TestDecription.txt

* Test #1
The for alignment with large deletion and micro insersion. Mismatches and
small deletions are present in each flanking sequence.

MATCH = 1, MISMATCH = -2, GAP OPEN = -2, GAP EXTEND = -1, INDEL

First  seq [1,2399] =>      2399 nucs 'seq1'
Second seq [1, 253] =>       253 nucs 'seq2'

Score:         177
Aligned:       201        nucs
Identic:       192 ( 96%) nucs =>        99 ( 99%)        93 ( 92%)
Gaps:            5 (  2%) nucs

Alignment:
 first  seq =>  [1, 99] EXCISED REGION [2299,2399]
 second seq =>  [1,100] EXCISED REGION [ 150, 246]

EXCISED REGION(S):
 first  seq =>      2199 nucs [100,2298]
 second seq =>        49 nucs [101,149]

Identity at breakpoints: 
 first  seq =>         0 nucs
 second seq =>         0 nucs
Identity outside breakpoints: 
 first  seq =>         0 nucs
 second seq =>         0 nucs
Identity inside breakpoints: 
 first  seq =>         3 nucs [100,102] to [2296,2298]
 second seq =>         0 nucs

        1 AGCCCCTCTTCTGAGGGGAGGGGGGACACTCAGCCCCGTTTTACCCC-CCCTGCCCTGCG 59
          ||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||
        1 AGCCCCTCTTCTGAGGGGAGGGGGGACACTCAGCCCCGTTTTACCCCTCCCTGCCCTGCG 60

       60 GGGGTGGGCTGAGCACGGAGGGTGGGCAGAGGAACAGAGG 99
          ||||||||||||||||||||||||||||||||||||||||
       61 GGGGTGGGCTGAGCACGGAGGGTGGGCAGAGGAACAGAGG 100

EXCISED REGION

     2299 AGTGCCTGTGTCTGGTGGGGGCCACTCAGGAGAGTTGGGTTTTCAGGGCAGAGATGGGCT 2358
          ||||||||||||||||||||||||||||||||||||||||||||||||||...|||||||
      150 AGTGCCTGTGTCTGGTGGGGGCCACTCAGGAGAGTTGGGTTTTCAGGGCACTCATGGGCT 209

     2359 TGATTCCACCTGGTGGGGTGGGTGGACCCTGGAGACTCTCA 2399
          |||||||    |||||||||||||||||||||||||||.||
      210 TGATTCC----GGTGGGGTGGGTGGACCCTGGAGACTCUCA 246

* Test #2
The for alignment with same size deletion and insersion.

MATCH = 1, MISMATCH = -2, GAP OPEN = -2, GAP EXTEND = -1, INDEL

First  seq [1,38] =>        38 nucs 'seq1'
Second seq [1,36] =>        36 nucs 'seq2'

Score:          27
Aligned:        32        nucs
Identic:        30 ( 94%) nucs =>         7 (100%)        23 ( 92%)
Gaps:            2 (  6%) nucs

Alignment:
 first  seq =>  [1,7] EXCISED REGION [14,38]
 second seq =>  [1,7] EXCISED REGION [14,36]

EXCISED REGION(S):
 first  seq =>         6 nucs [8,13]
 second seq =>         6 nucs [8,13]

Identity at breakpoints: 
 first  seq =>         0 nucs
 second seq =>         0 nucs
Identity outside breakpoints: 
 first  seq =>         1 nucs [7,7] to [14,14]
 second seq =>         1 nucs [7,7] to [14,14]
Identity inside breakpoints: 
 first  seq =>         3 nucs [8,10] to [11,13]
 second seq =>         3 nucs [8,10] to [11,13]

        1 AGCCGGA 7
          |||||||
        1 AGCCGGA 7

EXCISED REGION

       14 ACACTCAGCCCCGTTTTACCCCTCC 38
          ||||||||||||||||  |||||||
       14 ACACTCAGCCCCGTTT--CCCCTCC 36

* Test #3
The for alignment with large deletion, insersion and microhomology around
breakpoints.

MATCH = 1, MISMATCH = -2, GAP OPEN = -2, GAP EXTEND = -1, INDEL

First  seq [1,62] =>        62 nucs 'seq1'
Second seq [1,50] =>        50 nucs 'seq2'

Score:          46
Aligned:        49        nucs
Identic:        48 ( 98%) nucs =>        14 (100%)        34 ( 97%)
Gaps:            1 (  2%) nucs

Alignment:
 first  seq =>  [1,14] EXCISED REGION [28,62]
 second seq =>  [1,14] EXCISED REGION [17,50]

EXCISED REGION(S):
 first  seq =>        13 nucs [15,27]
 second seq =>         2 nucs [15,16]

Identity at breakpoints: 
 first  seq =>         2 nucs [15,16] to [28,29]
 second seq =>         0 nucs
Identity outside breakpoints: 
 first  seq =>         0 nucs
 second seq =>         0 nucs
Identity inside breakpoints: 
 first  seq =>         0 nucs
 second seq =>         1 nucs [15,15] to [16,16]

        1 TCTCTCTCAGCCGG 14
          ||||||||||||||
        1 TCTCTCTCAGCCGG 14

EXCISED REGION

       28 AGCCCCGTTTTACCCCTCCACTGGACCAAAAAAAA 62
          |||||||||||| ||||||||||||||||||||||
       17 AGCCCCGTTTTA-CCCTCCACTGGACCAAAAAAAA 50

* Test #4
Another test for homology around breakpoints.

MATCH = 1, MISMATCH = -2, GAP OPEN = -2, GAP EXTEND = -1, INDEL

First  seq [1,53] =>        53 nucs 'seq1'
Second seq [1,42] =>        42 nucs 'seq2'

Score:          36
Aligned:        42        nucs
Identic:        40 ( 95%) nucs =>        11 (100%)        29 ( 94%)
Gaps:            1 (  2%) nucs

Alignment:
 first  seq =>  [1,11] EXCISED REGION [23,53]
 second seq =>  [1,11] EXCISED REGION [13,42]

EXCISED REGION(S):
 first  seq =>        11 nucs [12,22]
 second seq =>         1 nucs [12,12]

Identity at breakpoints: 
 first  seq =>         6 nucs [9,14] to [20,25]
 second seq =>         0 nucs
Identity outside breakpoints: 
 first  seq =>         0 nucs
 second seq =>         0 nucs
Identity inside breakpoints: 
 first  seq =>         0 nucs
 second seq =>         0 nucs

        1 CTGTCTCCTGG 11
          |||||||||||
        1 CTGTCTCCTGG 11

EXCISED REGION

       23 AGGTGCCCCTCCACACCCTCTTGATCTTCCC 53
          |||||||||| ||||||||||||||.|||||
       13 AGGTGCCCCT-CACACCCTCTTGATTTTCCC 42

* Test #5
Test for microhomology inside and outside breakpoints.

MATCH = 1, MISMATCH = -2, GAP OPEN = -2, GAP EXTEND = -1, INDEL

First  seq [1,20] =>        20 nucs 'seq1'
Second seq [1,11] =>        11 nucs 'seq2'

Score:          11
Aligned:        11        nucs
Identic:        11 (100%) nucs =>         5 (100%)         6 (100%)
Gaps:            0 (  0%) nucs

Alignment:
 first  seq =>  [2,6] EXCISED REGION [14,19]
 second seq =>  [1,5] EXCISED REGION [ 6,11]

EXCISED REGION(S):
 first  seq =>         7 nucs [7,13]
 second seq =>         0 nucs

Identity at breakpoints: 
 first  seq =>         0 nucs
 second seq =>         0 nucs
Identity outside breakpoints: 
 first  seq =>         4 nucs [3,6] to [14,17]
 second seq =>         4 nucs [2,5] to [6,9]
Identity inside breakpoints: 
 first  seq =>         3 nucs [7,9] to [11,13]
 second seq =>         0 nucs

        2 CACTG 6
          |||||
        1 CACTG 5

EXCISED REGION

       14 ACTGAT 19
          ||||||
        6 ACTGAT 11

* Test #6
Test for an alternative alignment. There is a 2 bp homology at breakpoints.
Alternative breakpoint should be shifted by 2 bp.

MATCH = 1, MISMATCH = -2, GAP OPEN = -2, GAP EXTEND = -1, INDEL

First  seq [1,10] =>        10 nucs 'seq1'
Second seq [1, 6] =>         6 nucs 'seq2'

Score:           6
Aligned:         6        nucs
Identic:         6 (100%) nucs =>         3 (100%)         3 (100%)
Gaps:            0 (  0%) nucs

Alignment:
 first  seq =>  [1,3] EXCISED REGION [8,10]
 second seq =>  [1,3] EXCISED REGION [4, 6]

EXCISED REGION(S):
 first  seq =>         4 nucs [4,7]
 second seq =>         0 nucs
ALTERNATIVE REGION(S):
 first  seq =>         4 nucs [6,9]
 second seq =>         0 nucs

Identity at breakpoints: 
 first  seq =>         2 nucs [4,5] to [8,9]
 second seq =>         0 nucs
Identity outside breakpoints: 
 first  seq =>         1 nucs [3,3] to [8,8]
 second seq =>         1 nucs [3,3] to [4,4]
Identity inside breakpoints: 
 first  seq =>         0 nucs
 second seq =>         0 nucs

        1 GTA 3
          |||
        1 GTA 3

EXCISED REGION

        8 ACT 10
          |||
        4 ACT 6

* Test #7
Test for an alternative alignment. Right flanking sequence aligns at a
different place.

MATCH = 1, MISMATCH = -2, GAP OPEN = -2, GAP EXTEND = -1, INDEL

First  seq [1,12] =>        12 nucs 'seq1'
Second seq [1, 6] =>         6 nucs 'seq2'

Score:           6
Aligned:         6        nucs
Identic:         6 (100%) nucs =>         3 (100%)         3 (100%)
Gaps:            0 (  0%) nucs

Alignment:
 first  seq =>  [1,3] EXCISED REGION [7,9]
 second seq =>  [1,3] EXCISED REGION [4,6]

EXCISED REGION(S):
 first  seq =>         3 nucs [4,6]
 second seq =>         0 nucs
ALTERNATIVE REGION(S):
 first  seq =>         6 nucs [4,9]
 second seq =>         0 nucs

Identity at breakpoints: 
 first  seq =>         0 nucs
 second seq =>         0 nucs
Identity outside breakpoints: 
 first  seq =>         1 nucs [3,3] to [7,7]
 second seq =>         1 nucs [3,3] to [4,4]
Identity inside breakpoints: 
 first  seq =>         1 nucs [4,4] to [6,6]
 second seq =>         0 nucs

        1 GTA 3
          |||
        1 GTA 3

EXCISED REGION

        7 ACT 9
          |||
        4 ACT 6

* Test #8
Test for an alignment of reverse complement (second sequence).

MATCH = 1, MISMATCH = -2, GAP OPEN = -2, GAP EXTEND = -1, INDEL

First  seq [ 1,40] =>        40 nucs 'seq1'
Second seq [45, 1] =>        45 nucs 'seq2'

Score:          32
Aligned:        35        nucs
Identic:        34 ( 97%) nucs =>         8 (100%)        26 ( 96%)
Gaps:            1 (  3%) nucs

Alignment:
 first  seq =>  [ 1, 8] EXCISED REGION [15,40]
 second seq =>  [45,38] EXCISED REGION [27, 1]

EXCISED REGION(S):
 first  seq =>         6 nucs [9,14]
 second seq =>        10 nucs [37,28]

Identity at breakpoints: 
 first  seq =>         0 nucs
 second seq =>         4 nucs [39,36] to [29,26]
Identity outside breakpoints: 
 first  seq =>         2 nucs [7,8] to [15,16]
 second seq =>         2 nucs [39,38] to [27,26]
Identity inside breakpoints: 
 first  seq =>         3 nucs [9,11] to [12,14]
 second seq =>         5 nucs [37,33] to [32,28]

        1 AGCCGGAG 8
          ||||||||
       45 AGCCGGAG 38

EXCISED REGION

       15 AGACACTCAGCCCC-TTTTACCCCTCC 40
          |||||||||||||| ||||||||||||
       27 AGACACTCAGCCCCGTTTTACCCCTCC 1


* Test #9
Test for alignment with many indels/mismatches in flanking sequences.

MATCH = 1, MISMATCH = -2, GAP OPEN = -2, GAP EXTEND = -1, INDEL

First  seq [1,259] =>       259 nucs 'seq1'
Second seq [1,188] =>       188 nucs 'seq2'

Score:         169
Aligned:       199        nucs
Identic:       186 ( 93%) nucs =>       126 ( 91%)        60 (100%)
Gaps:           11 (  6%) nucs

Alignment:
 first  seq =>  [1,139] EXCISED REGION [200,259]
 second seq =>  [1,128] EXCISED REGION [129,188]

EXCISED REGION(S):
 first  seq =>        60 nucs [140,199]
 second seq =>         0 nucs
ALTERNATIVE REGION(S):
 first  seq =>        60 nucs [141,200]
 second seq =>         0 nucs

Identity at breakpoints: 
 first  seq =>         1 nucs [140,140] to [200,200]
 second seq =>         0 nucs
Identity outside breakpoints: 
 first  seq =>         0 nucs
 second seq =>         0 nucs
Identity inside breakpoints: 
 first  seq =>         0 nucs
 second seq =>         0 nucs

        1 ACTGCAATCTCTGCCTCCCAGGTTCAAGCAATTCTCCTACCTCAGCCTCCTGAGTAGCTG 60
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
        1 ACTGCAATCTCTGCCTCCCAGGTTCAAGCAATTCTCCTACCTCAGCCTCCTGAGTAGCTG 60

       61 AATGGTCAACTGGTCAGGGtaaaacctatgtaatgatgatgaattacatttttgatatgc 120
          |        |||||||   |||||||||||||||.|.|||||||||||||||||||||||
       61 A--------CTGGTCA---TAAAACCTATGTAATCACGATGAATTACATTTTTGATATGC 109

      121 tgatggatttggtttgcta 139
          |||||||||||||||||||
      110 TGATGGATTTGGTTTGCTA 128

EXCISED REGION

      200 gttgtttccttgctagattttagtgtcaggatgatactggttttgtagaatgagttagag 259
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
      129 GTTGTTTCCTTGCTAGATTTTAGTGTCAGGATGATACTGGTTTTGTAGAATGAGTTAGAG 188

* Test #10
Test for inversion.

MATCH = 1, MISMATCH = -2, GAP OPEN = -2, GAP EXTEND = -1, INVERSION

First  seq [1,9] =>         9 nucs 'seq1'
Second seq [1,8] =>         8 nucs 'seq2'

Score:           8
Aligned:         8        nucs
Identic:         8 (100%) nucs =>         4 (100%)         4 (100%)
Gaps:            0 (  0%) nucs

Alignment:
 first  seq =>  [2,5] EXCISED REGION [9,6]
 second seq =>  [1,4] EXCISED REGION [5,8]

EXCISED REGION(S):
 first  seq =>         4 nucs [6,9]
 second seq =>         0 nucs

Identity at breakpoints: 
 first  seq =>         0 nucs
 second seq =>         0 nucs
Identity outside breakpoints: 
 first  seq =>         0 nucs
 second seq =>         2 nucs [3,4] to [5,6]
Identity inside breakpoints: 
 first  seq =>         0 nucs
 second seq =>         0 nucs

        2 ACTG 5
          ||||
        1 ACTG 4

EXCISED REGION

        9 TGAC 6
          ||||
        5 TGAC 8

* Test #11
Test for inversion.

MATCH = 1, MISMATCH = -2, GAP OPEN = -2, GAP EXTEND = -1, INVERSION

First  seq [1,250] =>       250 nucs 'seq1'
Second seq [1, 86] =>        86 nucs 'seq2'

Score:          78
Aligned:        87        nucs
Identic:        84 ( 97%) nucs =>        48 ( 96%)        36 ( 97%)
Gaps:            1 (  1%) nucs

Alignment:
 first  seq =>  [1,50] EXCISED REGION [150,114]
 second seq =>  [1,49] EXCISED REGION [ 50, 86]

EXCISED REGION(S):
 first  seq =>       100 nucs [51,150]
 second seq =>         0 nucs

Identity at breakpoints: 
 first  seq =>         4 nucs [47,50] to [147,150]
 second seq =>         0 nucs
Identity outside breakpoints: 
 first  seq =>         0 nucs
 second seq =>         0 nucs
Identity inside breakpoints: 
 first  seq =>         0 nucs
 second seq =>         0 nucs

        1 AGCCCCTCTTCTGAGGGGAGGGGGGACACTCAGCCCCGTTTTACCCCTAA 50
          ||||||||.|||||||| ||||||||||||||||||||||||||||||||
        1 AGCCCCTCATCTGAGGG-AGGGGGGACACTCAGCCCCGTTTTACCCCTAA 49

EXCISED REGION

      150 TTAGTTTCTTGCTACTGGGAACCCACGTGCATGTCAC 114
          |||||||||||||||.|||||||||||||||||||||
       50 TTAGTTTCTTGCTACGGGGAACCCACGTGCATGTCAC 86

* Test #12
Test to demonstrate that linear pass to find optimal split between two local
alignments won't find correct alginment. This case is put in the paper.

MATCH = 1, MISMATCH = -2, GAP OPEN = -4, GAP EXTEND = -2, INDEL

First  seq [1,29] =>        29 nucs 'seq1'
Second seq [1,47] =>        47 nucs 'seq2'

Score:          26
Aligned:        29        nucs
Identic:        28 ( 97%) nucs =>        12 (100%)        16 ( 94%)
Gaps:            0 (  0%) nucs

Alignment:
 first  seq =>  [1,12] EXCISED REGION [13,29]
 second seq =>  [1,12] EXCISED REGION [31,47]

EXCISED REGION(S):
 first  seq =>         0 nucs
 second seq =>        18 nucs [13,30]

Identity at breakpoints: 
 first  seq =>         0 nucs
 second seq =>         0 nucs
Identity outside breakpoints: 
 first  seq =>         0 nucs
 second seq =>         0 nucs
Identity inside breakpoints: 
 first  seq =>         0 nucs
 second seq =>         0 nucs

        1 GACAGTCGACCT 12
          ||||||||||||
        1 GACAGTCGACCT 12

EXCISED REGION

       13 AAAAAAACTGGTCGGCA 29
          |||||.|||||||||||
       31 AAAAAGACTGGTCGGCA 47

* Test #13
Test for tandem duplication.

MATCH = 1, MISMATCH = -2, GAP OPEN = -2, GAP EXTEND = -1, TDUPLICATION

First  seq [1,289] =>       289 nucs 'seq1'
Second seq [1,104] =>       104 nucs 'seq2'

Score:          89
Aligned:       100        nucs
Identic:        96 ( 96%) nucs =>        48 ( 96%)        48 ( 96%)
Gaps:            3 (  3%) nucs

Alignment:
 first  seq =>  [173,222] EXCISED REGION [25, 72]
 second seq =>  [  1, 49] EXCISED REGION [55,104]

EXCISED REGION(S):
 first  seq =>       198 nucs [25,222]
 second seq =>         5 nucs [50,54]

Identity at breakpoints: 
 first  seq =>         4 nucs [25,28] to [223,226]
 second seq =>         0 nucs
Identity outside breakpoints: 
 first  seq =>         3 nucs [22,24] to [223,225]
 second seq =>         2 nucs [48,49] to [55,56]
Identity inside breakpoints: 
 first  seq =>         2 nucs [25,26] to [221,222]
 second seq =>         2 nucs [50,51] to [53,54]

      173 CTGCGCCTGGGGCACACACATGTGGCTTCCGCTTTCCAGAGCTCTACCAG 222
          ||||||||||| ||||||||||||.|||||||||||||||||||||||||
        1 CTGCGCCTGGG-CACACACATGTGACTTCCGCTTTCCAGAGCTCTACCAG 49

EXCISED REGION

       25 AGCTCCTCTTCTGAGGGGAC--GGGACACTCAGCCCCGTTTTACCCCCCG 72
          ||||||||||||||||||||  ||||||||||||||||||||||||||||
       55 AGCTCCTCTTCTGAGGGGACGGGGGACACTCAGCCCCGTTTTACCCCCCG 104

* Test #14
Inversion with conting over left breakpoint.

MATCH = 1, MISMATCH = -2, GAP OPEN = -2, GAP EXTEND = -1, INVERSION

First  seq [1,289] =>       289 nucs 'seq1'
Second seq [1, 74] =>        74 nucs 'seq2'

Score:          68
Aligned:        74        nucs
Identic:        72 ( 97%) nucs =>        23 ( 96%)        49 ( 98%)
Gaps:            1 (  1%) nucs

Alignment:
 first  seq =>  [1,23] EXCISED REGION [223,174]
 second seq =>  [1,24] EXCISED REGION [ 25, 74]

EXCISED REGION(S):
 first  seq =>       200 nucs [24,223]
 second seq =>         0 nucs

Identity at breakpoints: 
 first  seq =>         4 nucs [24,27] to [224,227]
 second seq =>         0 nucs
Identity outside breakpoints: 
 first  seq =>         3 nucs [21,23] to [224,226]
 second seq =>         1 nucs [24,24] to [25,25]
Identity inside breakpoints: 
 first  seq =>         2 nucs [24,25] to [222,223]
 second seq =>         0 nucs

        1 AGATGGGCTT-ATTCTTGATTAGC 23
          |||||||||| |||||||||||||
        1 AGATGGGCTTGATTCTTGATTAGC 24

EXCISED REGION

      223 CTGGTAGAGCTCTGGAAAGCGGAAGCCACATGTGTGTGCCCCAGGCGCAG 174
          |||||||||||||||||||.||||||||||||||||||||||||||||||
       25 CTGGTAGAGCTCTGGAAAGGGGAAGCCACATGTGTGTGCCCCAGGCGCAG 74

* Test #15
Inversion with conting over right breakpoint.

MATCH = 1, MISMATCH = -2, GAP OPEN = -2, GAP EXTEND = -1, INVERSION

First  seq [1,288] =>       288 nucs 'seq1'
Second seq [1, 99] =>        99 nucs 'seq2'

Score:          88
Aligned:        99        nucs
Identic:        95 ( 96%) nucs =>        49 ( 98%)        46 ( 94%)
Gaps:            2 (  2%) nucs

Alignment:
 first  seq =>  [74,25] EXCISED REGION [225,271]
 second seq =>  [ 1,50] EXCISED REGION [ 51, 99]

EXCISED REGION(S):
 first  seq =>       200 nucs [25,224]
 second seq =>         0 nucs

Identity at breakpoints: 
 first  seq =>         4 nucs [25,28] to [225,228]
 second seq =>         0 nucs
Identity outside breakpoints: 
 first  seq =>         3 nucs [22,24] to [225,227]
 second seq =>         4 nucs [47,50] to [51,54]
Identity inside breakpoints: 
 first  seq =>         2 nucs [25,26] to [223,224]
 second seq =>         0 nucs

       74 CGGGGGGTAAAACGGGGCTGAGTGTCCCCCGTCCCCTCATAAGAGGAGCT 25
          |||||||||||||||||||||||||||||||||||||||.||||||||||
        1 CGGGGGGTAAAACGGGGCTGAGTGTCCCCCGTCCCCTCAGAAGAGGAGCT 50

EXCISED REGION

      225 AGCTAGAGC--GCAGCTTACAAGGAGCTAGGCTTCAAGCGGTGACTGGG 271
          |||||||||  |||||||||||||||||||||||||||||||||.||||
       51 AGCTAGAGCAAGCAGCTTACAAGGAGCTAGGCTTCAAGCGGTGAGTGGG 99