral breakpoints
Working set size: 2092 Mb
Pagefile usage: 1537 Mb
performing a gapped alignment
0%..1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..47%..48%..49%..
50%..51%..52%..53%..54%..55%..56%..57%..58%..59%..
60%..61%..62%..63%..64%..65%..66%..67%..68%..69%..
70%..71%..72%..73%..74%..75%..76%..77%..78%..79%..
80%..81%..82%..83%..84%..85%..86%..87%..88%..89%..
90%..91%..92%..93%..94%..95%..96%..97%..98%..99%..
100%..Working set size: 2316 Mb
Pagefile usage: 1750 Mb
Fix left ends
Working set size: 2316 Mb
Pagefile usage: 1750 Mb
done.
Working set size: 2316 Mb
Pagefile usage: 1750 Mb
Aligning node 5 to 10 via 4!
Working set size: 2032 Mb
Pagefile usage: 1489 Mb
get ancestral matches
Working set size: 2072 Mb
Pagefile usage: 1529 Mb
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 2073 Mb
Pagefile usage: 1534 Mb
construct LCB tracking matches
There are 65423 tracking matches
There are 512656 / 3990803 components used
Working set size: 2433 Mb
Pagefile usage: 1869 Mb
init tracking match LCB tracking
Working set size: 2436 Mb
Pagefile usage: 1872 Mb
pairwise score tracking matches
Working set size: 2439 Mb
Pagefile usage: 1875 Mb
get pairwise LCBs

there are 58100 pairwise LCBs

Working set size: 2449 Mb
Pagefile usage: 1885 Mb
scaling bp penalty by conservation weight:
0.10184 0.0779986
0.105794
0.0813018
0.0957466
0.0739364
scaling bp penalty by bp weight:
0.0214286
0.0214286
0.0214286
0.0214286
0.107143
0.0428571
Greedy BPE
Scoring with scaled breakpoint penalty: 93500.8
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..done
Working set size: 2070 Mb
Pagefile usage: 1510 Mb
Arrived at 32 intervals
Adding unaligned intervals
addUnalignedIntervals yields 93 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(5) has 9 intervals
descendant 1(10) has 1 intervals
propagateDescendantBreakpoints yields 40 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 4.50164e+008
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 583 new matches outside LCBs
0,1 have 567 new matches outside LCBs
1,0 have 625 new matches outside LCBs
1,1 have 533 new matches outside LCBs
2,0 have 837 new matches outside LCBs
2,1 have 477 new matches outside LCBs
0,0 has an additional 3183 matches
0,1 has an additional 3105 matches
1,0 has an additional 3533 matches
1,1 has an additional 2915 matches
2,0 has an additional 3303 matches
2,1 has an additional 2988 matches
Restoring backed up alignment tree...
29,19 has 3183 pairwise matches
29,30 has 3105 pairwise matches
12,19 has 3533 pairwise matches
12,30 has 2915 pairwise matches
21,19 has 3303 pairwise matches
21,30 has 2988 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 2137 Mb
Pagefile usage: 1577 Mb
construct LCB tracking matches
There are 57025 tracking matches
There are 449840 / 3478525 components used
Working set size: 2395 Mb

Pagefile usage: 1827 Mb

init tracking match LCB tracking
Working set size: 2397 Mb
Pagefile usage: 1830 Mb
pairwise score tracking matches
Working set size: 2401 Mb
Pagefile usage: 1833 Mb
get pairwise LCBs
there are 12660 pairwise LCBs
Working set size: 2406 Mb
Pagefile usage: 1838 Mb
scaling bp penalty by conservation weight:
0.10184 0.0779986
0.105794
0.0813018
0.0957466
0.0739364
scaling bp penalty by bp weight:
0.0214286
0.0214286
0.0214286
0.0214286
0.107143
0.0428571
Greedy BPE
Scoring with scaled breakpoint penalty: 93500.8
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..done
Working set size: 2126 Mb
Pagefile usage: 1592 Mb
Arrived at 30 intervals
Adding unaligned intervals
addUnalignedIntervals yields 82 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(5) has 9 intervals
descendant 1(10) has 1 intervals
propagateDescendantBreakpoints yields 38 intervals
Creating ancestral ordering
Previous anchoring score: 4.50164e+008, new anchor score: 5.68453e+008
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 664 new matches outside LCBs
0,1 have 908 new matches outside LCBs
1,0 have 818 new matches outside LCBs
1,1 have 626 new matches outside LCBs
2,0 have 830 new matches outside LCBs
2,1 have 757 new matches outside LCBs
0,0 has an additional 1951 matches
0,1 has an additional 1902 matches
1,0 has an additional 2521 matches
1,1 has an additional 1916 matches
2,0 has an additional 2197 matches
2,1 has an additional 1953 matches
Restoring backed up alignment tree...
29,19 has 1951 pairwise matches
29,30 has 1902 pairwise matches
12,19 has 2521 pairwise matches
12,30 has 1916 pairwise matches

21,19 has 2197 pairwise matches

21,30 has 1953 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 2154 Mb
Pagefile usage: 1620 Mb
construct LCB tracking matches
There are 56713 tracking matches
There are 447699 / 3459493 components used
Working set size: 2363 Mb
Pagefile usage: 1795 Mb
init tracking match LCB tracking
Working set size: 2366 Mb
Pagefile usage: 1798 Mb
pairwise score tracking matches
Working set size: 2368 Mb
Pagefile usage: 1801 Mb
get pairwise LCBs
there are 11229 pairwise LCBs
Working set size: 2376 Mb
Pagefile usage: 1808 Mb
scaling bp penalty by conservation weight:
0.10184 0.0779986
0.105794
0.0813018
0.0957466
0.0739364
scaling bp penalty by bp weight:
0.0214286
0.0214286
0.0214286
0.0214286
0.107143
0.0428571
Greedy BPE
Scoring with scaled breakpoint penalty: 93500.8
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..done
Working set size: 2108 Mb
Pagefile usage: 1563 Mb
Arrived at 23 intervals
Adding unaligned intervals
addUnalignedIntervals yields 61 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(5) has 9 intervals
descendant 1(10) has 1 intervals
propagateDescendantBreakpoints yields 31 intervals
Creating ancestral ordering
Previous anchoring score: 5.68453e+008, new anchor score: 5.71272e+008
Working set size: 2114 Mb
Pagefile usage: 1572 Mb
propagating ancestral breakpoints
Working set size: 2115 Mb
Pagefile usage: 1573 Mb
performing a gapped alignment
0%..1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..

40%..41%..42%..43%..44%..45%..46%..47%..48%..49%..
50%..51%..52%..53%..54%..55%..56%..57%..58%..59%..
60%..61%..62%..63%..64%..65%..66%..67%..68%..69%..
70%..71%..72%..73%..74%..75%..76%..77%..78%..79%..
80%..81%..82%..83%..84%..85%..86%..87%..88%..89%..
90%..91%..92%..93%..94%..95%..96%..97%..98%..99%..
100%..Working set size: 2298 Mb
Pagefile usage: 1736 Mb
Fix left ends
Working set size: 2298 Mb
Pagefile usage: 1736 Mb
done.
performing iterative refinement
0%..1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..15%..16%..17%..18%..
20%..21%..22%..23%..24%..26%..27%..28%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..
40%..41%..42%..43%..44%..45%..47%..49%..
50%..51%..52%..53%..54%..55%..56%..57%..58%..59%..
61%..62%..63%..64%..65%..66%..67%..68%..69%..
70%..71%..72%..73%..74%..75%..76%..78%..79%..
81%..82%..83%..84%..86%..87%..88%..89%..
90%..91%..92%..93%..94%..95%..96%..97%..98%..99%..
100%..Working set size: 2322 Mb
Pagefile usage: 1753 Mb
Fix left ends
Working set size: 2322 Mb
Pagefile usage: 1753 Mb
done.
Working set size: 2322 Mb
Pagefile usage: 1753 Mb
Aligning node 19 to 20 via 18!
Working set size: 2031 Mb
Pagefile usage: 1476 Mb
get ancestral matches
Working set size: 2035 Mb
Pagefile usage: 1480 Mb
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 2035 Mb
Pagefile usage: 1480 Mb
construct LCB tracking matches
There are 8617 tracking matches
There are 17234 / 525637 components used
Working set size: 2047 Mb
Pagefile usage: 1492 Mb
init tracking match LCB tracking
Working set size: 2047 Mb
Pagefile usage: 1492 Mb
pairwise score tracking matches
Working set size: 2048 Mb
Pagefile usage: 1492 Mb
get pairwise LCBs
there are 1431 pairwise LCBs
Working set size: 2048 Mb
Pagefile usage: 1493 Mb
scaling bp penalty by conservation weight:
0.0708613

scaling bp penalty by bp weight:

0.0214286
Greedy BPE
Scoring with scaled breakpoint penalty: 107084
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..47%..48%..49%..
50%..51%..52%..53%..54%..55%..56%..57%..58%..59%..
60%..61%..62%..63%..done
Working set size: 2049 Mb
Pagefile usage: 1505 Mb
Arrived at 4 intervals
Adding unaligned intervals
addUnalignedIntervals yields 10 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(19) has 1 intervals
descendant 1(20) has 1 intervals
propagateDescendantBreakpoints yields 4 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 1.61279e+008
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 229 new matches outside LCBs
0,0 has an additional 1891 matches
Restoring backed up alignment tree...
10,5 has 1891 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 2082 Mb
Pagefile usage: 1537 Mb
construct LCB tracking matches
There are 9236 tracking matches
There are 18472 / 563396 components used
Working set size: 2091 Mb
Pagefile usage: 1545 Mb
init tracking match LCB tracking
Working set size: 2091 Mb
Pagefile usage: 1545 Mb
pairwise score tracking matches
Working set size: 2091 Mb
Pagefile usage: 1545 Mb
get pairwise LCBs
there are 1533 pairwise LCBs
Working set size: 2091 Mb
Pagefile usage: 1545 Mb
scaling bp penalty by conservation weight:
0.0708613
scaling bp penalty by bp weight:
0.0214286
Greedy BPE

Scoring with scaled breakpoint penalty: 107084

1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..47%..48%..49%..
50%..51%..52%..53%..54%..55%..56%..57%..58%..59%..
60%..61%..62%..63%..64%..65%..66%..67%..68%..69%..
70%..71%..72%..73%..74%..75%..76%..77%..78%..79%..
80%..81%..82%..83%..done
Working set size: 2092 Mb
Pagefile usage: 1546 Mb
Arrived at 1 intervals
Adding unaligned intervals
addUnalignedIntervals yields 1 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(19) has 1 intervals
descendant 1(20) has 1 intervals
propagateDescendantBreakpoints yields 1 intervals
Creating ancestral ordering
Previous anchoring score: 1.61279e+008, new anchor score: 1.89827e+008
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 0 new matches outside LCBs
0,0 has an additional 584 matches
Restoring backed up alignment tree...
10,5 has 584 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 2118 Mb
Pagefile usage: 1579 Mb
construct LCB tracking matches
There are 8385 tracking matches
There are 16770 / 511485 components used
Working set size: 2119 Mb
Pagefile usage: 1580 Mb
init tracking match LCB tracking
Working set size: 2119 Mb
Pagefile usage: 1580 Mb
pairwise score tracking matches
Working set size: 2119 Mb
Pagefile usage: 1580 Mb
get pairwise LCBs
there are 584 pairwise LCBs
Working set size: 2119 Mb
Pagefile usage: 1580 Mb
scaling bp penalty by conservation weight:
0.0708613
scaling bp penalty by bp weight:
0.0214286
Greedy BPE
Scoring with scaled breakpoint penalty: 107084
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..

30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..47%..48%..49%..
50%..51%..52%..53%..54%..55%..56%..57%..58%..59%..
60%..61%..62%..63%..64%..65%..66%..67%..68%..69%..
70%..71%..72%..73%..74%..75%..76%..77%..78%..done
Working set size: 2119 Mb
Pagefile usage: 1580 Mb
Arrived at 1 intervals
Adding unaligned intervals
addUnalignedIntervals yields 1 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(19) has 1 intervals
descendant 1(20) has 1 intervals
propagateDescendantBreakpoints yields 1 intervals
Creating ancestral ordering
Previous anchoring score: 1.89827e+008, new anchor score: 1.89551e+008
Working set size: 2119 Mb
Pagefile usage: 1580 Mb
propagating ancestral breakpoints
Working set size: 2119 Mb
Pagefile usage: 1580 Mb
performing a gapped alignment
0%..1%..2%..3%..4%..5%..6%..8%..9%..
10%..11%..12%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..25%..26%..27%..29%..
30%..32%..34%..35%..37%..39%..
41%..42%..43%..44%..46%..47%..48%..49%..
50%..52%..53%..54%..55%..56%..57%..59%..
60%..61%..62%..63%..64%..66%..67%..68%..69%..
70%..72%..73%..74%..75%..76%..77%..78%..79%..
80%..81%..82%..83%..84%..85%..86%..87%..88%..89%..
90%..91%..92%..93%..94%..95%..96%..97%..98%..
100%..Working set size: 2064 Mb
Pagefile usage: 1517 Mb
Fix left ends
Working set size: 2064 Mb
Pagefile usage: 1517 Mb
done.
Working set size: 2064 Mb
Pagefile usage: 1517 Mb
Aligning node 18 to 21 via 17!
Working set size: 2061 Mb
Pagefile usage: 1526 Mb
get ancestral matches
Working set size: 2091 Mb
Pagefile usage: 1554 Mb
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 2091 Mb
Pagefile usage: 1554 Mb
construct LCB tracking matches
There are 20050 tracking matches
There are 78125 / 1223050 components used
Working set size: 2147 Mb
Pagefile usage: 1600 Mb
init tracking match LCB tracking
Working set size: 2147 Mb

Pagefile usage: 1600 Mb

pairwise score tracking matches
Working set size: 2147 Mb
Pagefile usage: 1600 Mb
get pairwise LCBs
there are 5519 pairwise LCBs
Working set size: 2149 Mb
Pagefile usage: 1602 Mb
scaling bp penalty by conservation weight:
0.0840168
0.0794776
scaling bp penalty by bp weight:
0.0214286
0.0857143
Greedy BPE
Scoring with scaled breakpoint penalty: 101146
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..done
Working set size: 2147 Mb
Pagefile usage: 1603 Mb
Arrived at 13 intervals
Adding unaligned intervals
addUnalignedIntervals yields 37 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(18) has 1 intervals
descendant 1(21) has 1 intervals
propagateDescendantBreakpoints yields 13 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 2.80081e+008
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 163 new matches outside LCBs
1,0 have 135 new matches outside LCBs
0,0 has an additional 2906 matches
1,0 has an additional 2881 matches
Restoring backed up alignment tree...
5,1 has 2906 pairwise matches
10,1 has 2881 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 2161 Mb
Pagefile usage: 1615 Mb
construct LCB tracking matches
There are 20644 tracking matches
There are 80372 / 1259284 components used
Working set size: 2176 Mb
Pagefile usage: 1631 Mb
init tracking match LCB tracking
Working set size: 2176 Mb
Pagefile usage: 1631 Mb
pairwise score tracking matches
Working set size: 2176 Mb
Pagefile usage: 1631 Mb

get pairwise LCBs

there are 4347 pairwise LCBs
Working set size: 2177 Mb
Pagefile usage: 1631 Mb
scaling bp penalty by conservation weight:
0.0840168
0.0794776
scaling bp penalty by bp weight:
0.0214286
0.0857143
Greedy BPE
Scoring with scaled breakpoint penalty: 101146
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..47%..48%..49%..
50%..51%..52%..53%..54%..55%..done
Working set size: 2175 Mb
Pagefile usage: 1627 Mb
Arrived at 27 intervals
Adding unaligned intervals
addUnalignedIntervals yields 78 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(18) has 1 intervals
descendant 1(21) has 1 intervals
propagateDescendantBreakpoints yields 27 intervals
Creating ancestral ordering
Previous anchoring score: 2.80081e+008, new anchor score: 3.52598e+008
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 401 new matches outside LCBs
1,0 have 427 new matches outside LCBs
0,0 has an additional 1420 matches
1,0 has an additional 1628 matches
Restoring backed up alignment tree...
5,1 has 1420 pairwise matches
10,1 has 1628 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 2085 Mb
Pagefile usage: 1525 Mb
construct LCB tracking matches
There are 20014 tracking matches
There are 78011 / 1220854 components used
Working set size: 2113 Mb
Pagefile usage: 1552 Mb
init tracking match LCB tracking
Working set size: 2113 Mb
Pagefile usage: 1552 Mb
pairwise score tracking matches
Working set size: 2114 Mb
Pagefile usage: 1553 Mb
get pairwise LCBs
there are 2944 pairwise LCBs

Working set size: 2114 Mb

Pagefile usage: 1553 Mb
scaling bp penalty by conservation weight:
0.0840168
0.0794776
scaling bp penalty by bp weight:
0.0214286
0.0857143
Greedy BPE
Scoring with scaled breakpoint penalty: 101146
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..47%..48%..49%..
50%..51%..52%..53%..54%..55%..56%..57%..58%..done
Working set size: 2114 Mb
Pagefile usage: 1556 Mb
Arrived at 17 intervals
Adding unaligned intervals
addUnalignedIntervals yields 49 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(18) has 1 intervals
descendant 1(21) has 1 intervals
propagateDescendantBreakpoints yields 17 intervals
Creating ancestral ordering
Previous anchoring score: 3.52598e+008, new anchor score: 3.52418e+008
Working set size: 2114 Mb
Pagefile usage: 1556 Mb
propagating ancestral breakpoints
Working set size: 2114 Mb
Pagefile usage: 1556 Mb
performing a gapped alignment
0%..1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..42%..43%..44%..45%..46%..47%..48%..49%..
50%..51%..52%..53%..54%..55%..56%..57%..58%..59%..
60%..61%..63%..64%..65%..66%..67%..68%..69%..
70%..71%..72%..73%..74%..75%..76%..77%..78%..79%..
80%..81%..82%..83%..84%..85%..86%..87%..89%..
90%..91%..92%..93%..94%..95%..96%..97%..98%..99%..
100%..Working set size: 2279 Mb
Pagefile usage: 1715 Mb
Fix left ends
Working set size: 2279 Mb
Pagefile usage: 1715 Mb
done.
Working set size: 2279 Mb
Pagefile usage: 1715 Mb
Aligning node 17 to 22 via 16!
Working set size: 2273 Mb

Pagefile usage: 1708 Mb

get ancestral matches
Working set size: 2275 Mb
Pagefile usage: 1712 Mb
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 2275 Mb
Pagefile usage: 1712 Mb
construct LCB tracking matches
There are 25518 tracking matches
There are 146903 / 1556598 components used
Working set size: 2283 Mb
Pagefile usage: 1718 Mb
init tracking match LCB tracking
Working set size: 2283 Mb
Pagefile usage: 1718 Mb
pairwise score tracking matches
Working set size: 2283 Mb
Pagefile usage: 1718 Mb
get pairwise LCBs
there are 10355 pairwise LCBs
Working set size: 2283 Mb
Pagefile usage: 1718 Mb
scaling bp penalty by conservation weight:
0.0889019
0.0861026
0.0769267
scaling bp penalty by bp weight:
0.0214286
0.0857143
0.0214286
Greedy BPE
Scoring with scaled breakpoint penalty: 99005.9
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..done
Working set size: 2279 Mb
Pagefile usage: 1714 Mb
Arrived at 35 intervals
Adding unaligned intervals
addUnalignedIntervals yields 104 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(17) has 27 intervals
descendant 1(22) has 1 intervals
propagateDescendantBreakpoints yields 61 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 4.27753e+008
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 1677 new matches outside LCBs
1,0 have 1020 new matches outside LCBs
2,0 have 1713 new matches outside LCBs
0,0 has an additional 3484 matches
1,0 has an additional 2787 matches
2,0 has an additional 3686 matches

Restoring backed up alignment tree...

1,11 has 3484 pairwise matches
5,11 has 2787 pairwise matches
10,11 has 3686 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 2280 Mb
Pagefile usage: 1714 Mb
construct LCB tracking matches
There are 24673 tracking matches
There are 142819 / 1505053 components used
Working set size: 2280 Mb
Pagefile usage: 1714 Mb
init tracking match LCB tracking
Working set size: 2280 Mb
Pagefile usage: 1714 Mb
pairwise score tracking matches
Working set size: 2280 Mb
Pagefile usage: 1714 Mb
get pairwise LCBs
there are 5911 pairwise LCBs
Working set size: 2280 Mb
Pagefile usage: 1714 Mb
scaling bp penalty by conservation weight:
0.0889019
0.0861026
0.0769267
scaling bp penalty by bp weight:
0.0214286
0.0857143
0.0214286
Greedy BPE
Scoring with scaled breakpoint penalty: 99005.9
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..done
Working set size: 2280 Mb
Pagefile usage: 1714 Mb
Arrived at 25 intervals
Adding unaligned intervals
addUnalignedIntervals yields 72 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(17) has 27 intervals
descendant 1(22) has 1 intervals
propagateDescendantBreakpoints yields 51 intervals
Creating ancestral ordering
Previous anchoring score: 4.27753e+008, new anchor score: 5.12778e+008
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 1476 new matches outside LCBs
1,0 have 1165 new matches outside LCBs
2,0 have 1471 new matches outside LCBs
0,0 has an additional 2273 matches

1,0 has an additional 2097 matches

2,0 has an additional 2661 matches
Restoring backed up alignment tree...
1,11 has 2273 pairwise matches
5,11 has 2097 pairwise matches
10,11 has 2661 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 2094 Mb
Pagefile usage: 1536 Mb
construct LCB tracking matches
There are 24907 tracking matches
There are 144031 / 1519327 components used
Working set size: 2144 Mb
Pagefile usage: 1577 Mb
init tracking match LCB tracking
Working set size: 2144 Mb
Pagefile usage: 1578 Mb
pairwise score tracking matches
Working set size: 2145 Mb
Pagefile usage: 1579 Mb
get pairwise LCBs
there are 6131 pairwise LCBs
Working set size: 2147 Mb
Pagefile usage: 1580 Mb
scaling bp penalty by conservation weight:
0.0889019
0.0861026
0.0769267
scaling bp penalty by bp weight:
0.0214286
0.0857143
0.0214286
Greedy BPE
Scoring with scaled breakpoint penalty: 99005.9
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..done
Working set size: 2151 Mb
Pagefile usage: 1585 Mb
Arrived at 21 intervals
Adding unaligned intervals
addUnalignedIntervals yields 61 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(17) has 27 intervals
descendant 1(22) has 1 intervals
propagateDescendantBreakpoints yields 47 intervals
Creating ancestral ordering
Previous anchoring score: 5.12778e+008, new anchor score: 5.14668e+008
Working set size: 2151 Mb
Pagefile usage: 1586 Mb
propagating ancestral breakpoints
Working set size: 2151 Mb
Pagefile usage: 1586 Mb

performing a gapped alignment

0%..1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..46%..47%..48%..49%..
50%..51%..52%..53%..54%..55%..56%..57%..58%..59%..
60%..61%..63%..64%..65%..66%..67%..68%..69%..
70%..71%..72%..73%..74%..75%..76%..77%..78%..79%..
80%..81%..82%..83%..84%..85%..86%..87%..88%..89%..
90%..91%..92%..93%..94%..95%..96%..97%..98%..99%..
100%..Working set size: 2217 Mb
Pagefile usage: 1652 Mb
Fix left ends
Working set size: 2217 Mb
Pagefile usage: 1652 Mb
done.
performing iterative refinement
0%..1%..2%..3%..4%..5%..6%..7%..8%..9%..
11%..12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
31%..32%..33%..35%..36%..37%..38%..39%..
40%..42%..43%..45%..46%..47%..49%..
50%..51%..52%..54%..55%..56%..57%..58%..59%..
60%..61%..62%..64%..65%..66%..67%..68%..69%..
70%..71%..72%..73%..75%..77%..78%..79%..
80%..82%..83%..85%..87%..88%..
90%..91%..92%..93%..94%..95%..96%..97%..98%..99%..
100%..Working set size: 2224 Mb
Pagefile usage: 1658 Mb
Fix left ends
Working set size: 2224 Mb
Pagefile usage: 1658 Mb
done.
Working set size: 2224 Mb
Pagefile usage: 1658 Mb
Aligning node 1 to 16 via 2!
Working set size: 2036 Mb
Pagefile usage: 1471 Mb
get ancestral matches
Working set size: 2123 Mb
Pagefile usage: 1558 Mb
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 2124 Mb
Pagefile usage: 1558 Mb
construct LCB tracking matches
There are 58026 tracking matches
There are 2215831 / 3539586 components used
Working set size: 2496 Mb
Pagefile usage: 1929 Mb
init tracking match LCB tracking
Working set size: 2532 Mb
Pagefile usage: 1964 Mb
pairwise score tracking matches
Working set size: 2567 Mb
Pagefile usage: 2000 Mb

get pairwise LCBs

there are 643179 pairwise LCBs
Working set size: 2637 Mb
Pagefile usage: 2070 Mb
scaling bp penalty by conservation weight:
0.0881852
0.0893187
0.0836282
0.0838612
0.0767015
0.0821319
0.0807882
0.0754883
0.0970206
0.0958969
0.0943953
0.0913972
0.0973544
0.096647
0.0950708
0.0940651
0.0850173
0.0906945
0.0925139
0.087128
0.0860071
0.0877608
0.0928098
0.0856076
0.0909022
0.0901356
0.0967589
0.0911229
0.0905788
0.0901022
0.0969789
0.0913077
0.0908548
0.0919648
0.084419
0.0892142
0.0836369
0.0858967
0.0798986
0.0824367
0.0829345
0.0869083
0.0784669
0.0839898
0.105201
0.11925 0.11517 0.108144
0.0915505
0.108511
0.103687
0.098376
0.0948901
0.111424
0.104292
0.0986491
0.0774124
0.078916
0.0790345
0.0709197
0.0883791
0.0859643
0.077914
0.0841536
0.0957532
0.09739 0.0953984
0.0883452
0.0848315
0.0874218
0.0817807
0.0790048
0.0857448
0.0960438
0.0814209
0.0890572
0.0859581
0.0957886
0.0829029
0.0900769
scaling bp penalty by bp weight:
0.0857143
0.0214286
0.15
0.0214286
0.0857143
0.0214286
0.0857143
0.0214286
0.0857143
0.0857143
0.15
0.0857143
0.0857143
0.0857143
0.15
0.0857143
0.0857143
0.0214286
0.0857143
0.0214286
0.0857143
0.0857143
0.0857143
0.0214286
0.0857143
0.0857143
0.0857143
0.0214286
0.0857143
0.0857143
0.0857143
0.0214286
0.0857143
0.0857143
0.15
0.0857143
0.0857143
0.0214286
0.15
0.0214286
0.0857143
0.0214286
0.15
0.0214286
0.0857143
0.0214286
0.0857143
0.0857143
0.0857143
0.0214286
0.0857143
0.0214286
0.0857143
0.0857143
0.107143
0.0857143
0.0214286
0.0214286
0.0214286
0.0214286
0.0857143
0.0857143
0.15
0.0214286
0.0857143
0.0214286
0.0857143
0.0857143
0.0214286
0.0214286
0.0214286
0.0857143
0.0857143
0.0214286
0.15
0.0214286
0.0857143
0.0214286
0.15
0.0214286
Greedy BPE
Scoring with scaled breakpoint penalty: 86697.4
1%..done
Working set size: 2232 Mb
Pagefile usage: 1717 Mb
Arrived at 212 intervals
Adding unaligned intervals
addUnalignedIntervals yields 632 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints

descendant 0(1) has 254 intervals

descendant 1(16) has 51 intervals
propagateDescendantBreakpoints yields 515 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 8.82628e+009
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 3017 new matches outside LCBs
0,1 have 3112 new matches outside LCBs
0,2 have 2512 new matches outside LCBs
0,3 have 2718 new matches outside LCBs
1,0 have 2354 new matches outside LCBs
1,1 have 2739 new matches outside LCBs
1,2 have 2348 new matches outside LCBs
1,3 have 2360 new matches outside LCBs
2,0 have 3070 new matches outside LCBs
2,1 have 3255 new matches outside LCBs
2,2 have 2889 new matches outside LCBs
2,3 have 3212 new matches outside LCBs
3,0 have 3073 new matches outside LCBs
3,1 have 3254 new matches outside LCBs
3,2 have 2890 new matches outside LCBs
3,3 have 3208 new matches outside LCBs
4,0 have 2638 new matches outside LCBs
4,1 have 3085 new matches outside LCBs
4,2 have 2830 new matches outside LCBs
4,3 have 2831 new matches outside LCBs
5,0 have 2863 new matches outside LCBs
5,1 have 3077 new matches outside LCBs
5,2 have 3151 new matches outside LCBs
5,3 have 2941 new matches outside LCBs
6,0 have 3108 new matches outside LCBs
6,1 have 3187 new matches outside LCBs
6,2 have 3336 new matches outside LCBs
6,3 have 3223 new matches outside LCBs
7,0 have 3114 new matches outside LCBs
7,1 have 3186 new matches outside LCBs
7,2 have 3357 new matches outside LCBs
7,3 have 3232 new matches outside LCBs
8,0 have 2922 new matches outside LCBs
8,1 have 3172 new matches outside LCBs
8,2 have 2520 new matches outside LCBs
8,3 have 3270 new matches outside LCBs
9,0 have 2786 new matches outside LCBs
9,1 have 2747 new matches outside LCBs
9,2 have 2221 new matches outside LCBs
9,3 have 2944 new matches outside LCBs
10,0 have 2672 new matches outside LCBs
10,1 have 2853 new matches outside LCBs
10,2 have 2260 new matches outside LCBs
10,3 have 3088 new matches outside LCBs
11,0 have 3360 new matches outside LCBs
11,1 have 4719 new matches outside LCBs
11,2 have 4430 new matches outside LCBs
11,3 have 3985 new matches outside LCBs
12,0 have 2511 new matches outside LCBs
12,1 have 3657 new matches outside LCBs
12,2 have 3250 new matches outside LCBs
12,3 have 3136 new matches outside LCBs

13,0 have 2808 new matches

13,1 have 4225 new matches
13,2 have 3757 new matches
13,3 have 3490 new matches
14,0 have 2173 new matches
14,1 have 2262 new matches
14,2 have 1996 new matches
14,3 have 1802 new matches
15,0 have 2980 new matches
15,1 have 2895 new matches
15,2 have 2379 new matches
15,3 have 2710 new matches
16,0 have 2516 new matches
16,1 have 2782 new matches
16,2 have 2503 new matches
16,3 have 2281 new matches
17,0 have 2730 new matches
17,1 have 3112 new matches
17,2 have 2662 new matches
17,3 have 2670 new matches
18,0 have 2864 new matches
18,1 have 3689 new matches
18,2 have 2772 new matches
18,3 have 3137 new matches
19,0 have 2871 new matches
19,1 have 3687 new matches
19,2 have 2766 new matches
19,3 have 3133 new matches
0,0 has an additional 6041
0,1 has an additional 5798
0,2 has an additional 5057
0,3 has an additional 5179
1,0 has an additional 5099
1,1 has an additional 5183
1,2 has an additional 4745
1,3 has an additional 4633
2,0 has an additional 6145
2,1 has an additional 6271
2,2 has an additional 5699
2,3 has an additional 5945
3,0 has an additional 6148
3,1 has an additional 6272
3,2 has an additional 5702
3,3 has an additional 5945
4,0 has an additional 5644
4,1 has an additional 5708
4,2 has an additional 5583
4,3 has an additional 5390
5,0 has an additional 5804
5,1 has an additional 5680
5,2 has an additional 5697
5,3 has an additional 5555
6,0 has an additional 6165
6,1 has an additional 6094
6,2 has an additional 6166
6,3 has an additional 5961
7,0 has an additional 6170
7,1 has an additional 6093
7,2 has an additional 6187
7,3 has an additional 5970

outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches

LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs

8,0 has an additional 5939 matches

8,1 has an additional 6016 matches
8,2 has an additional 5117 matches
8,3 has an additional 6209 matches
9,0 has an additional 5721 matches
9,1 has an additional 5528 matches
9,2 has an additional 5009 matches
9,3 has an additional 5796 matches
10,0 has an additional 5691 matches
10,1 has an additional 5611 matches
10,2 has an additional 5000 matches
10,3 has an additional 6007 matches
11,0 has an additional 6784 matches
11,1 has an additional 7673 matches
11,2 has an additional 7474 matches
11,3 has an additional 6893 matches
12,0 has an additional 5584 matches
12,1 has an additional 6426 matches
12,2 has an additional 5914 matches
12,3 has an additional 5846 matches
13,0 has an additional 5719 matches
13,1 has an additional 6963 matches
13,2 has an additional 6638 matches
13,3 has an additional 6040 matches
14,0 has an additional 4739 matches
14,1 has an additional 4620 matches
14,2 has an additional 4338 matches
14,3 has an additional 3956 matches
15,0 has an additional 5615 matches
15,1 has an additional 5684 matches
15,2 has an additional 5018 matches
15,3 has an additional 5176 matches
16,0 has an additional 5471 matches
16,1 has an additional 5517 matches
16,2 has an additional 5389 matches
16,3 has an additional 4716 matches
17,0 has an additional 5862 matches
17,1 has an additional 5949 matches
17,2 has an additional 5340 matches
17,3 has an additional 5354 matches
18,0 has an additional 5994 matches
18,1 has an additional 6598 matches
18,2 has an additional 5489 matches
18,3 has an additional 6006 matches
19,0 has an additional 6002 matches
19,1 has an additional 6593 matches
19,2 has an additional 5484 matches
19,3 has an additional 5999 matches
Restoring backed up alignment tree...
6,11 has 6041 pairwise matches
6,1 has 5798 pairwise matches
6,5 has 5057 pairwise matches
6,10 has 5179 pairwise matches
4,11 has 5099 pairwise matches
4,1 has 5183 pairwise matches
4,5 has 4745 pairwise matches
4,10 has 4633 pairwise matches
7,11 has 6145 pairwise matches
7,1 has 6271 pairwise matches
7,5 has 5699 pairwise matches

7,10 has 5945 pairwise matches

8,11 has 6148 pairwise matches
8,1 has 6272 pairwise matches
8,5 has 5702 pairwise matches
8,10 has 5945 pairwise matches
17,11 has 5644 pairwise matches
17,1 has 5708 pairwise matches
17,5 has 5583 pairwise matches
17,10 has 5390 pairwise matches
0,11 has 5804 pairwise matches
0,1 has 5680 pairwise matches
0,5 has 5697 pairwise matches
0,10 has 5555 pairwise matches
15,11 has 6165 pairwise matches
15,1 has 6094 pairwise matches
15,5 has 6166 pairwise matches
15,10 has 5961 pairwise matches
16,11 has 6170 pairwise matches
16,1 has 6093 pairwise matches
16,5 has 6187 pairwise matches
16,10 has 5970 pairwise matches
2,11 has 5939 pairwise matches
2,1 has 6016 pairwise matches
2,5 has 5117 pairwise matches
2,10 has 6209 pairwise matches
13,11 has 5721 pairwise matches
13,1 has 5528 pairwise matches
13,5 has 5009 pairwise matches
13,10 has 5796 pairwise matches
14,11 has 5691 pairwise matches
14,1 has 5611 pairwise matches
14,5 has 5000 pairwise matches
14,10 has 6007 pairwise matches
22,11 has 6784 pairwise matches
22,1 has 7673 pairwise matches
22,5 has 7474 pairwise matches
22,10 has 6893 pairwise matches
20,11 has 5584 pairwise matches
20,1 has 6426 pairwise matches
20,5 has 5914 pairwise matches
20,10 has 5846 pairwise matches
25,11 has 5719 pairwise matches
25,1 has 6963 pairwise matches
25,5 has 6638 pairwise matches
25,10 has 6040 pairwise matches
28,11 has 4739 pairwise matches
28,1 has 4620 pairwise matches
28,5 has 4338 pairwise matches
28,10 has 3956 pairwise matches
18,11 has 5615 pairwise matches
18,1 has 5684 pairwise matches
18,5 has 5018 pairwise matches
18,10 has 5176 pairwise matches
26,11 has 5471 pairwise matches
26,1 has 5517 pairwise matches
26,5 has 5389 pairwise matches
26,10 has 4716 pairwise matches
3,11 has 5862 pairwise matches
3,1 has 5949 pairwise matches
3,5 has 5340 pairwise matches

3,10 has 5354 pairwise matches

23,11 has 5994 pairwise matches
23,1 has 6598 pairwise matches
23,5 has 5489 pairwise matches
23,10 has 6006 pairwise matches
24,11 has 6002 pairwise matches
24,1 has 6593 pairwise matches
24,5 has 5484 pairwise matches
24,10 has 5999 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 2265 Mb
Pagefile usage: 1691 Mb
construct LCB tracking matches
There are 39665 tracking matches
There are 1656667 / 2419565 components used
Working set size: 2463 Mb
Pagefile usage: 1886 Mb
init tracking match LCB tracking
Working set size: 2488 Mb
Pagefile usage: 1911 Mb
pairwise score tracking matches
Working set size: 2512 Mb
Pagefile usage: 1935 Mb
get pairwise LCBs
there are 57767 pairwise LCBs
Working set size: 2533 Mb
Pagefile usage: 1947 Mb
scaling bp penalty by conservation weight:
0.0881852
0.0893187
0.0836282
0.0838612
0.0767015
0.0821319
0.0807882
0.0754883
0.0970206
0.0958969
0.0943953
0.0913972
0.0973544
0.096647
0.0950708
0.0940651
0.0850173
0.0906945
0.0925139
0.087128
0.0860071
0.0877608
0.0928098
0.0856076
0.0909022
0.0901356
0.0967589
0.0911229
0.0905788
0.0901022
0.0969789
0.0913077
0.0908548
0.0919648
0.084419
0.0892142
0.0836369
0.0858967
0.0798986
0.0824367
0.0829345
0.0869083
0.0784669
0.0839898
0.105201
0.11925 0.11517 0.108144
0.0915505
0.108511
0.103687
0.098376
0.0948901
0.111424
0.104292
0.0986491
0.0774124
0.078916
0.0790345
0.0709197
0.0883791
0.0859643
0.077914
0.0841536
0.0957532
0.09739 0.0953984
0.0883452
0.0848315
0.0874218
0.0817807
0.0790048
0.0857448
0.0960438
0.0814209
0.0890572
0.0859581
0.0957886
0.0829029
0.0900769
scaling bp penalty by bp weight:
0.0857143
0.0214286
0.15
0.0214286
0.0857143
0.0214286
0.0857143
0.0214286
0.0857143
0.0857143
0.15
0.0857143
0.0857143
0.0857143
0.15
0.0857143
0.0857143
0.0214286
0.0857143
0.0214286
0.0857143
0.0857143
0.0857143
0.0214286
0.0857143
0.0857143
0.0857143
0.0214286
0.0857143
0.0857143
0.0857143
0.0214286
0.0857143
0.0857143
0.15
0.0857143

0.0857143
0.0857143
0.0857143
0.0857143
0.0857143
0.0214286
0.0857143
0.0857143
0.0214286
0.0857143
0.0857143

0.0214286
0.0214286
0.0214286
0.0214286
0.0857143
0.0214286
0.0857143
0.0214286
0.0214286
0.0214286
0.0214286

0.15
0.0214286
0.15
0.0214286
0.0857143
0.0857143
0.0857143
0.0214286
0.107143
0.0857143
0.0214286
0.0214286
0.15
0.0214286
0.0857143
0.0857143
0.0214286
0.0857143
0.15
0.0214286
0.15
0.0214286

Greedy BPE
Scoring with scaled breakpoint penalty: 86697.4
1%..2%..3%..4%..5%..6%..7%..done
Working set size: 2318 Mb
Pagefile usage: 1793 Mb
Arrived at 190 intervals
Adding unaligned intervals
addUnalignedIntervals yields 504 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(1) has 254 intervals
descendant 1(16) has 51 intervals
propagateDescendantBreakpoints yields 489 intervals
Creating ancestral ordering
Previous anchoring score: 8.82628e+009, new anchor score: 1.16895e+010
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 2117 new matches outside LCBs
0,1 have 1976 new matches outside LCBs
0,2 have 1571 new matches outside LCBs
0,3 have 1793 new matches outside LCBs
1,0 have 1594 new matches outside LCBs
1,1 have 1631 new matches outside LCBs
1,2 have 1419 new matches outside LCBs
1,3 have 1436 new matches outside LCBs
2,0 have 2221 new matches outside LCBs
2,1 have 2081 new matches outside LCBs
2,2 have 1954 new matches outside LCBs
2,3 have 2219 new matches outside LCBs
3,0 have 2220 new matches outside LCBs
3,1 have 2082 new matches outside LCBs
3,2 have 1956 new matches outside LCBs
3,3 have 2213 new matches outside LCBs
4,0 have 1814 new matches outside LCBs
4,1 have 1917 new matches outside LCBs
4,2 have 1874 new matches outside LCBs
4,3 have 1891 new matches outside LCBs
5,0 have 2017 new matches outside LCBs
5,1 have 1928 new matches outside LCBs
5,2 have 2153 new matches outside LCBs
5,3 have 2005 new matches outside LCBs
6,0 have 2223 new matches outside LCBs
6,1 have 1989 new matches outside LCBs
6,2 have 2332 new matches outside LCBs
6,3 have 2235 new matches outside LCBs
7,0 have 2221 new matches outside LCBs

7,1 have 1991 new matches outside LCBs

7,2 have 2332 new matches outside LCBs
7,3 have 2234 new matches outside LCBs
8,0 have 2249 new matches outside LCBs
8,1 have 2232 new matches outside LCBs
8,2 have 1888 new matches outside LCBs
8,3 have 2406 new matches outside LCBs
9,0 have 2081 new matches outside LCBs
9,1 have 2017 new matches outside LCBs
9,2 have 1615 new matches outside LCBs
9,3 have 2167 new matches outside LCBs
10,0 have 1984 new matches outside LCBs
10,1 have 2076 new matches outside LCBs
10,2 have 1652 new matches outside LCBs
10,3 have 2347 new matches outside LCBs
11,0 have 2541 new matches outside LCBs
11,1 have 3400 new matches outside LCBs
11,2 have 3565 new matches outside LCBs
11,3 have 3272 new matches outside LCBs
12,0 have 1839 new matches outside LCBs
12,1 have 2567 new matches outside LCBs
12,2 have 2469 new matches outside LCBs
12,3 have 2513 new matches outside LCBs
13,0 have 2055 new matches outside LCBs
13,1 have 3181 new matches outside LCBs
13,2 have 2991 new matches outside LCBs
13,3 have 2889 new matches outside LCBs
14,0 have 1457 new matches outside LCBs
14,1 have 1176 new matches outside LCBs
14,2 have 1206 new matches outside LCBs
14,3 have 1048 new matches outside LCBs
15,0 have 2222 new matches outside LCBs
15,1 have 1859 new matches outside LCBs
15,2 have 1606 new matches outside LCBs
15,3 have 1964 new matches outside LCBs
16,0 have 1799 new matches outside LCBs
16,1 have 1737 new matches outside LCBs
16,2 have 1655 new matches outside LCBs
16,3 have 1533 new matches outside LCBs
17,0 have 1987 new matches outside LCBs
17,1 have 1997 new matches outside LCBs
17,2 have 1876 new matches outside LCBs
17,3 have 1906 new matches outside LCBs
18,0 have 2071 new matches outside LCBs
18,1 have 2544 new matches outside LCBs
18,2 have 2025 new matches outside LCBs
18,3 have 2348 new matches outside LCBs
19,0 have 2070 new matches outside LCBs
19,1 have 2541 new matches outside LCBs
19,2 have 2025 new matches outside LCBs
19,3 have 2347 new matches outside LCBs
0,0 has an additional 2827 matches
0,1 has an additional 2996 matches
0,2 has an additional 2495 matches
0,3 has an additional 2433 matches
1,0 has an additional 2247 matches
1,1 has an additional 2504 matches
1,2 has an additional 2169 matches
1,3 has an additional 2086 matches
2,0 has an additional 2826 matches

2,1 has an additional 3287 matches

2,2 has an additional 3119 matches
2,3 has an additional 3050 matches
3,0 has an additional 2826 matches
3,1 has an additional 3289 matches
3,2 has an additional 3121 matches
3,3 has an additional 3044 matches
4,0 has an additional 2537 matches
4,1 has an additional 2857 matches
4,2 has an additional 2744 matches
4,3 has an additional 2709 matches
5,0 has an additional 2794 matches
5,1 has an additional 2937 matches
5,2 has an additional 3094 matches
5,3 has an additional 2871 matches
6,0 has an additional 3093 matches
6,1 has an additional 3271 matches
6,2 has an additional 3585 matches
6,3 has an additional 3104 matches
7,0 has an additional 3109 matches
7,1 has an additional 3275 matches
7,2 has an additional 3606 matches
7,3 has an additional 3122 matches
8,0 has an additional 3064 matches
8,1 has an additional 3294 matches
8,2 has an additional 3117 matches
8,3 has an additional 3283 matches
9,0 has an additional 2814 matches
9,1 has an additional 2966 matches
9,2 has an additional 2780 matches
9,3 has an additional 2969 matches
10,0 has an additional 2801 matches
10,1 has an additional 3099 matches
10,2 has an additional 2756 matches
10,3 has an additional 3129 matches
11,0 has an additional 3656 matches
11,1 has an additional 4408 matches
11,2 has an additional 4909 matches
11,3 has an additional 4427 matches
12,0 has an additional 2824 matches
12,1 has an additional 3631 matches
12,2 has an additional 3647 matches
12,3 has an additional 3378 matches
13,0 has an additional 2932 matches
13,1 has an additional 4106 matches
13,2 has an additional 4020 matches
13,3 has an additional 3618 matches
14,0 has an additional 2137 matches
14,1 has an additional 2042 matches
14,2 has an additional 2049 matches
14,3 has an additional 1664 matches
15,0 has an additional 2884 matches
15,1 has an additional 2838 matches
15,2 has an additional 2723 matches
15,3 has an additional 2650 matches
16,0 has an additional 2611 matches
16,1 has an additional 2734 matches
16,2 has an additional 3198 matches
16,3 has an additional 2157 matches
17,0 has an additional 2764 matches

17,1 has an additional 3006 matches

17,2 has an additional 2825 matches
17,3 has an additional 2652 matches
18,0 has an additional 3037 matches
18,1 has an additional 3608 matches
18,2 has an additional 3107 matches
18,3 has an additional 3167 matches
19,0 has an additional 3037 matches
19,1 has an additional 3604 matches
19,2 has an additional 3109 matches
19,3 has an additional 3166 matches
Restoring backed up alignment tree...
6,11 has 2827 pairwise matches
6,1 has 2996 pairwise matches
6,5 has 2495 pairwise matches
6,10 has 2433 pairwise matches
4,11 has 2247 pairwise matches
4,1 has 2504 pairwise matches
4,5 has 2169 pairwise matches
4,10 has 2086 pairwise matches
7,11 has 2826 pairwise matches
7,1 has 3287 pairwise matches
7,5 has 3119 pairwise matches
7,10 has 3050 pairwise matches
8,11 has 2826 pairwise matches
8,1 has 3289 pairwise matches
8,5 has 3121 pairwise matches
8,10 has 3044 pairwise matches
17,11 has 2537 pairwise matches
17,1 has 2857 pairwise matches
17,5 has 2744 pairwise matches
17,10 has 2709 pairwise matches
0,11 has 2794 pairwise matches
0,1 has 2937 pairwise matches
0,5 has 3094 pairwise matches
0,10 has 2871 pairwise matches
15,11 has 3093 pairwise matches
15,1 has 3271 pairwise matches
15,5 has 3585 pairwise matches
15,10 has 3104 pairwise matches
16,11 has 3109 pairwise matches
16,1 has 3275 pairwise matches
16,5 has 3606 pairwise matches
16,10 has 3122 pairwise matches
2,11 has 3064 pairwise matches
2,1 has 3294 pairwise matches
2,5 has 3117 pairwise matches
2,10 has 3283 pairwise matches
13,11 has 2814 pairwise matches
13,1 has 2966 pairwise matches
13,5 has 2780 pairwise matches
13,10 has 2969 pairwise matches
14,11 has 2801 pairwise matches
14,1 has 3099 pairwise matches
14,5 has 2756 pairwise matches
14,10 has 3129 pairwise matches
22,11 has 3656 pairwise matches
22,1 has 4408 pairwise matches
22,5 has 4909 pairwise matches
22,10 has 4427 pairwise matches

20,11 has 2824 pairwise matches

20,1 has 3631 pairwise matches
20,5 has 3647 pairwise matches
20,10 has 3378 pairwise matches
25,11 has 2932 pairwise matches
25,1 has 4106 pairwise matches
25,5 has 4020 pairwise matches
25,10 has 3618 pairwise matches
28,11 has 2137 pairwise matches
28,1 has 2042 pairwise matches
28,5 has 2049 pairwise matches
28,10 has 1664 pairwise matches
18,11 has 2884 pairwise matches
18,1 has 2838 pairwise matches
18,5 has 2723 pairwise matches
18,10 has 2650 pairwise matches
26,11 has 2611 pairwise matches
26,1 has 2734 pairwise matches
26,5 has 3198 pairwise matches
26,10 has 2157 pairwise matches
3,11 has 2764 pairwise matches
3,1 has 3006 pairwise matches
3,5 has 2825 pairwise matches
3,10 has 2652 pairwise matches
23,11 has 3037 pairwise matches
23,1 has 3608 pairwise matches
23,5 has 3107 pairwise matches
23,10 has 3167 pairwise matches
24,11 has 3037 pairwise matches
24,1 has 3604 pairwise matches
24,5 has 3109 pairwise matches
24,10 has 3166 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 2374 Mb
Pagefile usage: 1839 Mb
construct LCB tracking matches
There are 39684 tracking matches
There are 1649296 / 2420724 components used
Working set size: 2479 Mb
Pagefile usage: 1920 Mb
init tracking match LCB tracking
Working set size: 2503 Mb
Pagefile usage: 1944 Mb
pairwise score tracking matches
Working set size: 2528 Mb
Pagefile usage: 1968 Mb
get pairwise LCBs
there are 45138 pairwise LCBs
Working set size: 2536 Mb
Pagefile usage: 1973 Mb
scaling bp penalty by conservation weight:
0.0881852
0.0893187
0.0836282
0.0838612
0.0767015
0.0821319
0.0807882
0.0754883
0.0970206
0.0958969
0.0943953
0.0913972
0.0973544
0.096647
0.0950708
0.0940651
0.0850173
0.0906945
0.0925139
0.087128
0.0860071
0.0877608
0.0928098
0.0856076
0.0909022
0.0901356
0.0967589
0.0911229
0.0905788
0.0901022
0.0969789
0.0913077
0.0908548
0.0919648
0.084419
0.0892142

0.0836369
0.0829345
0.105201
0.0915505
0.0948901
0.0774124
0.0883791
0.0957532
0.0848315
0.0857448
0.0859581

0.0858967
0.0798986
0.0824367
0.0869083
0.0784669
0.0839898
0.11925 0.11517 0.108144
0.108511
0.103687
0.098376
0.111424
0.104292
0.0986491
0.078916
0.0790345
0.0709197
0.0859643
0.077914
0.0841536
0.09739 0.0953984
0.0883452
0.0874218
0.0817807
0.0790048
0.0960438
0.0814209
0.0890572
0.0957886
0.0829029
0.0900769

scaling bp penalty by bp weight:

0.0857143
0.0214286
0.15
0.0214286
0.0857143
0.0214286
0.0857143
0.0214286
0.0857143
0.0857143
0.15
0.0857143
0.0857143
0.0857143
0.15
0.0857143
0.0857143
0.0214286
0.0857143
0.0214286
0.0857143
0.0857143
0.0857143
0.0214286
0.0857143
0.0857143
0.0857143
0.0214286
0.0857143
0.0857143
0.0857143
0.0214286
0.0857143
0.0857143
0.15
0.0857143
0.0857143
0.0214286
0.15
0.0214286
0.0857143
0.0214286
0.15
0.0214286
0.0857143
0.0214286
0.0857143
0.0857143
0.0857143
0.0214286
0.0857143
0.0214286
0.0857143
0.0857143
0.107143
0.0857143
0.0214286
0.0214286
0.0214286
0.0214286
0.0857143
0.0857143
0.15
0.0214286
0.0857143
0.0214286
0.0857143
0.0857143
0.0214286
0.0214286
0.0214286
0.0857143
0.0857143
0.0214286
0.15
0.0214286
0.0857143
0.0214286
0.15
0.0214286
Greedy BPE
Scoring with scaled breakpoint penalty: 86697.4
1%..2%..3%..4%..5%..6%..7%..8%..9%..done
Working set size: 2277 Mb
Pagefile usage: 1702 Mb
Arrived at 182 intervals
Adding unaligned intervals
addUnalignedIntervals yields 481 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(1) has 254 intervals
descendant 1(16) has 51 intervals
propagateDescendantBreakpoints yields 476 intervals
Creating ancestral ordering
Previous anchoring score: 1.16895e+010, new anchor score: 1.16967e+010
Working set size: 2279 Mb
Pagefile usage: 1712 Mb
propagating ancestral breakpoints
Working set size: 2282 Mb
Pagefile usage: 1717 Mb
performing a gapped alignment
0%..9%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..

20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..47%..48%..49%..
50%..51%..52%..53%..54%..55%..56%..57%..58%..59%..
60%..61%..62%..63%..64%..65%..66%..67%..68%..69%..
70%..71%..72%..73%..74%..75%..76%..77%..78%..79%..
80%..81%..82%..83%..84%..85%..86%..87%..88%..89%..
90%..91%..92%..93%..94%..95%..96%..97%..98%..99%..Working set size: 2453 Mb
Pagefile usage: 1880 Mb
Fix left ends
Working set size: 2453 Mb
Pagefile usage: 1880 Mb
done.
Working set size: 2453 Mb
Pagefile usage: 1880 Mb
Aligning node 2 to 4 via 3!
Working set size: 2157 Mb
Pagefile usage: 1601 Mb
get ancestral matches
Working set size: 2232 Mb
Pagefile usage: 1676 Mb
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 2232 Mb
Pagefile usage: 1678 Mb
construct LCB tracking matches
There are 88578 tracking matches
There are 4120997 / 5403258 components used
Working set size: 2809 Mb
Pagefile usage: 2230 Mb
init tracking match LCB tracking
Working set size: 2891 Mb
Pagefile usage: 2311 Mb
pairwise score tracking matches
Working set size: 2972 Mb
Pagefile usage: 2392 Mb
get pairwise LCBs
there are 2200005 pairwise LCBs
Working set size: 3203 Mb
Pagefile usage: 2623 Mb
scaling bp penalty by conservation weight:
0.104308
0.082926
0.0876522
0.0962354
0.0802696
0.11446 0.0946115
0.106509
0.107388
0.094341
0.112542
0.0922735
0.0928351
0.0989504
0.0849337
0.105547
0.0835203
0.0915094
0.100781
0.0862605
0.110383
0.0898347
0.0827252
0.0978867
0.0866425
0.105835
0.0725374
0.0751431
0.0868568
0.0819164
0.123097
0.09628 0.0846801
0.091687
0.0902899
0.123985
0.0973955
0.0850126
0.0919313
0.0905321
0.115725
0.0848423
0.0834596
0.0851524
0.0878706
0.116667
0.0847359
0.0838756
0.0870396
0.0897507
0.12062 0.0922209
0.089806
0.0914911
0.0940886
0.120639
0.0922576
0.0897393
0.0914776
0.0940719
0.117177
0.0918824
0.0829517
0.0922173
0.0814833
0.111262
0.0835397
0.0775097
0.0924478
0.0820491
0.109597
0.0855969
0.074238
0.0905392
0.0778284
0.128618
0.109212
0.109025
0.10664 0.106846
0.118799
0.0962708
0.0946893
0.0937439
0.093455
0.12035 0.0960072
0.0953667
0.0917209
0.0953641
0.100428
0.0778868
0.080101
0.0979779
0.0834132

0.112299
0.122783
0.104971
0.110196
0.111165

0.0898108
0.0923052
0.0876447
0.0866611
0.0880644

0.0806593
0.0951004
0.0781697
0.0728839
0.0734292

scaling bp penalty by bp weight:

0.0214286
0.0857143
0.0857143
0.0214286
0.0214286
0.0214286
0.0214286
0.0857143
0.15
0.15
0.0214286
0.0214286
0.0214286
0.0857143
0.0214286
0.15
0.15
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0857143
0.0214286
0.0214286
0.0857143
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0857143
0.0214286
0.0214286
0.0214286
0.0857143
0.0214286
0.0857143
0.0857143
0.0214286
0.0857143
0.0857143
0.0214286
0.128571
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.15
0.15
0.0214286
0.0214286
0.0857143
0.0214286
0.0214286
0.0857143

0.0980504
0.110921
0.095474
0.0884578
0.0889674

0.0853317
0.102196
0.0829028
0.0817822
0.0822248

0.0857143
0.0214286
0.107143
0.0214286
0.107143
0.0214286
0.0857143
0.0857143
0.0214286
0.0214286
0.0214286
0.0214286
0.0857143
0.0857143
0.0214286
0.128571
0.128571
0.171429
0.0214286
0.0214286
0.0214286
0.107143
0.0857143
0.0857143

0.0428571
0.0428571
0.0428571
0.0428571
0.107143
0.107143
0.107143
0.0428571
0.0428571
0.0428571
0.0428571
0.107143
0.0428571
0.0428571
0.0428571
0.0857143
0.0428571
0.0428571
0.0428571
0.0428571
0.0428571

Greedy BPE
Scoring with scaled breakpoint penalty: 92477.2
done
Working set size: 2341 Mb
Pagefile usage: 1807 Mb
Arrived at 306 intervals
Adding unaligned intervals
addUnalignedIntervals yields 909 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(2) has 489 intervals
descendant 1(4) has 38 intervals
propagateDescendantBreakpoints yields 830 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 3.67048e+009
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 2613 new matches outside LCBs
0,1 have 2515 new matches outside LCBs
0,2 have 2482 new matches outside LCBs
0,3 have 2778 new matches outside LCBs
0,4 have 2635 new matches outside LCBs
1,0 have 2910 new matches outside LCBs
1,1 have 2718 new matches outside LCBs
1,2 have 2595 new matches outside LCBs

1,3 have 3098 new matches outside LCBs

1,4 have 2922 new matches outside LCBs
2,0 have 2654 new matches outside LCBs
2,1 have 2532 new matches outside LCBs
2,2 have 2498 new matches outside LCBs
2,3 have 2823 new matches outside LCBs
2,4 have 2739 new matches outside LCBs
3,0 have 2709 new matches outside LCBs
3,1 have 2480 new matches outside LCBs
3,2 have 2378 new matches outside LCBs
3,3 have 2870 new matches outside LCBs
3,4 have 2745 new matches outside LCBs
4,0 have 3081 new matches outside LCBs
4,1 have 2873 new matches outside LCBs
4,2 have 2386 new matches outside LCBs
4,3 have 3275 new matches outside LCBs
4,4 have 2970 new matches outside LCBs
5,0 have 2880 new matches outside LCBs
5,1 have 2609 new matches outside LCBs
5,2 have 2064 new matches outside LCBs
5,3 have 2788 new matches outside LCBs
5,4 have 2777 new matches outside LCBs
6,0 have 3123 new matches outside LCBs
6,1 have 2810 new matches outside LCBs
6,2 have 2190 new matches outside LCBs
6,3 have 2986 new matches outside LCBs
6,4 have 2894 new matches outside LCBs
7,0 have 3116 new matches outside LCBs
7,1 have 2808 new matches outside LCBs
7,2 have 2189 new matches outside LCBs
7,3 have 2988 new matches outside LCBs
7,4 have 2891 new matches outside LCBs
8,0 have 3009 new matches outside LCBs
8,1 have 2684 new matches outside LCBs
8,2 have 2189 new matches outside LCBs
8,3 have 2886 new matches outside LCBs
8,4 have 2906 new matches outside LCBs
9,0 have 3063 new matches outside LCBs
9,1 have 2721 new matches outside LCBs
9,2 have 2247 new matches outside LCBs
9,3 have 2927 new matches outside LCBs
9,4 have 2949 new matches outside LCBs
10,0 have 3243 new matches outside LCBs
10,1 have 2804 new matches outside LCBs
10,2 have 2326 new matches outside LCBs
10,3 have 3041 new matches outside LCBs
10,4 have 3053 new matches outside LCBs
11,0 have 3242 new matches outside LCBs
11,1 have 2802 new matches outside LCBs
11,2 have 2324 new matches outside LCBs
11,3 have 3041 new matches outside LCBs
11,4 have 3054 new matches outside LCBs
12,0 have 3030 new matches outside LCBs
12,1 have 2852 new matches outside LCBs
12,2 have 2257 new matches outside LCBs
12,3 have 3176 new matches outside LCBs
12,4 have 3010 new matches outside LCBs
13,0 have 3017 new matches outside LCBs
13,1 have 2790 new matches outside LCBs
13,2 have 2287 new matches outside LCBs

13,3 have 3071 new matches

13,4 have 2979 new matches
14,0 have 3038 new matches
14,1 have 2828 new matches
14,2 have 2235 new matches
14,3 have 3062 new matches
14,4 have 2895 new matches
15,0 have 3312 new matches
15,1 have 2880 new matches
15,2 have 2829 new matches
15,3 have 3152 new matches
15,4 have 3073 new matches
16,0 have 2949 new matches
16,1 have 2635 new matches
16,2 have 2397 new matches
16,3 have 2683 new matches
16,4 have 2712 new matches
17,0 have 3055 new matches
17,1 have 2682 new matches
17,2 have 2416 new matches
17,3 have 2723 new matches
17,4 have 2754 new matches
18,0 have 2732 new matches
18,1 have 2590 new matches
18,2 have 2051 new matches
18,3 have 2897 new matches
18,4 have 2803 new matches
19,0 have 2940 new matches
19,1 have 2743 new matches
19,2 have 2207 new matches
19,3 have 3105 new matches
19,4 have 2945 new matches
20,0 have 2957 new matches
20,1 have 2612 new matches
20,2 have 2164 new matches
20,3 have 3005 new matches
20,4 have 2968 new matches
21,0 have 2916 new matches
21,1 have 2866 new matches
21,2 have 2264 new matches
21,3 have 3200 new matches
21,4 have 3102 new matches
22,0 have 3067 new matches
22,1 have 2828 new matches
22,2 have 2187 new matches
22,3 have 3135 new matches
22,4 have 3052 new matches
23,0 have 3064 new matches
23,1 have 2821 new matches
23,2 have 2190 new matches
23,3 have 3144 new matches
23,4 have 3057 new matches
0,0 has an additional 7256
0,1 has an additional 6769
0,2 has an additional 7229
0,3 has an additional 7644
0,4 has an additional 7156
1,0 has an additional 7624
1,1 has an additional 7193
1,2 has an additional 7471

outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
matches
matches
matches
matches
matches
matches
matches
matches

LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs

1,3 has an additional 8020 matches

1,4 has an additional 7785 matches
2,0 has an additional 7896 matches
2,1 has an additional 7356 matches
2,2 has an additional 7895 matches
2,3 has an additional 8166 matches
2,4 has an additional 7849 matches
3,0 has an additional 7275 matches
3,1 has an additional 6571 matches
3,2 has an additional 7016 matches
3,3 has an additional 7727 matches
3,4 has an additional 7234 matches
4,0 has an additional 7835 matches
4,1 has an additional 7332 matches
4,2 has an additional 6901 matches
4,3 has an additional 8338 matches
4,4 has an additional 7774 matches
5,0 has an additional 7497 matches
5,1 has an additional 6925 matches
5,2 has an additional 6452 matches
5,3 has an additional 7666 matches
5,4 has an additional 7388 matches
6,0 has an additional 8178 matches
6,1 has an additional 7511 matches
6,2 has an additional 7086 matches
6,3 has an additional 8432 matches
6,4 has an additional 7967 matches
7,0 has an additional 8175 matches
7,1 has an additional 7512 matches
7,2 has an additional 7087 matches
7,3 has an additional 8440 matches
7,4 has an additional 7968 matches
8,0 has an additional 7878 matches
8,1 has an additional 7127 matches
8,2 has an additional 6707 matches
8,3 has an additional 7910 matches
8,4 has an additional 7640 matches
9,0 has an additional 7998 matches
9,1 has an additional 7238 matches
9,2 has an additional 6827 matches
9,3 has an additional 8090 matches
9,4 has an additional 7800 matches
10,0 has an additional 8333 matches
10,1 has an additional 7576 matches
10,2 has an additional 7209 matches
10,3 has an additional 8502 matches
10,4 has an additional 8113 matches
11,0 has an additional 8336 matches
11,1 has an additional 7573 matches
11,2 has an additional 7208 matches
11,3 has an additional 8503 matches
11,4 has an additional 8121 matches
12,0 has an additional 7977 matches
12,1 has an additional 7280 matches
12,2 has an additional 6611 matches
12,3 has an additional 8142 matches
12,4 has an additional 7634 matches
13,0 has an additional 8042 matches
13,1 has an additional 7363 matches
13,2 has an additional 6802 matches

13,3 has an additional 8390 matches

13,4 has an additional 7962 matches
14,0 has an additional 8072 matches
14,1 has an additional 7439 matches
14,2 has an additional 6636 matches
14,3 has an additional 8271 matches
14,4 has an additional 7845 matches
15,0 has an additional 8451 matches
15,1 has an additional 7354 matches
15,2 has an additional 8030 matches
15,3 has an additional 8404 matches
15,4 has an additional 8025 matches
16,0 has an additional 8444 matches
16,1 has an additional 7785 matches
16,2 has an additional 7952 matches
16,3 has an additional 8263 matches
16,4 has an additional 7872 matches
17,0 has an additional 8153 matches
17,1 has an additional 7322 matches
17,2 has an additional 7387 matches
17,3 has an additional 7732 matches
17,4 has an additional 7370 matches
18,0 has an additional 7321 matches
18,1 has an additional 6870 matches
18,2 has an additional 6211 matches
18,3 has an additional 7696 matches
18,4 has an additional 7332 matches
19,0 has an additional 7828 matches
19,1 has an additional 7544 matches
19,2 has an additional 7198 matches
19,3 has an additional 8711 matches
19,4 has an additional 8079 matches
20,0 has an additional 8536 matches
20,1 has an additional 7665 matches
20,2 has an additional 7679 matches
20,3 has an additional 9049 matches
20,4 has an additional 8804 matches
21,0 has an additional 8082 matches
21,1 has an additional 7603 matches
21,2 has an additional 7171 matches
21,3 has an additional 8819 matches
21,4 has an additional 8602 matches
22,0 has an additional 8224 matches
22,1 has an additional 7589 matches
22,2 has an additional 7279 matches
22,3 has an additional 8931 matches
22,4 has an additional 8750 matches
23,0 has an additional 8220 matches
23,1 has an additional 7583 matches
23,2 has an additional 7284 matches
23,3 has an additional 8938 matches
23,4 has an additional 8753 matches
Restoring backed up alignment tree...
11,19 has 7256 pairwise matches
11,30 has 6769 pairwise matches
11,29 has 7229 pairwise matches
11,12 has 7644 pairwise matches
11,21 has 7156 pairwise matches
1,19 has 7624 pairwise matches
1,30 has 7193 pairwise matches

1,29 has 7471 pairwise matches

1,12 has 8020 pairwise matches
1,21 has 7785 pairwise matches
5,19 has 7896 pairwise matches
5,30 has 7356 pairwise matches
5,29 has 7895 pairwise matches
5,12 has 8166 pairwise matches
5,21 has 7849 pairwise matches
10,19 has 7275 pairwise matches
10,30 has 6571 pairwise matches
10,29 has 7016 pairwise matches
10,12 has 7727 pairwise matches
10,21 has 7234 pairwise matches
6,19 has 7835 pairwise matches
6,30 has 7332 pairwise matches
6,29 has 6901 pairwise matches
6,12 has 8338 pairwise matches
6,21 has 7774 pairwise matches
4,19 has 7497 pairwise matches
4,30 has 6925 pairwise matches
4,29 has 6452 pairwise matches
4,12 has 7666 pairwise matches
4,21 has 7388 pairwise matches
7,19 has 8178 pairwise matches
7,30 has 7511 pairwise matches
7,29 has 7086 pairwise matches
7,12 has 8432 pairwise matches
7,21 has 7967 pairwise matches
8,19 has 8175 pairwise matches
8,30 has 7512 pairwise matches
8,29 has 7087 pairwise matches
8,12 has 8440 pairwise matches
8,21 has 7968 pairwise matches
17,19 has 7878 pairwise matches
17,30 has 7127 pairwise matches
17,29 has 6707 pairwise matches
17,12 has 7910 pairwise matches
17,21 has 7640 pairwise matches
0,19 has 7998 pairwise matches
0,30 has 7238 pairwise matches
0,29 has 6827 pairwise matches
0,12 has 8090 pairwise matches
0,21 has 7800 pairwise matches
15,19 has 8333 pairwise matches
15,30 has 7576 pairwise matches
15,29 has 7209 pairwise matches
15,12 has 8502 pairwise matches
15,21 has 8113 pairwise matches
16,19 has 8336 pairwise matches
16,30 has 7573 pairwise matches
16,29 has 7208 pairwise matches
16,12 has 8503 pairwise matches
16,21 has 8121 pairwise matches
2,19 has 7977 pairwise matches
2,30 has 7280 pairwise matches
2,29 has 6611 pairwise matches
2,12 has 8142 pairwise matches
2,21 has 7634 pairwise matches
13,19 has 8042 pairwise matches
13,30 has 7363 pairwise matches

13,29 has 6802 pairwise matches

13,12 has 8390 pairwise matches
13,21 has 7962 pairwise matches
14,19 has 8072 pairwise matches
14,30 has 7439 pairwise matches
14,29 has 6636 pairwise matches
14,12 has 8271 pairwise matches
14,21 has 7845 pairwise matches
22,19 has 8451 pairwise matches
22,30 has 7354 pairwise matches
22,29 has 8030 pairwise matches
22,12 has 8404 pairwise matches
22,21 has 8025 pairwise matches
20,19 has 8444 pairwise matches
20,30 has 7785 pairwise matches
20,29 has 7952 pairwise matches
20,12 has 8263 pairwise matches
20,21 has 7872 pairwise matches
25,19 has 8153 pairwise matches
25,30 has 7322 pairwise matches
25,29 has 7387 pairwise matches
25,12 has 7732 pairwise matches
25,21 has 7370 pairwise matches
28,19 has 7321 pairwise matches
28,30 has 6870 pairwise matches
28,29 has 6211 pairwise matches
28,12 has 7696 pairwise matches
28,21 has 7332 pairwise matches
18,19 has 7828 pairwise matches
18,30 has 7544 pairwise matches
18,29 has 7198 pairwise matches
18,12 has 8711 pairwise matches
18,21 has 8079 pairwise matches
26,19 has 8536 pairwise matches
26,30 has 7665 pairwise matches
26,29 has 7679 pairwise matches
26,12 has 9049 pairwise matches
26,21 has 8804 pairwise matches
3,19 has 8082 pairwise matches
3,30 has 7603 pairwise matches
3,29 has 7171 pairwise matches
3,12 has 8819 pairwise matches
3,21 has 8602 pairwise matches
23,19 has 8224 pairwise matches
23,30 has 7589 pairwise matches
23,29 has 7279 pairwise matches
23,12 has 8931 pairwise matches
23,21 has 8750 pairwise matches
24,19 has 8220 pairwise matches
24,30 has 7583 pairwise matches
24,29 has 7284 pairwise matches
24,12 has 8938 pairwise matches
24,21 has 8753 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 2629 Mb
Pagefile usage: 2078 Mb
construct LCB tracking matches
There are 27240 tracking matches
There are 1390312 / 1661640 components used
Working set size: 2695 Mb

Pagefile usage: 2136 Mb

init tracking match LCB tracking
Working set size: 2720 Mb
Pagefile usage: 2161 Mb
pairwise score tracking matches
Working set size: 2745 Mb
Pagefile usage: 2186 Mb
get pairwise LCBs
there are 44235 pairwise LCBs
Working set size: 2751 Mb
Pagefile usage: 2186 Mb
scaling bp penalty by conservation weight:
0.104308
0.082926
0.0876522
0.0962354
0.0802696
0.11446 0.0946115
0.106509
0.107388
0.094341
0.112542
0.0922735
0.0928351
0.0989504
0.0849337
0.105547
0.0835203
0.0915094
0.100781
0.0862605
0.110383
0.0898347
0.0827252
0.0978867
0.0866425
0.105835
0.0725374
0.0751431
0.0868568
0.0819164
0.123097
0.09628 0.0846801
0.091687
0.0902899
0.123985
0.0973955
0.0850126
0.0919313
0.0905321
0.115725
0.0848423
0.0834596
0.0851524
0.0878706
0.116667
0.0847359
0.0838756
0.0870396
0.0897507
0.12062 0.0922209
0.089806
0.0914911
0.0940886
0.120639
0.0922576
0.0897393
0.0914776
0.0940719
0.117177
0.0918824
0.0829517
0.0922173
0.0814833
0.111262
0.0835397
0.0775097
0.0924478
0.0820491
0.109597
0.0855969
0.074238
0.0905392
0.0778284
0.128618
0.109212
0.109025
0.10664 0.106846
0.118799
0.0962708
0.0946893
0.0937439
0.093455
0.12035 0.0960072
0.0953667
0.0917209
0.0953641
0.100428
0.0778868
0.080101
0.0979779
0.0834132
0.112299
0.0898108
0.0806593
0.0980504
0.0853317
0.122783
0.0923052
0.0951004
0.110921
0.102196
0.104971
0.0876447
0.0781697
0.095474
0.0829028
0.110196
0.0866611
0.0728839
0.0884578
0.0817822
0.111165
0.0880644
0.0734292
0.0889674
0.0822248
scaling bp penalty by bp weight:
0.0214286
0.0857143
0.0857143
0.0214286
0.0214286
0.0214286
0.0214286
0.0857143
0.15
0.15
0.0214286
0.0214286
0.0214286
0.0857143
0.0214286
0.15
0.15
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0857143
0.0214286
0.0214286
0.0857143
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0857143
0.0214286
0.0214286
0.0214286
0.0857143
0.0214286
0.0857143
0.0857143
0.0214286
0.0857143
0.0857143
0.0214286
0.128571
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286

0.0857143
0.0214286
0.107143
0.0214286
0.107143
0.0214286
0.0857143
0.0857143
0.0214286
0.0214286
0.0214286
0.0214286
0.0857143
0.0857143
0.0214286
0.128571
0.128571
0.171429
0.0214286
0.0214286
0.0214286

0.0428571
0.0428571
0.0428571
0.0428571
0.107143
0.107143
0.107143
0.0428571
0.0428571
0.0428571
0.0428571
0.107143
0.0428571
0.0428571
0.0428571
0.0857143
0.0428571
0.0428571
0.0428571

0.0214286
0.0214286
0.0214286

0.0214286
0.0214286
0.0214286

0.15
0.15
0.0857143
0.0857143

0.107143
0.0857143
0.0857143

0.0428571
0.0428571

Greedy BPE
Scoring with scaled breakpoint penalty: 92477.2
1%..2%..3%..4%..done
Working set size: 2602 Mb
Pagefile usage: 2025 Mb
Arrived at 276 intervals
Adding unaligned intervals
addUnalignedIntervals yields 734 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(2) has 489 intervals
descendant 1(4) has 38 intervals
propagateDescendantBreakpoints yields 792 intervals
Creating ancestral ordering
Previous anchoring score: 3.67048e+009, new anchor score: 1.49038e+010
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 2028 new matches outside LCBs
0,1 have 1754 new matches outside LCBs
0,2 have 2144 new matches outside LCBs
0,3 have 2578 new matches outside LCBs
0,4 have 1978 new matches outside LCBs
1,0 have 2680 new matches outside LCBs
1,1 have 2203 new matches outside LCBs
1,2 have 2992 new matches outside LCBs
1,3 have 3193 new matches outside LCBs
1,4 have 2618 new matches outside LCBs
2,0 have 2452 new matches outside LCBs
2,1 have 2051 new matches outside LCBs
2,2 have 2263 new matches outside LCBs
2,3 have 2767 new matches outside LCBs
2,4 have 2103 new matches outside LCBs
3,0 have 2591 new matches outside LCBs
3,1 have 2022 new matches outside LCBs
3,2 have 2636 new matches outside LCBs
3,3 have 3228 new matches outside LCBs
3,4 have 2533 new matches outside LCBs
4,0 have 2655 new matches outside LCBs
4,1 have 2071 new matches outside LCBs
4,2 have 2306 new matches outside LCBs
4,3 have 2777 new matches outside LCBs
4,4 have 1979 new matches outside LCBs
5,0 have 2470 new matches outside LCBs
5,1 have 1365 new matches outside LCBs
5,2 have 1640 new matches outside LCBs
5,3 have 1704 new matches outside LCBs
5,4 have 1766 new matches outside LCBs
6,0 have 3023 new matches outside LCBs
6,1 have 1964 new matches outside LCBs
6,2 have 1916 new matches outside LCBs
6,3 have 2216 new matches outside LCBs
6,4 have 1952 new matches outside LCBs
7,0 have 3015 new matches outside LCBs
7,1 have 1958 new matches outside LCBs

7,2 have 1914 new matches outside LCBs

7,3 have 2209 new matches outside LCBs
7,4 have 1951 new matches outside LCBs
8,0 have 2835 new matches outside LCBs
8,1 have 1604 new matches outside LCBs
8,2 have 2037 new matches outside LCBs
8,3 have 1730 new matches outside LCBs
8,4 have 1949 new matches outside LCBs
9,0 have 3044 new matches outside LCBs
9,1 have 1698 new matches outside LCBs
9,2 have 2239 new matches outside LCBs
9,3 have 2106 new matches outside LCBs
9,4 have 2247 new matches outside LCBs
10,0 have 3305 new matches outside LCBs
10,1 have 1908 new matches outside LCBs
10,2 have 2537 new matches outside LCBs
10,3 have 2484 new matches outside LCBs
10,4 have 2458 new matches outside LCBs
11,0 have 3299 new matches outside LCBs
11,1 have 1901 new matches outside LCBs
11,2 have 2535 new matches outside LCBs
11,3 have 2489 new matches outside LCBs
11,4 have 2463 new matches outside LCBs
12,0 have 2917 new matches outside LCBs
12,1 have 2183 new matches outside LCBs
12,2 have 2136 new matches outside LCBs
12,3 have 2797 new matches outside LCBs
12,4 have 1951 new matches outside LCBs
13,0 have 2680 new matches outside LCBs
13,1 have 1868 new matches outside LCBs
13,2 have 2155 new matches outside LCBs
13,3 have 2751 new matches outside LCBs
13,4 have 2206 new matches outside LCBs
14,0 have 2604 new matches outside LCBs
14,1 have 1929 new matches outside LCBs
14,2 have 2035 new matches outside LCBs
14,3 have 2690 new matches outside LCBs
14,4 have 1973 new matches outside LCBs
15,0 have 3374 new matches outside LCBs
15,1 have 2093 new matches outside LCBs
15,2 have 3561 new matches outside LCBs
15,3 have 3871 new matches outside LCBs
15,4 have 3285 new matches outside LCBs
16,0 have 2660 new matches outside LCBs
16,1 have 1716 new matches outside LCBs
16,2 have 2457 new matches outside LCBs
16,3 have 2403 new matches outside LCBs
16,4 have 2328 new matches outside LCBs
17,0 have 2875 new matches outside LCBs
17,1 have 1786 new matches outside LCBs
17,2 have 2608 new matches outside LCBs
17,3 have 2626 new matches outside LCBs
17,4 have 2534 new matches outside LCBs
18,0 have 1774 new matches outside LCBs
18,1 have 1474 new matches outside LCBs
18,2 have 1770 new matches outside LCBs
18,3 have 2228 new matches outside LCBs
18,4 have 1784 new matches outside LCBs
19,0 have 2520 new matches outside LCBs
19,1 have 1801 new matches outside LCBs

19,2 have 2030 new matches

19,3 have 2721 new matches
19,4 have 2046 new matches
20,0 have 2499 new matches
20,1 have 1271 new matches
20,2 have 2008 new matches
20,3 have 2644 new matches
20,4 have 2243 new matches
21,0 have 2153 new matches
21,1 have 2109 new matches
21,2 have 1921 new matches
21,3 have 2699 new matches
21,4 have 2155 new matches
22,0 have 2459 new matches
22,1 have 1701 new matches
22,2 have 1670 new matches
22,3 have 2439 new matches
22,4 have 2052 new matches
23,0 have 2456 new matches
23,1 have 1692 new matches
23,2 have 1666 new matches
23,3 have 2435 new matches
23,4 have 2047 new matches
0,0 has an additional 3231
0,1 has an additional 2510
0,2 has an additional 3084
0,3 has an additional 3668
0,4 has an additional 3154
1,0 has an additional 3525
1,1 has an additional 3083
1,2 has an additional 3921
1,3 has an additional 4476
1,4 has an additional 3840
2,0 has an additional 3301
2,1 has an additional 2714
2,2 has an additional 3352
2,3 has an additional 3791
2,4 has an additional 3141
3,0 has an additional 3369
3,1 has an additional 2738
3,2 has an additional 3441
3,3 has an additional 4236
3,4 has an additional 3573
4,0 has an additional 3619
4,1 has an additional 2938
4,2 has an additional 3012
4,3 has an additional 3908
4,4 has an additional 3119
5,0 has an additional 3158
5,1 has an additional 2093
5,2 has an additional 2235
5,3 has an additional 2682
5,4 has an additional 2697
6,0 has an additional 4420
6,1 has an additional 2869
6,2 has an additional 2831
6,3 has an additional 3586
6,4 has an additional 3118
7,0 has an additional 4411
7,1 has an additional 2863

outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
outside
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches
matches

LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs
LCBs

7,2 has an additional 2842 matches

7,3 has an additional 3579 matches
7,4 has an additional 3127 matches
8,0 has an additional 3820 matches
8,1 has an additional 2430 matches
8,2 has an additional 2773 matches
8,3 has an additional 2858 matches
8,4 has an additional 2994 matches
9,0 has an additional 4003 matches
9,1 has an additional 2549 matches
9,2 has an additional 2950 matches
9,3 has an additional 3299 matches
9,4 has an additional 3270 matches
10,0 has an additional 4657 matches
10,1 has an additional 2826 matches
10,2 has an additional 3417 matches
10,3 has an additional 3863 matches
10,4 has an additional 3634 matches
11,0 has an additional 4645 matches
11,1 has an additional 2811 matches
11,2 has an additional 3415 matches
11,3 has an additional 3849 matches
11,4 has an additional 3623 matches
12,0 has an additional 3902 matches
12,1 has an additional 3084 matches
12,2 has an additional 3111 matches
12,3 has an additional 4148 matches
12,4 has an additional 3039 matches
13,0 has an additional 3708 matches
13,1 has an additional 2812 matches
13,2 has an additional 3150 matches
13,3 has an additional 4275 matches
13,4 has an additional 3656 matches
14,0 has an additional 3659 matches
14,1 has an additional 2923 matches
14,2 has an additional 3109 matches
14,3 has an additional 4263 matches
14,4 has an additional 3512 matches
15,0 has an additional 4930 matches
15,1 has an additional 3220 matches
15,2 has an additional 5095 matches
15,3 has an additional 5365 matches
15,4 has an additional 4775 matches
16,0 has an additional 3951 matches
16,1 has an additional 2850 matches
16,2 has an additional 3484 matches
16,3 has an additional 3757 matches
16,4 has an additional 3626 matches
17,0 has an additional 4039 matches
17,1 has an additional 2676 matches
17,2 has an additional 3720 matches
17,3 has an additional 3820 matches
17,4 has an additional 3684 matches
18,0 has an additional 2641 matches
18,1 has an additional 2377 matches
18,2 has an additional 2472 matches
18,3 has an additional 3368 matches
18,4 has an additional 2949 matches
19,0 has an additional 3550 matches
19,1 has an additional 2863 matches

19,2 has an additional 3097 matches

19,3 has an additional 4282 matches
19,4 has an additional 3435 matches
20,0 has an additional 3856 matches
20,1 has an additional 2295 matches
20,2 has an additional 3238 matches
20,3 has an additional 4452 matches
20,4 has an additional 3843 matches
21,0 has an additional 3389 matches
21,1 has an additional 3013 matches
21,2 has an additional 2847 matches
21,3 has an additional 4163 matches
21,4 has an additional 3691 matches
22,0 has an additional 3770 matches
22,1 has an additional 2697 matches
22,2 has an additional 2703 matches
22,3 has an additional 4113 matches
22,4 has an additional 3674 matches
23,0 has an additional 3766 matches
23,1 has an additional 2691 matches
23,2 has an additional 2728 matches
23,3 has an additional 4111 matches
23,4 has an additional 3671 matches
Restoring backed up alignment tree...
11,19 has 3231 pairwise matches
11,30 has 2510 pairwise matches
11,29 has 3084 pairwise matches
11,12 has 3668 pairwise matches
11,21 has 3154 pairwise matches
1,19 has 3525 pairwise matches
1,30 has 3083 pairwise matches
1,29 has 3921 pairwise matches
1,12 has 4476 pairwise matches
1,21 has 3840 pairwise matches
5,19 has 3301 pairwise matches
5,30 has 2714 pairwise matches
5,29 has 3352 pairwise matches
5,12 has 3791 pairwise matches
5,21 has 3141 pairwise matches
10,19 has 3369 pairwise matches
10,30 has 2738 pairwise matches
10,29 has 3441 pairwise matches
10,12 has 4236 pairwise matches
10,21 has 3573 pairwise matches
6,19 has 3619 pairwise matches
6,30 has 2938 pairwise matches
6,29 has 3012 pairwise matches
6,12 has 3908 pairwise matches
6,21 has 3119 pairwise matches
4,19 has 3158 pairwise matches
4,30 has 2093 pairwise matches
4,29 has 2235 pairwise matches
4,12 has 2682 pairwise matches
4,21 has 2697 pairwise matches
7,19 has 4420 pairwise matches
7,30 has 2869 pairwise matches
7,29 has 2831 pairwise matches
7,12 has 3586 pairwise matches
7,21 has 3118 pairwise matches
8,19 has 4411 pairwise matches

8,30 has 2863 pairwise matches

8,29 has 2842 pairwise matches
8,12 has 3579 pairwise matches
8,21 has 3127 pairwise matches
17,19 has 3820 pairwise matches
17,30 has 2430 pairwise matches
17,29 has 2773 pairwise matches
17,12 has 2858 pairwise matches
17,21 has 2994 pairwise matches
0,19 has 4003 pairwise matches
0,30 has 2549 pairwise matches
0,29 has 2950 pairwise matches
0,12 has 3299 pairwise matches
0,21 has 3270 pairwise matches
15,19 has 4657 pairwise matches
15,30 has 2826 pairwise matches
15,29 has 3417 pairwise matches
15,12 has 3863 pairwise matches
15,21 has 3634 pairwise matches
16,19 has 4645 pairwise matches
16,30 has 2811 pairwise matches
16,29 has 3415 pairwise matches
16,12 has 3849 pairwise matches
16,21 has 3623 pairwise matches
2,19 has 3902 pairwise matches
2,30 has 3084 pairwise matches
2,29 has 3111 pairwise matches
2,12 has 4148 pairwise matches
2,21 has 3039 pairwise matches
13,19 has 3708 pairwise matches
13,30 has 2812 pairwise matches
13,29 has 3150 pairwise matches
13,12 has 4275 pairwise matches
13,21 has 3656 pairwise matches
14,19 has 3659 pairwise matches
14,30 has 2923 pairwise matches
14,29 has 3109 pairwise matches
14,12 has 4263 pairwise matches
14,21 has 3512 pairwise matches
22,19 has 4930 pairwise matches
22,30 has 3220 pairwise matches
22,29 has 5095 pairwise matches
22,12 has 5365 pairwise matches
22,21 has 4775 pairwise matches
20,19 has 3951 pairwise matches
20,30 has 2850 pairwise matches
20,29 has 3484 pairwise matches
20,12 has 3757 pairwise matches
20,21 has 3626 pairwise matches
25,19 has 4039 pairwise matches
25,30 has 2676 pairwise matches
25,29 has 3720 pairwise matches
25,12 has 3820 pairwise matches
25,21 has 3684 pairwise matches
28,19 has 2641 pairwise matches
28,30 has 2377 pairwise matches
28,29 has 2472 pairwise matches
28,12 has 3368 pairwise matches
28,21 has 2949 pairwise matches
18,19 has 3550 pairwise matches

18,30 has 2863 pairwise matches

18,29 has 3097 pairwise matches
18,12 has 4282 pairwise matches
18,21 has 3435 pairwise matches
26,19 has 3856 pairwise matches
26,30 has 2295 pairwise matches
26,29 has 3238 pairwise matches
26,12 has 4452 pairwise matches
26,21 has 3843 pairwise matches
3,19 has 3389 pairwise matches
3,30 has 3013 pairwise matches
3,29 has 2847 pairwise matches
3,12 has 4163 pairwise matches
3,21 has 3691 pairwise matches
23,19 has 3770 pairwise matches
23,30 has 2697 pairwise matches
23,29 has 2703 pairwise matches
23,12 has 4113 pairwise matches
23,21 has 3674 pairwise matches
24,19 has 3766 pairwise matches
24,30 has 2691 pairwise matches
24,29 has 2728 pairwise matches
24,12 has 4111 pairwise matches
24,21 has 3671 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 2659 Mb
Pagefile usage: 2087 Mb
construct LCB tracking matches
There are 28734 tracking matches
There are 1408002 / 1752774 components used
Working set size: 2678 Mb
Pagefile usage: 2105 Mb
init tracking match LCB tracking
Working set size: 2704 Mb
Pagefile usage: 2131 Mb
pairwise score tracking matches
Working set size: 2731 Mb
Pagefile usage: 2158 Mb
get pairwise LCBs
there are 41687 pairwise LCBs
Working set size: 2732 Mb
Pagefile usage: 2159 Mb
scaling bp penalty by conservation weight:
0.104308
0.082926
0.0876522
0.0962354
0.0802696
0.11446 0.0946115
0.106509
0.107388
0.094341
0.112542
0.0922735
0.0928351
0.0989504
0.0849337
0.105547
0.0835203
0.0915094
0.100781
0.0862605
0.110383
0.0898347
0.0827252
0.0978867
0.0866425
0.105835
0.0725374
0.0751431
0.0868568
0.0819164
0.123097
0.09628 0.0846801
0.091687
0.0902899
0.123985
0.0973955
0.0850126
0.0919313
0.0905321
0.115725
0.0848423
0.0834596
0.0851524
0.0878706
0.116667
0.0847359
0.0838756
0.0870396
0.0897507
0.12062 0.0922209
0.089806
0.0914911
0.0940886
0.120639
0.0922576
0.0897393
0.0914776
0.0940719
0.117177
0.0918824
0.0829517
0.0922173
0.0814833
0.111262
0.0835397
0.0775097
0.0924478
0.0820491
0.109597
0.0855969
0.074238
0.0905392
0.0778284
0.128618
0.109212
0.109025
0.10664 0.106846
0.118799
0.0962708
0.0946893
0.0937439
0.093455

0.12035 0.0960072
0.0953667
0.0917209
0.0953641
0.100428
0.0778868
0.080101
0.0979779
0.0834132
0.112299
0.0898108
0.0806593
0.0980504
0.0853317
0.122783
0.0923052
0.0951004
0.110921
0.102196
0.104971
0.0876447
0.0781697
0.095474
0.0829028
0.110196
0.0866611
0.0728839
0.0884578
0.0817822
0.111165
0.0880644
0.0734292
0.0889674
0.0822248
scaling bp penalty by bp weight:
0.0214286
0.0857143
0.0857143
0.0214286
0.0214286
0.0214286
0.0214286
0.0857143
0.15
0.15
0.0214286
0.0214286
0.0214286
0.0857143
0.0214286
0.15
0.15
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0857143
0.0214286
0.0214286
0.0857143
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0857143
0.0214286
0.0214286
0.0214286
0.0857143
0.0214286
0.0857143
0.0857143
0.0214286
0.0857143
0.0857143
0.0214286
0.128571
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.15
0.15
0.0214286
0.0214286
0.0857143
0.0214286
0.0214286
0.0857143

0.0857143
0.0214286
0.107143
0.0214286
0.107143
0.0214286
0.0857143
0.0857143
0.0214286
0.0214286
0.0214286
0.0214286
0.0857143
0.0857143
0.0214286
0.128571
0.128571
0.171429
0.0214286
0.0214286
0.0214286
0.107143
0.0857143
0.0857143

0.0428571
0.0428571
0.0428571
0.0428571
0.107143
0.107143
0.107143
0.0428571
0.0428571
0.0428571
0.0428571
0.107143
0.0428571
0.0428571
0.0428571
0.0857143
0.0428571
0.0428571
0.0428571
0.0428571
0.0428571

Greedy BPE
Scoring with scaled breakpoint penalty: 92477.2
1%..2%..3%..4%..5%..6%..7%..8%..9%..done
Working set size: 2728 Mb
Pagefile usage: 2135 Mb
Arrived at 285 intervals
Adding unaligned intervals
addUnalignedIntervals yields 757 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(2) has 489 intervals
descendant 1(4) has 38 intervals
propagateDescendantBreakpoints yields 805 intervals
Creating ancestral ordering
Previous anchoring score: 1.49038e+010, new anchor score: 1.49101e+010
Working set size: 2532 Mb
Pagefile usage: 1944 Mb
propagating ancestral breakpoints
Working set size: 2534 Mb
Pagefile usage: 1949 Mb
performing a gapped alignment
0%..
10%..11%..12%..13%..14%..15%..16%..17%..18%..19%..

20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..47%..48%..49%..
50%..51%..52%..53%..54%..55%..56%..57%..58%..59%..
60%..61%..62%..63%..64%..65%..66%..67%..68%..69%..
70%..71%..72%..73%..74%..75%..76%..77%..78%..79%..
80%..81%..82%..83%..84%..85%..86%..87%..88%..89%..
90%..91%..92%..93%..94%..95%..96%..97%..98%..99%..
100%..Working set size: 2703 Mb
Pagefile usage: 2120 Mb
Fix left ends
Working set size: 2703 Mb
Pagefile usage: 2120 Mb
done.
performing iterative refinement
0%..
12%..13%..14%..15%..16%..17%..18%..19%..
20%..21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..47%..48%..49%..
50%..51%..52%..53%..54%..55%..56%..57%..58%..59%..
60%..61%..62%..63%..64%..65%..66%..67%..68%..69%..
70%..71%..72%..73%..74%..75%..76%..77%..78%..79%..
80%..81%..82%..83%..84%..85%..86%..87%..88%..89%..
90%..91%..92%..93%..94%..95%..96%..97%..98%..99%..
100%..Working set size: 2723 Mb
Pagefile usage: 2135 Mb
Fix left ends
Working set size: 2723 Mb
Pagefile usage: 2135 Mb
done.
Working set size: 2723 Mb
Pagefile usage: 2135 Mb
Aligning node 3 to 15 via 13!
Working set size: 2389 Mb
Pagefile usage: 1907 Mb
get ancestral matches
Working set size: 2407 Mb
Pagefile usage: 1924 Mb
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 2407 Mb
Pagefile usage: 1925 Mb
construct LCB tracking matches
There are 48098 tracking matches
There are 2334569 / 2933978 components used
Working set size: 2632 Mb
Pagefile usage: 2089 Mb
init tracking match LCB tracking
Working set size: 2642 Mb
Pagefile usage: 2100 Mb
pairwise score tracking matches
Working set size: 2653 Mb
Pagefile usage: 2110 Mb
get pairwise LCBs
there are 225517 pairwise LCBs
Working set size: 2678 Mb
Pagefile usage: 2126 Mb

scaling bp penalty by conservation weight:

0.113291
0.0846678
0.0862361
0.0945604
0.0837625
0.0906053
0.097461
0.0925116
0.0953735
0.0949548
0.0842998
0.0950338
0.0950436
0.0921694
0.0923713
0.098213
0.0983914
0.0849803
0.0812594
0.0770087
0.118185
0.104075
0.104177
0.088317
0.0888407
0.102329
0.0895244
0.0794664
0.0792547
scaling bp penalty by bp weight:
0.0214286
0.0214286
0.0214286
0.0214286
0.0428571
0.0857143
0.0214286
0.15
0.0214286
0.0857143
0.0214286
0.0857143
0.0857143
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0857143
0.0214286
0.0214286
0.0214286
0.0642857
0.0214286
0.0214286
0.0214286
0.0857143

0.0214286
0.0214286
Greedy BPE
Scoring with scaled breakpoint penalty: 88822.9
1%..2%..3%..done
Working set size: 2396 Mb
Pagefile usage: 1823 Mb
Arrived at 342 intervals
Adding unaligned intervals
addUnalignedIntervals yields 1000 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(3) has 792 intervals
descendant 1(15) has 1 intervals
propagateDescendantBreakpoints yields 1131 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 3.39394e+009
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 2983 new matches outside LCBs
1,0 have 2062 new matches outside LCBs
2,0 have 2591 new matches outside LCBs
3,0 have 3199 new matches outside LCBs
4,0 have 2604 new matches outside LCBs
5,0 have 3273 new matches outside LCBs
6,0 have 3830 new matches outside LCBs
7,0 have 3310 new matches outside LCBs
8,0 have 3565 new matches outside LCBs
9,0 have 3505 new matches outside LCBs
10,0 have 2884 new matches outside LCBs
11,0 have 3382 new matches outside LCBs
12,0 have 3381 new matches outside LCBs
13,0 have 3212 new matches outside LCBs
14,0 have 3554 new matches outside LCBs
15,0 have 3889 new matches outside LCBs
16,0 have 3900 new matches outside LCBs
17,0 have 3154 new matches outside LCBs
18,0 have 3163 new matches outside LCBs
19,0 have 2848 new matches outside LCBs
20,0 have 5142 new matches outside LCBs
21,0 have 3787 new matches outside LCBs
22,0 have 4111 new matches outside LCBs
23,0 have 2782 new matches outside LCBs
24,0 have 3179 new matches outside LCBs
25,0 have 3173 new matches outside LCBs
26,0 have 3402 new matches outside LCBs
27,0 have 2912 new matches outside LCBs
28,0 have 2912 new matches outside LCBs
0,0 has an additional 5812 matches
1,0 has an additional 4504 matches
2,0 has an additional 5435 matches
3,0 has an additional 6322 matches
4,0 has an additional 5510 matches
5,0 has an additional 5810 matches
6,0 has an additional 6489 matches
7,0 has an additional 5975 matches
8,0 has an additional 6151 matches

9,0 has an additional 6345 matches

10,0 has an additional 5543 matches
11,0 has an additional 6201 matches
12,0 has an additional 6201 matches
13,0 has an additional 6054 matches
14,0 has an additional 6310 matches
15,0 has an additional 6792 matches
16,0 has an additional 6802 matches
17,0 has an additional 5724 matches
18,0 has an additional 6096 matches
19,0 has an additional 5660 matches
20,0 has an additional 8547 matches
21,0 has an additional 6851 matches
22,0 has an additional 7189 matches
23,0 has an additional 5439 matches
24,0 has an additional 6154 matches
25,0 has an additional 6214 matches
26,0 has an additional 6384 matches
27,0 has an additional 6092 matches
28,0 has an additional 6089 matches
Restoring backed up alignment tree...
19,9 has 5812 pairwise matches
30,9 has 4504 pairwise matches
29,9 has 5435 pairwise matches
12,9 has 6322 pairwise matches
21,9 has 5510 pairwise matches
11,9 has 5810 pairwise matches
1,9 has 6489 pairwise matches
5,9 has 5975 pairwise matches
10,9 has 6151 pairwise matches
6,9 has 6345 pairwise matches
4,9 has 5543 pairwise matches
7,9 has 6201 pairwise matches
8,9 has 6201 pairwise matches
17,9 has 6054 pairwise matches
0,9 has 6310 pairwise matches
15,9 has 6792 pairwise matches
16,9 has 6802 pairwise matches
2,9 has 5724 pairwise matches
13,9 has 6096 pairwise matches
14,9 has 5660 pairwise matches
22,9 has 8547 pairwise matches
20,9 has 6851 pairwise matches
25,9 has 7189 pairwise matches
28,9 has 5439 pairwise matches
18,9 has 6154 pairwise matches
26,9 has 6214 pairwise matches
3,9 has 6384 pairwise matches
23,9 has 6092 pairwise matches
24,9 has 6089 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 2456 Mb
Pagefile usage: 1899 Mb
construct LCB tracking matches
There are 37350 tracking matches
There are 1998203 / 2278350 components used
Working set size: 2595 Mb
Pagefile usage: 2031 Mb
init tracking match LCB tracking
Working set size: 2603 Mb

Pagefile usage: 2040 Mb

pairwise score tracking matches
Working set size: 2612 Mb
Pagefile usage: 2049 Mb
get pairwise LCBs
there are 28210 pairwise LCBs
Working set size: 2620 Mb
Pagefile usage: 2055 Mb
scaling bp penalty by conservation weight:
0.113291
0.0846678
0.0862361
0.0945604
0.0837625
0.0906053
0.097461
0.0925116
0.0953735
0.0949548
0.0842998
0.0950338
0.0950436
0.0921694
0.0923713
0.098213
0.0983914
0.0849803
0.0812594
0.0770087
0.118185
0.104075
0.104177
0.088317
0.0888407
0.102329
0.0895244
0.0794664
0.0792547
scaling bp penalty by bp weight:
0.0214286
0.0214286
0.0214286
0.0214286
0.0428571
0.0857143
0.0214286
0.15
0.0214286
0.0857143
0.0214286
0.0857143
0.0857143
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0857143

0.0214286
0.0214286
0.0214286
0.0642857
0.0214286
0.0214286
0.0214286
0.0857143
0.0214286
0.0214286
Greedy BPE
Scoring with scaled breakpoint penalty: 88822.9
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..done
Working set size: 2459 Mb
Pagefile usage: 1883 Mb
Arrived at 310 intervals
Adding unaligned intervals
addUnalignedIntervals yields 797 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(3) has 792 intervals
descendant 1(15) has 1 intervals
propagateDescendantBreakpoints yields 1095 intervals
Creating ancestral ordering
Previous anchoring score: 3.39394e+009, new anchor score: 4.15166e+009
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 2403 new matches outside LCBs
1,0 have 1563 new matches outside LCBs
2,0 have 2056 new matches outside LCBs
3,0 have 2466 new matches outside LCBs
4,0 have 1949 new matches outside LCBs
5,0 have 2547 new matches outside LCBs
6,0 have 2892 new matches outside LCBs
7,0 have 2508 new matches outside LCBs
8,0 have 2920 new matches outside LCBs
9,0 have 2881 new matches outside LCBs
10,0 have 2167 new matches outside LCBs
11,0 have 2659 new matches outside LCBs
12,0 have 2658 new matches outside LCBs
13,0 have 2554 new matches outside LCBs
14,0 have 2816 new matches outside LCBs
15,0 have 3171 new matches outside LCBs
16,0 have 3176 new matches outside LCBs
17,0 have 2523 new matches outside LCBs
18,0 have 2484 new matches outside LCBs
19,0 have 2182 new matches outside LCBs
20,0 have 4450 new matches outside LCBs
21,0 have 3193 new matches outside LCBs
22,0 have 3484 new matches outside LCBs
23,0 have 2247 new matches outside LCBs
24,0 have 2617 new matches outside LCBs
25,0 have 2431 new matches outside LCBs
26,0 have 2773 new matches outside LCBs
27,0 have 2296 new matches outside LCBs
28,0 have 2288 new matches outside LCBs

0,0 has an additional 3116 matches

1,0 has an additional 2210 matches
2,0 has an additional 3164 matches
3,0 has an additional 3931 matches
4,0 has an additional 3109 matches
5,0 has an additional 3170 matches
6,0 has an additional 3543 matches
7,0 has an additional 3357 matches
8,0 has an additional 3433 matches
9,0 has an additional 3867 matches
10,0 has an additional 3133 matches
11,0 has an additional 3830 matches
12,0 has an additional 3827 matches
13,0 has an additional 3713 matches
14,0 has an additional 3960 matches
15,0 has an additional 4444 matches
16,0 has an additional 4454 matches
17,0 has an additional 3507 matches
18,0 has an additional 3455 matches
19,0 has an additional 3200 matches
20,0 has an additional 5998 matches
21,0 has an additional 4302 matches
22,0 has an additional 4745 matches
23,0 has an additional 2912 matches
24,0 has an additional 3823 matches
25,0 has an additional 3713 matches
26,0 has an additional 3743 matches
27,0 has an additional 3493 matches
28,0 has an additional 3478 matches
Restoring backed up alignment tree...
19,9 has 3116 pairwise matches
30,9 has 2210 pairwise matches
29,9 has 3164 pairwise matches
12,9 has 3931 pairwise matches
21,9 has 3109 pairwise matches
11,9 has 3170 pairwise matches
1,9 has 3543 pairwise matches
5,9 has 3357 pairwise matches
10,9 has 3433 pairwise matches
6,9 has 3867 pairwise matches
4,9 has 3133 pairwise matches
7,9 has 3830 pairwise matches
8,9 has 3827 pairwise matches
17,9 has 3713 pairwise matches
0,9 has 3960 pairwise matches
15,9 has 4444 pairwise matches
16,9 has 4454 pairwise matches
2,9 has 3507 pairwise matches
13,9 has 3455 pairwise matches
14,9 has 3200 pairwise matches
22,9 has 5998 pairwise matches
20,9 has 4302 pairwise matches
25,9 has 4745 pairwise matches
28,9 has 2912 pairwise matches
18,9 has 3823 pairwise matches
26,9 has 3713 pairwise matches
3,9 has 3743 pairwise matches
23,9 has 3493 pairwise matches
24,9 has 3478 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination

Working set size: 2501 Mb

Pagefile usage: 1942 Mb
construct LCB tracking matches
There are 36737 tracking matches
There are 1984779 / 2240957 components used
Working set size: 2579 Mb
Pagefile usage: 2020 Mb
init tracking match LCB tracking
Working set size: 2587 Mb
Pagefile usage: 2029 Mb
pairwise score tracking matches
Working set size: 2596 Mb
Pagefile usage: 2037 Mb
get pairwise LCBs
there are 19698 pairwise LCBs
Working set size: 2600 Mb
Pagefile usage: 2038 Mb
scaling bp penalty by conservation weight:
0.113291
0.0846678
0.0862361
0.0945604
0.0837625
0.0906053
0.097461
0.0925116
0.0953735
0.0949548
0.0842998
0.0950338
0.0950436
0.0921694
0.0923713
0.098213
0.0983914
0.0849803
0.0812594
0.0770087
0.118185
0.104075
0.104177
0.088317
0.0888407
0.102329
0.0895244
0.0794664
0.0792547
scaling bp penalty by bp weight:
0.0214286
0.0214286
0.0214286
0.0214286
0.0428571
0.0857143
0.0214286
0.15
0.0214286
0.0857143

0.0214286
0.0857143
0.0857143
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0857143
0.0214286
0.0214286
0.0214286
0.0642857
0.0214286
0.0214286
0.0214286
0.0857143
0.0214286
0.0214286
Greedy BPE
Scoring with scaled breakpoint penalty: 88822.9
1%..2%..3%..4%..5%..6%..7%..8%..9%..
10%..11%..12%..done
Working set size: 2435 Mb
Pagefile usage: 1859 Mb
Arrived at 332 intervals
Adding unaligned intervals
addUnalignedIntervals yields 841 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(3) has 792 intervals
descendant 1(15) has 1 intervals
propagateDescendantBreakpoints yields 1115 intervals
Creating ancestral ordering
Previous anchoring score: 4.15166e+009, new anchor score: 4.17072e+009
Working set size: 2435 Mb
Pagefile usage: 1863 Mb
propagating ancestral breakpoints
Working set size: 2437 Mb
Pagefile usage: 1867 Mb
performing a gapped alignment
0%..
21%..22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..47%..48%..49%..
50%..51%..52%..53%..54%..55%..56%..57%..58%..59%..
60%..61%..62%..63%..64%..65%..66%..67%..68%..69%..
70%..71%..72%..73%..74%..75%..76%..77%..78%..79%..
80%..81%..82%..83%..84%..85%..86%..87%..88%..89%..
90%..91%..92%..93%..94%..95%..96%..97%..98%..99%..
100%..Working set size: 2627 Mb
Pagefile usage: 2042 Mb
Fix left ends
Working set size: 2627 Mb
Pagefile usage: 2042 Mb
done.

Working set size: 2627 Mb

Pagefile usage: 2042 Mb
Aligning node 13 to 14 via 0!
Working set size: 2614 Mb
Pagefile usage: 2041 Mb
get ancestral matches
Working set size: 2617 Mb
Pagefile usage: 2043 Mb
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 2617 Mb
Pagefile usage: 2043 Mb
construct LCB tracking matches
There are 79089 tracking matches
There are 3604364 / 4824429 components used
Working set size: 2820 Mb
Pagefile usage: 2227 Mb
init tracking match LCB tracking
Working set size: 2838 Mb
Pagefile usage: 2245 Mb
pairwise score tracking matches
Working set size: 2856 Mb
Pagefile usage: 2264 Mb
get pairwise LCBs
there are 1489015 pairwise LCBs
Working set size: 3010 Mb
Pagefile usage: 2416 Mb
scaling bp penalty by conservation weight:
0.205179
0.228646
0.209714
0.209466
0.215562
0.211976
0.215442
0.218912
0.220993
0.220597
0.211523
0.204423
0.217683
0.217746
0.209334
0.208912
0.212248
0.212265
0.21042
0.208876
0.207869
0.224429
0.219419
0.220067
0.210748
0.214328
0.221401
0.210706
0.20562
0.205443
scaling bp penalty by bp weight:

0.0214286
0.0214286
0.0214286
0.0857143
0.0857143
0.0428571
0.0857143
0.0214286
0.0857143
0.0214286
0.0857143
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0857143
0.0857143
0.128571
0.0214286
0.0214286
0.0214286
0.0857143
0.0857143
0.0857143
Greedy BPE
Scoring with scaled breakpoint penalty: 57342.8
1%..2%..3%..done
Working set size: 2376 Mb
Pagefile usage: 1802 Mb
Arrived at 161 intervals
Adding unaligned intervals
addUnalignedIntervals yields 479 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(13) has 1095 intervals
descendant 1(14) has 1 intervals
propagateDescendantBreakpoints yields 1255 intervals
Creating ancestral ordering
Previous anchoring score: -1.79769e+308, new anchor score: 4.37453e+007
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 22962 new matches outside LCBs
1,0 have 24347 new matches outside LCBs
2,0 have 24064 new matches outside LCBs
3,0 have 23836 new matches outside LCBs
4,0 have 24601 new matches outside LCBs
5,0 have 24370 new matches outside LCBs
6,0 have 24721 new matches outside LCBs
7,0 have 24905 new matches outside LCBs
8,0 have 24803 new matches outside LCBs
9,0 have 25065 new matches outside LCBs

10,0 have 23745 new matches outside LCBs

11,0 have 23862 new matches outside LCBs
12,0 have 24493 new matches outside LCBs
13,0 have 24493 new matches outside LCBs
14,0 have 24077 new matches outside LCBs
15,0 have 24183 new matches outside LCBs
16,0 have 24418 new matches outside LCBs
17,0 have 24419 new matches outside LCBs
18,0 have 24463 new matches outside LCBs
19,0 have 24661 new matches outside LCBs
20,0 have 24526 new matches outside LCBs
21,0 have 25719 new matches outside LCBs
22,0 have 24708 new matches outside LCBs
23,0 have 24818 new matches outside LCBs
24,0 have 24169 new matches outside LCBs
25,0 have 24679 new matches outside LCBs
26,0 have 24406 new matches outside LCBs
27,0 have 24554 new matches outside LCBs
28,0 have 24594 new matches outside LCBs
29,0 have 24598 new matches outside LCBs
0,0 has an additional 36550 matches
1,0 has an additional 37773 matches
2,0 has an additional 36381 matches
3,0 has an additional 36815 matches
4,0 has an additional 38497 matches
5,0 has an additional 37769 matches
6,0 has an additional 38346 matches
7,0 has an additional 38024 matches
8,0 has an additional 38721 matches
9,0 has an additional 38420 matches
10,0 has an additional 37991 matches
11,0 has an additional 36939 matches
12,0 has an additional 38676 matches
13,0 has an additional 38673 matches
14,0 has an additional 37476 matches
15,0 has an additional 37722 matches
16,0 has an additional 38124 matches
17,0 has an additional 38127 matches
18,0 has an additional 38079 matches
19,0 has an additional 37983 matches
20,0 has an additional 37861 matches
21,0 has an additional 40617 matches
22,0 has an additional 38355 matches
23,0 has an additional 38694 matches
24,0 has an additional 36792 matches
25,0 has an additional 38337 matches
26,0 has an additional 38668 matches
27,0 has an additional 38336 matches
28,0 has an additional 39205 matches
29,0 has an additional 39215 matches
Restoring backed up alignment tree...
9,27 has 36550 pairwise matches
19,27 has 37773 pairwise matches
30,27 has 36381 pairwise matches
29,27 has 36815 pairwise matches
12,27 has 38497 pairwise matches
21,27 has 37769 pairwise matches
11,27 has 38346 pairwise matches
1,27 has 38024 pairwise matches
5,27 has 38721 pairwise matches

10,27 has 38420 pairwise matches

6,27 has 37991 pairwise matches
4,27 has 36939 pairwise matches
7,27 has 38676 pairwise matches
8,27 has 38673 pairwise matches
17,27 has 37476 pairwise matches
0,27 has 37722 pairwise matches
15,27 has 38124 pairwise matches
16,27 has 38127 pairwise matches
2,27 has 38079 pairwise matches
13,27 has 37983 pairwise matches
14,27 has 37861 pairwise matches
22,27 has 40617 pairwise matches
20,27 has 38355 pairwise matches
25,27 has 38694 pairwise matches
28,27 has 36792 pairwise matches
18,27 has 38337 pairwise matches
26,27 has 38668 pairwise matches
3,27 has 38336 pairwise matches
23,27 has 39205 pairwise matches
24,27 has 39215 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 2715 Mb
Pagefile usage: 2242 Mb
construct LCB tracking matches
There are 37052 tracking matches
There are 1794779 / 2260172 components used
Working set size: 2798 Mb
Pagefile usage: 2318 Mb
init tracking match LCB tracking
Working set size: 2807 Mb
Pagefile usage: 2327 Mb
pairwise score tracking matches
Working set size: 2815 Mb
Pagefile usage: 2335 Mb
get pairwise LCBs
there are 529908 pairwise LCBs
Working set size: 2867 Mb
Pagefile usage: 2385 Mb
scaling bp penalty by conservation weight:
0.205179
0.228646
0.209714
0.209466
0.215562
0.211976
0.215442
0.218912
0.220993
0.220597
0.211523
0.204423
0.217683
0.217746
0.209334
0.208912
0.212248
0.212265
0.21042
0.208876

0.207869
0.224429
0.219419
0.220067
0.210748
0.214328
0.221401
0.210706
0.20562
0.205443
scaling bp penalty by bp weight:
0.0214286
0.0214286
0.0214286
0.0857143
0.0857143
0.0428571
0.0857143
0.0214286
0.0857143
0.0214286
0.0857143
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0857143
0.0857143
0.128571
0.0214286
0.0214286
0.0214286
0.0857143
0.0857143
0.0857143
Greedy BPE
Scoring with scaled breakpoint penalty: 57342.8
1%..2%..3%..done
Working set size: 2650 Mb
Pagefile usage: 2166 Mb
Arrived at 258 intervals
Adding unaligned intervals
addUnalignedIntervals yields 693 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(13) has 1095 intervals
descendant 1(14) has 1 intervals
propagateDescendantBreakpoints yields 1350 intervals
Creating ancestral ordering
Previous anchoring score: 4.37453e+007, new anchor score: 3.56833e+009

Backing up alignment tree...

propagating ancestral breakpoints
recursive anchor search
0,0 have 3504 new matches outside LCBs
1,0 have 3592 new matches outside LCBs
2,0 have 2925 new matches outside LCBs
3,0 have 2997 new matches outside LCBs
4,0 have 3633 new matches outside LCBs
5,0 have 3346 new matches outside LCBs
6,0 have 3569 new matches outside LCBs
7,0 have 3825 new matches outside LCBs
8,0 have 3881 new matches outside LCBs
9,0 have 4278 new matches outside LCBs
10,0 have 4055 new matches outside LCBs
11,0 have 3007 new matches outside LCBs
12,0 have 3988 new matches outside LCBs
13,0 have 3991 new matches outside LCBs
14,0 have 3316 new matches outside LCBs
15,0 have 3553 new matches outside LCBs
16,0 have 3883 new matches outside LCBs
17,0 have 3886 new matches outside LCBs
18,0 have 3639 new matches outside LCBs
19,0 have 3701 new matches outside LCBs
20,0 have 3483 new matches outside LCBs
21,0 have 4841 new matches outside LCBs
22,0 have 3737 new matches outside LCBs
23,0 have 3928 new matches outside LCBs
24,0 have 3238 new matches outside LCBs
25,0 have 4109 new matches outside LCBs
26,0 have 3576 new matches outside LCBs
27,0 have 3798 new matches outside LCBs
28,0 have 3585 new matches outside LCBs
29,0 have 3580 new matches outside LCBs
0,0 has an additional 8868 matches
1,0 has an additional 9027 matches
2,0 has an additional 8144 matches
3,0 has an additional 8541 matches
4,0 has an additional 9175 matches
5,0 has an additional 8551 matches
6,0 has an additional 8667 matches
7,0 has an additional 8891 matches
8,0 has an additional 9178 matches
9,0 has an additional 9508 matches
10,0 has an additional 9315 matches
11,0 has an additional 8396 matches
12,0 has an additional 9597 matches
13,0 has an additional 9598 matches
14,0 has an additional 8808 matches
15,0 has an additional 9076 matches
16,0 has an additional 9462 matches
17,0 has an additional 9459 matches
18,0 has an additional 8745 matches
19,0 has an additional 8835 matches
20,0 has an additional 8652 matches
21,0 has an additional 10652 matches
22,0 has an additional 9353 matches
23,0 has an additional 9759 matches
24,0 has an additional 8314 matches
25,0 has an additional 9686 matches
26,0 has an additional 9236 matches

27,0 has an additional 9033 matches

28,0 has an additional 9035 matches
29,0 has an additional 9012 matches
Restoring backed up alignment tree...
9,27 has 8868 pairwise matches
19,27 has 9027 pairwise matches
30,27 has 8144 pairwise matches
29,27 has 8541 pairwise matches
12,27 has 9175 pairwise matches
21,27 has 8551 pairwise matches
11,27 has 8667 pairwise matches
1,27 has 8891 pairwise matches
5,27 has 9178 pairwise matches
10,27 has 9508 pairwise matches
6,27 has 9315 pairwise matches
4,27 has 8396 pairwise matches
7,27 has 9597 pairwise matches
8,27 has 9598 pairwise matches
17,27 has 8808 pairwise matches
0,27 has 9076 pairwise matches
15,27 has 9462 pairwise matches
16,27 has 9459 pairwise matches
2,27 has 8745 pairwise matches
13,27 has 8835 pairwise matches
14,27 has 8652 pairwise matches
22,27 has 10652 pairwise matches
20,27 has 9353 pairwise matches
25,27 has 9759 pairwise matches
28,27 has 8314 pairwise matches
18,27 has 9686 pairwise matches
26,27 has 9236 pairwise matches
3,27 has 9033 pairwise matches
23,27 has 9035 pairwise matches
24,27 has 9012 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 2673 Mb
Pagefile usage: 2237 Mb
construct LCB tracking matches
There are 29306 tracking matches
There are 1497321 / 1787666 components used
Working set size: 2702 Mb
Pagefile usage: 2263 Mb
init tracking match LCB tracking
Working set size: 2708 Mb
Pagefile usage: 2270 Mb
pairwise score tracking matches
Working set size: 2715 Mb
Pagefile usage: 2276 Mb
get pairwise LCBs
there are 175039 pairwise LCBs
Working set size: 2730 Mb
Pagefile usage: 2279 Mb
scaling bp penalty by conservation weight:
0.205179
0.228646
0.209714
0.209466
0.215562
0.211976
0.215442

0.218912
0.220993
0.220597
0.211523
0.204423
0.217683
0.217746
0.209334
0.208912
0.212248
0.212265
0.21042
0.208876
0.207869
0.224429
0.219419
0.220067
0.210748
0.214328
0.221401
0.210706
0.20562
0.205443
scaling bp penalty by bp weight:
0.0214286
0.0214286
0.0214286
0.0857143
0.0857143
0.0428571
0.0857143
0.0214286
0.0857143
0.0214286
0.0857143
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0857143
0.0857143
0.128571
0.0214286
0.0214286
0.0214286
0.0857143
0.0857143
0.0857143
Greedy BPE
Scoring with scaled breakpoint penalty: 57342.8
1%..2%..3%..4%..done

Working set size: 2732 Mb

Pagefile usage: 2270 Mb
Arrived at 235 intervals
Adding unaligned intervals
addUnalignedIntervals yields 622 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(13) has 1095 intervals
descendant 1(14) has 1 intervals
propagateDescendantBreakpoints yields 1326 intervals
Creating ancestral ordering
Previous anchoring score: 3.56833e+009, new anchor score: 3.73076e+009
Backing up alignment tree...
propagating ancestral breakpoints
recursive anchor search
0,0 have 2929 new matches outside LCBs
1,0 have 3456 new matches outside LCBs
2,0 have 2490 new matches outside LCBs
3,0 have 2833 new matches outside LCBs
4,0 have 3359 new matches outside LCBs
5,0 have 2892 new matches outside LCBs
6,0 have 3182 new matches outside LCBs
7,0 have 3361 new matches outside LCBs
8,0 have 3566 new matches outside LCBs
9,0 have 3897 new matches outside LCBs
10,0 have 3513 new matches outside LCBs
11,0 have 2606 new matches outside LCBs
12,0 have 3394 new matches outside LCBs
13,0 have 3394 new matches outside LCBs
14,0 have 2821 new matches outside LCBs
15,0 have 3038 new matches outside LCBs
16,0 have 3285 new matches outside LCBs
17,0 have 3286 new matches outside LCBs
18,0 have 3237 new matches outside LCBs
19,0 have 3376 new matches outside LCBs
20,0 have 3121 new matches outside LCBs
21,0 have 4542 new matches outside LCBs
22,0 have 3500 new matches outside LCBs
23,0 have 3731 new matches outside LCBs
24,0 have 2854 new matches outside LCBs
25,0 have 3628 new matches outside LCBs
26,0 have 3117 new matches outside LCBs
27,0 have 3629 new matches outside LCBs
28,0 have 3344 new matches outside LCBs
29,0 have 3331 new matches outside LCBs
0,0 has an additional 4810 matches
1,0 has an additional 5316 matches
2,0 has an additional 4143 matches
3,0 has an additional 4626 matches
4,0 has an additional 5266 matches
5,0 has an additional 4522 matches
6,0 has an additional 4761 matches
7,0 has an additional 4945 matches
8,0 has an additional 5239 matches
9,0 has an additional 5543 matches
10,0 has an additional 5243 matches
11,0 has an additional 4256 matches
12,0 has an additional 5146 matches
13,0 has an additional 5146 matches

14,0 has an additional 4547 matches

15,0 has an additional 4726 matches
16,0 has an additional 5153 matches
17,0 has an additional 5163 matches
18,0 has an additional 4889 matches
19,0 has an additional 5034 matches
20,0 has an additional 4771 matches
21,0 has an additional 6804 matches
22,0 has an additional 5592 matches
23,0 has an additional 5780 matches
24,0 has an additional 4450 matches
25,0 has an additional 5548 matches
26,0 has an additional 5296 matches
27,0 has an additional 5338 matches
28,0 has an additional 5283 matches
29,0 has an additional 5267 matches
Restoring backed up alignment tree...
9,27 has 4810 pairwise matches
19,27 has 5316 pairwise matches
30,27 has 4143 pairwise matches
29,27 has 4626 pairwise matches
12,27 has 5266 pairwise matches
21,27 has 4522 pairwise matches
11,27 has 4761 pairwise matches
1,27 has 4945 pairwise matches
5,27 has 5239 pairwise matches
10,27 has 5543 pairwise matches
6,27 has 5243 pairwise matches
4,27 has 4256 pairwise matches
7,27 has 5146 pairwise matches
8,27 has 5146 pairwise matches
17,27 has 4547 pairwise matches
0,27 has 4726 pairwise matches
15,27 has 5153 pairwise matches
16,27 has 5163 pairwise matches
2,27 has 4889 pairwise matches
13,27 has 5034 pairwise matches
14,27 has 4771 pairwise matches
22,27 has 6804 pairwise matches
20,27 has 5592 pairwise matches
25,27 has 5780 pairwise matches
28,27 has 4450 pairwise matches
18,27 has 5548 pairwise matches
26,27 has 5296 pairwise matches
3,27 has 5338 pairwise matches
23,27 has 5283 pairwise matches
24,27 has 5267 pairwise matches
Performing Sum-of-pairs Greedy Breakpoint Elimination
Working set size: 2582 Mb
Pagefile usage: 2118 Mb
construct LCB tracking matches
There are 26260 tracking matches
There are 1340915 / 1601860 components used
Working set size: 2617 Mb
Pagefile usage: 2151 Mb
init tracking match LCB tracking
Working set size: 2623 Mb
Pagefile usage: 2157 Mb
pairwise score tracking matches
Working set size: 2630 Mb

Pagefile usage: 2163 Mb

get pairwise LCBs
there are 62970 pairwise LCBs
Working set size: 2635 Mb
Pagefile usage: 2166 Mb
scaling bp penalty by conservation weight:
0.205179
0.228646
0.209714
0.209466
0.215562
0.211976
0.215442
0.218912
0.220993
0.220597
0.211523
0.204423
0.217683
0.217746
0.209334
0.208912
0.212248
0.212265
0.21042
0.208876
0.207869
0.224429
0.219419
0.220067
0.210748
0.214328
0.221401
0.210706
0.20562
0.205443
scaling bp penalty by bp weight:
0.0214286
0.0214286
0.0214286
0.0857143
0.0857143
0.0428571
0.0857143
0.0214286
0.0857143
0.0214286
0.0857143
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286
0.0214286

0.0857143
0.0857143
0.128571
0.0214286
0.0214286
0.0214286
0.0857143
0.0857143
0.0857143
Greedy BPE
Scoring with scaled breakpoint penalty: 57342.8
1%..2%..3%..4%..5%..6%..7%..done
Working set size: 2637 Mb
Pagefile usage: 2171 Mb
Arrived at 198 intervals
Adding unaligned intervals
addUnalignedIntervals yields 541 intervals
Merging unaligned intervals
Marbling gaps
Propagating descendant breakpoints
descendant 0(13) has 1095 intervals
descendant 1(14) has 1 intervals
propagateDescendantBreakpoints yields 1287 intervals
Creating ancestral ordering
Previous anchoring score: 3.73076e+009, new anchor score: 3.74715e+009
Working set size: 2635 Mb
Pagefile usage: 2177 Mb
propagating ancestral breakpoints
Working set size: 2635 Mb
Pagefile usage: 2177 Mb
performing a gapped alignment
0%..
22%..23%..24%..25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..47%..48%..49%..
50%..51%..52%..53%..54%..55%..56%..57%..58%..59%..
60%..61%..62%..63%..64%..65%..66%..67%..68%..69%..
70%..71%..72%..73%..74%..75%..76%..77%..78%..79%..
80%..81%..82%..83%..84%..85%..86%..87%..88%..89%..
90%..91%..92%..93%..94%..95%..96%..97%..98%..99%..
100%..Working set size: 2747 Mb
Pagefile usage: 2257 Mb
Fix left ends
Working set size: 2747 Mb
Pagefile usage: 2257 Mb
done.
Working set size: 2747 Mb
Pagefile usage: 2257 Mb
Performing final pass iterative refinement
0%..
25%..26%..27%..28%..29%..
30%..31%..32%..33%..34%..35%..36%..37%..38%..39%..
40%..41%..42%..43%..44%..45%..46%..47%..48%..49%..
50%..51%..52%..53%..54%..55%..56%..57%..58%..59%..
60%..61%..62%..63%..64%..65%..66%..67%..68%..69%..
70%..71%..72%..73%..74%..75%..76%..77%..78%..79%..

80%..81%..82%..83%..84%..85%..86%..87%..88%..89%..
90%..91%..92%..93%..94%..95%..96%..97%..98%..99%..
100%..Working set size: 2685 Mb
Pagefile usage: 2193 Mb
Fix left ends
Working set size: 2685 Mb
Pagefile usage: 2193 Mb
done.
root alignment has 1326 superintervals
root alignment length: 5684374
Organisms have 32.8% GC
Completed without error.