Alignment Reference

Insertion into Reference

Insertion into Query

R: AB
Q: AIB

A
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B

R: ARB
Q: ARRB

A R

A R

A R B
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w/Insertion

w/ Insertion

Exact tandem
alignment if I=R

R: ARB
Q: ARIRB

A R

R: ARIRB
Q: ARB

A R I

R B

A R R

R: ARRB
Q: ARB

R B

Exact tandem
alignment if I=R

A R

R: AIB
Q: AB

A R

R: ARRB
Q: ARRRB

A R R R

Rearrangement

Inversion

w/ Disagreement

A B' C

R: ABC
Q: AB'C

A R R

R: ABCDE
Q: AFCBE

A B C

A F C B E

R: ARRRB
Q: ARRB

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A R R B

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R R B

A R B

A B C D

Michael Schatz mschatz [a t] umiacs.umd.edu