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Alignment Reference
Insertion into Query
Insertion into Reference
Collapse Query
Collapse Query
w/ Insertion
Collapse Query
A
A
Inversion
Rearrangement
w/ Disagreement
Collapse Reference
Collapse Reference w/Insertion
Collapse Reference
R
R
B
R
B
R
R
A
R
B
I
R
A
R
B
A
R
B
A
B
A
R
B
R
A
I
B
A
B
C
A
R
R
R
B
C
B'
A
R
R
A
B
A
R
I
R
B
A
R
R
B
A
I
B
R
A
B
R
A
B
A
B
R: AIB
Q: AB
R: ARRB
Q: ARB
R: ARIRB
Q: ARB
Exact tandem alignment if I=R
R: ARRRB
Q: ARRB
R: ABC
Q: AB'C
R: AB
Q: AIB
R: ARB
Q: ARRB
R: ARB
Q: ARIRB
Exact tandem alignment if I=R
R: ARRB
Q: ARRRB
R: ABCDE
Q: AFCBE
Michael Schatz mschatz [a t] umiacs.umd.edu
A
B
C
D
E
C
F
A
B
E