Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 76 of 216
Found at i:23209512 original size:32 final size:32
Alignment explanation
Indices: 23209462--23209708 Score: 173
Period size: 32 Copynumber: 7.7 Consensus size: 32
23209452 TACAATAATG
* **
23209462 TGATTGGCACA-AAGCCATCAGTAGTAGTGATA
1 TGATCGGCACACAA-CCATCAGTAACAGTGATA
* * * *
23209494 TGACCGGCACACAACCATCAGTAACGGTAACA
1 TGATCGGCACACAACCATCAGTAACAGTGATA
* * *
23209526 TGATCGGTA-AAAAGCCATCAGTAGCAGTGATA
1 TGATCGGCACACAA-CCATCAGTAACAGTGATA
* ** * *
23209558 TGATCGGTACACAGTCATCATTAACAGTGAAA
1 TGATCGGCACACAACCATCAGTAACAGTGATA
* ** *
23209590 TGATCGGCACACAACCATCGGTAATGGTAATA
1 TGATCGGCACACAACCATCAGTAACAGTGATA
* *
23209622 TGATCGGTACAAAACCATCAGTAACAGT-ACTA
1 TGATCGGCACACAACCATCAGTAACAGTGA-TA
* * *
23209654 TGATTGGCATA-AAGCCATCAGTAACGGT-ACTA
1 TGATCGGCACACAA-CCATCAGTAACAGTGA-TA
*
23209686 TGACCGGCACA-AAGCCATCAGTA
1 TGATCGGCACACAA-CCATCAGTA
23209709 GCATCGCAGT
Statistics
Matches: 169, Mismatches: 41, Indels: 10
0.77 0.19 0.05
Matches are distributed among these distances:
31 6 0.04
32 159 0.94
33 4 0.02
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (32 bp):
TGATCGGCACACAACCATCAGTAACAGTGATA
Found at i:23209642 original size:253 final size:254
Alignment explanation
Indices: 23209170--23209676 Score: 748
Period size: 253 Copynumber: 2.0 Consensus size: 254
23209160 TAGCTATAAG
* *
23209170 CTATAAACAGAATGGTTACAAGCCATAAGTACAATAATGTGATTGGCACAAAGCCATTAGTAGCA
1 CTATAAACAGAATGGCTACAAGCCATAAGTACAATAATGTGATTGGCACAAAGCCATCAGTAGCA
* *
23209235 GCGATATGACTGGCACACAACCATCAGTAACGGTAACATGAACGACATAAAGCCATCAGTAACGA
66 GCGATATGACCGGCACACAACCATCAGTAACGGTAACATGAACGACAAAAAGCCATCAGTAACGA
* * * *
23209300 TAACATGATCGGCATAAAGCCATCAGTAATAGTGAAATGATCGGCACATAGCCATCGGTAACGGT
131 TAACATGATCGGCACAAAGCCATCAGTAACAGTGAAATGATCGGCACACAACCATCGGTAACGGT
* *
23209365 AATATGATTGACACAAAGCCATCAGTAACAGTACTATGATCGACATAAAGCCATCAGTA
196 AATATGATCGACACAAAACCATCAGTAACAGTACTATGATCGACATAAAGCCATCAGTA
*
23209424 CTATAAACAGAATGGCTACAA-CCATAAGTACAATAATGTGATTGGCACAAAGCCATCAGTAGTA
1 CTATAAACAGAATGGCTACAAGCCATAAGTACAATAATGTGATTGGCACAAAGCCATCAGTAGCA
* * ** *
23209488 GTGATATGACCGGCACACAACCATCAGTAACGGTAACATGATCGGTAAAAAGCCATCAGTAGC-A
66 GCGATATGACCGGCACACAACCATCAGTAACGGTAACATGAACGACAAAAAGCCATCAGTAACGA
* * * * * * *
23209552 GTGATATGATCGGTACACAGTCATCATTAACAGTGAAATGATCGGCACACAACCATCGGTAATGG
131 -TAACATGATCGGCACAAAGCCATCAGTAACAGTGAAATGATCGGCACACAACCATCGGTAACGG
** * *
23209617 TAATATGATCGGTACAAAACCATCAGTAACAGTACTATGATTGGCATAAAGCCATCAGTA
195 TAATATGATCGACACAAAACCATCAGTAACAGTACTATGATCGACATAAAGCCATCAGTA
23209677 ACGGTACTAT
Statistics
Matches: 225, Mismatches: 27, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
252 1 0.00
253 204 0.91
254 20 0.09
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.21
Consensus pattern (254 bp):
CTATAAACAGAATGGCTACAAGCCATAAGTACAATAATGTGATTGGCACAAAGCCATCAGTAGCA
GCGATATGACCGGCACACAACCATCAGTAACGGTAACATGAACGACAAAAAGCCATCAGTAACGA
TAACATGATCGGCACAAAGCCATCAGTAACAGTGAAATGATCGGCACACAACCATCGGTAACGGT
AATATGATCGACACAAAACCATCAGTAACAGTACTATGATCGACATAAAGCCATCAGTA
Found at i:23209673 original size:96 final size:96
Alignment explanation
Indices: 23209462--23209708 Score: 286
Period size: 96 Copynumber: 2.6 Consensus size: 96
23209452 TACAATAATG
** *
23209462 TGATTGGCACAAAGCCATCAGTAGTAGTGATATGACCGGCACACAACCATCAGTAACGGTAACAT
1 TGATTGGCACAAAGCCATCAGTAACAGTGAAATGACCGGCACACAACCATCAGTAACGGTAACAT
*
23209527 GATCGGTAAAAAGCCATCAGTAGCAGTGATA
66 GATCGGTAAAAAGCCATCAGTAACAGTGATA
* * * * * * * * *
23209558 TGATCGGTACACAGTCATCATTAACAGTGAAATGATCGGCACACAACCATCGGTAATGGTAATAT
1 TGATTGGCACAAAGCCATCAGTAACAGTGAAATGACCGGCACACAACCATCAGTAACGGTAACAT
23209623 GATCGGTACAAAA-CCATCAGTAACAGT-ACTA
66 GATCGGTA-AAAAGCCATCAGTAACAGTGA-TA
* * *
23209654 TGATTGGCATAAAGCCATCAGTAACGGT-ACTATGACCGGCACA-AAGCCATCAGTA
1 TGATTGGCACAAAGCCATCAGTAACAGTGA-AATGACCGGCACACAA-CCATCAGTA
23209709 GCATCGCAGT
Statistics
Matches: 124, Mismatches: 23, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
95 4 0.03
96 116 0.94
97 4 0.03
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (96 bp):
TGATTGGCACAAAGCCATCAGTAACAGTGAAATGACCGGCACACAACCATCAGTAACGGTAACAT
GATCGGTAAAAAGCCATCAGTAACAGTGATA
Found at i:23209913 original size:24 final size:23
Alignment explanation
Indices: 23209879--23209961 Score: 85
Period size: 24 Copynumber: 3.5 Consensus size: 23
23209869 GCCATGCTCA
23209879 AAATCAGTCATTCAAATCACAGAC
1 AAATCAGTCATTCAAA-CACAGAC
* * *
23209903 AAATCATTCATACCAGACACAGAC
1 AAATCAGTCAT-TCAAACACAGAC
* *
23209927 AAATCAGTCATTTAACCACAGAC
1 AAATCAGTCATTCAAACACAGAC
* *
23209950 AAAACAATCATT
1 AAATCAGTCATT
23209962 TGACCTCGAG
Statistics
Matches: 48, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
23 18 0.38
24 27 0.56
25 3 0.06
ACGTcount: A:0.47, C:0.25, G:0.07, T:0.20
Consensus pattern (23 bp):
AAATCAGTCATTCAAACACAGAC
Found at i:23210040 original size:27 final size:27
Alignment explanation
Indices: 23210009--23210287 Score: 265
Period size: 27 Copynumber: 10.4 Consensus size: 27
23209999 GGCATTACAA
23210009 TCATTTTACCCTACAGGGGTATTATGG
1 TCATTTTACCCTACAGGGGTATTATGG
* * * *
23210036 TCATTTTACCCTACAAGGGCATTACGA
1 TCATTTTACCCTACAGGGGTATTATGG
* *
23210063 TCATTTTACCCTACATGGGTATT-TAG
1 TCATTTTACCCTACAGGGGTATTATGG
* *
23210089 TCATTTTACCCTACAGGGGCATTATAG
1 TCATTTTACCCTACAGGGGTATTATGG
* * ***
23210116 TCATTTTACTCTACAGGGGCATTACAA
1 TCATTTTACCCTACAGGGGTATTATGG
* *
23210143 TCAGTTTACCCTACAGGGGTATTACGG
1 TCATTTTACCCTACAGGGGTATTATGG
* * * * *
23210170 TTATTTTACCCTATAAGGGCATTATAG
1 TCATTTTACCCTACAGGGGTATTATGG
* * *
23210197 TCATTTCACCCTACAAGGGTATTACGG
1 TCATTTTACCCTACAGGGGTATTATGG
* * * *
23210224 TCATTTTACCTTATAAGGGTATTTTGG
1 TCATTTTACCCTACAGGGGTATTATGG
* * * *
23210251 T-ATTCTACCCTACGGGGGTATTTTGA
1 TCATTTTACCCTACAGGGGTATTATGG
23210277 TCATTTTACCC
1 TCATTTTACCC
23210288 ATAAAGGATA
Statistics
Matches: 206, Mismatches: 44, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
26 41 0.20
27 165 0.80
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.37
Consensus pattern (27 bp):
TCATTTTACCCTACAGGGGTATTATGG
Found at i:23218480 original size:17 final size:16
Alignment explanation
Indices: 23218456--23218507 Score: 61
Period size: 17 Copynumber: 3.2 Consensus size: 16
23218446 AGGCAATTCA
23218456 CATA-AAATAACAGTT
1 CATACAAATAACAGTT
*
23218471 CATACGAAATAATAGTT
1 CATAC-AAATAACAGTT
*
23218488 CATTCAATATAACAGTT
1 CATACAA-ATAACAGTT
23218505 CAT
1 CAT
23218508 TCAATATAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
15 4 0.13
16 2 0.06
17 25 0.81
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (16 bp):
CATACAAATAACAGTT
Found at i:23218508 original size:17 final size:17
Alignment explanation
Indices: 23218462--23218516 Score: 76
Period size: 17 Copynumber: 3.2 Consensus size: 17
23218452 TTCACATAAA
*
23218462 ATAACAGTTCATACGAA-
1 ATAACAGTTCATTC-AAT
*
23218479 ATAATAGTTCATTCAAT
1 ATAACAGTTCATTCAAT
23218496 ATAACAGTTCATTCAAT
1 ATAACAGTTCATTCAAT
23218513 ATAA
1 ATAA
23218517 TAATTCATCC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
16 2 0.06
17 32 0.94
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (17 bp):
ATAACAGTTCATTCAAT
Found at i:23218523 original size:17 final size:17
Alignment explanation
Indices: 23218479--23218524 Score: 74
Period size: 17 Copynumber: 2.7 Consensus size: 17
23218469 TTCATACGAA
23218479 ATAATAGTTCATTCAAT
1 ATAATAGTTCATTCAAT
*
23218496 ATAACAGTTCATTCAAT
1 ATAATAGTTCATTCAAT
*
23218513 ATAATAATTCAT
1 ATAATAGTTCAT
23218525 CCATACAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.43, C:0.13, G:0.04, T:0.39
Consensus pattern (17 bp):
ATAATAGTTCATTCAAT
Found at i:23219234 original size:18 final size:18
Alignment explanation
Indices: 23219192--23219235 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
23219182 CACAATTTGG
**
23219192 CAAATTAATACAGTTCAC
1 CAAATTAATACAAATCAC
*
23219210 CATATTAATACAAATCAC
1 CAAATTAATACAAATCAC
*
23219228 TAAATTAA
1 CAAATTAA
23219236 CATAATTGGC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.50, C:0.18, G:0.02, T:0.30
Consensus pattern (18 bp):
CAAATTAATACAAATCAC
Found at i:23219551 original size:33 final size:31
Alignment explanation
Indices: 23219495--23219617 Score: 101
Period size: 31 Copynumber: 3.9 Consensus size: 31
23219485 CGCAAGCATT
*
23219495 ACAAAACTCATATACATATATATTATATAAA
1 ACAAAACCCATATACATATATATTATATAAA
23219526 ACAAAACCCATATATGCATATATATTATATATAA
1 ACAAAACCCATATA--CATATATATTATATA-AA
* * ** *
23219560 TCAAGACCC--ACGCATATATATTATACATATA
1 ACAAAACCCATATACATATATATTAT--ATAAA
* *
23219591 ACAAAACCCA-AGA-ATATATATTGTATA
1 ACAAAACCCATATACATATATATTATATA
23219618 TATACACATA
Statistics
Matches: 75, Mismatches: 11, Indels: 14
0.75 0.11 0.14
Matches are distributed among these distances:
29 3 0.04
30 12 0.16
31 31 0.41
32 5 0.07
33 15 0.20
34 9 0.12
ACGTcount: A:0.50, C:0.16, G:0.04, T:0.30
Consensus pattern (31 bp):
ACAAAACCCATATACATATATATTATATAAA
Found at i:23221258 original size:18 final size:18
Alignment explanation
Indices: 23221235--23221273 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
23221225 TTTTTCTCAA
* *
23221235 TTATTTTCAAACTTGATT
1 TTATTTTCAAAATTCATT
*
23221253 TTATTTTTAAAATTCATT
1 TTATTTTCAAAATTCATT
23221271 TTA
1 TTA
23221274 AGTTATTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.31, C:0.08, G:0.03, T:0.59
Consensus pattern (18 bp):
TTATTTTCAAAATTCATT
Found at i:23223100 original size:40 final size:40
Alignment explanation
Indices: 23223055--23223134 Score: 108
Period size: 42 Copynumber: 2.0 Consensus size: 40
23223045 CTATATGAAT
* * *
23223055 GGCACTAA-GTGTGAAATTAAAATGATGATGTTGAATAACA
1 GGCACTAAGGTGTGAAACTAAAATGACGATG-GGAATAACA
23223095 GGCACTAAGTGTGTGAAACTAAAATGACGATGGGAATAAC
1 GGCACTAAG-GTGTGAAACTAAAATGACGATGGGAATAAC
23223135 TTCATTATGG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
40 8 0.23
41 7 0.20
42 20 0.57
ACGTcount: A:0.41, C:0.10, G:0.25, T:0.24
Consensus pattern (40 bp):
GGCACTAAGGTGTGAAACTAAAATGACGATGGGAATAACA
Found at i:23229720 original size:23 final size:23
Alignment explanation
Indices: 23229676--23229722 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
23229666 GTTAAGTAAA
*
23229676 TATTTAAAAATAATAATTAAATT
1 TATTTAAAAATAATAATGAAATT
*
23229699 TATTTAAACATAA-AATAGAAATT
1 TATTTAAAAATAATAAT-GAAATT
23229722 T
1 T
23229723 CATTCAGTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
TATTTAAAAATAATAATGAAATT
Found at i:23232615 original size:23 final size:25
Alignment explanation
Indices: 23232571--23232616 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
23232561 AAGCTTTCTC
23232571 ATACCTATGTTATATTGTGAATAAA
1 ATACCTATGTTATATTGTGAATAAA
*
23232596 ATACTTATG-TAT-TTGTGAATA
1 ATACCTATGTTATATTGTGAATA
23232617 TGTTAATTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
24 3 0.15
25 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43
Consensus pattern (25 bp):
ATACCTATGTTATATTGTGAATAAA
Found at i:23234352 original size:54 final size:53
Alignment explanation
Indices: 23234296--23234753 Score: 360
Period size: 54 Copynumber: 8.5 Consensus size: 53
23234286 GAAAAATTAT
** * * * * * *
23234296 CGAAATACCATCGAATGGTAAAATTATCGAAATACCCCCGAAGGGTAAAATGA
1 CGAAATACCCCCGAAGGGTAAAATGACCAAAATACCCCCAAAAGGTAAAATGA
* * *
23234349 TCGAAATACCCCCGAAGGGTAAAATGACCAAAATAACCCTAAAAGATAAAATGA
1 -CGAAATACCCCCGAAGGGTAAAATGACCAAAATACCCCCAAAAGGTAAAATGA
* * * ** *
23234403 CTGAATTACCCCTGAAGGGTAAAATAACTGAATTACCCCCAAAAGGTAAAATGA
1 C-GAAATACCCCCGAAGGGTAAAATGACCAAAATACCCCCAAAAGGTAAAATGA
* * * * * * * *
23234457 TCGAATTACCCCCAAAGGGAAAAATGACCGAATTAACCCCGAAGGGTAAAATGA
1 -CGAAATACCCCCGAAGGGTAAAATGACCAAAATACCCCCAAAAGGTAAAATGA
* ** * * * *
23234511 CCAAATTACCCCTAAAGGGTAAAATTACCGAATTACCTCCAAAAGGTAAAATGA
1 CGAAA-TACCCCCGAAGGGTAAAATGACCAAAATACCCCCAAAAGGTAAAATGA
* * * ***
23234565 CTGAATTACCCCCTAAAGGTAAAATGACCAAAATACCCTTGAAAGGTAAAATGA
1 C-GAAATACCCCCGAAGGGTAAAATGACCAAAATACCCCCAAAAGGTAAAATGA
** * * * * * * *
23234619 CTGAAATACCCCTAAAGTGTAAAATAACTAAAATACCCTCGAAGGGTAAAATAA
1 C-GAAATACCCCCGAAGGGTAAAATGACCAAAATACCCCCAAAAGGTAAAATGA
* * * * *
23234673 TTGAAATACCCTCGAAAGGTAAAATGACCAAAATACCCCTAAAGGGTAAAATGA
1 -CGAAATACCCCCGAAGGGTAAAATGACCAAAATACCCCCAAAAGGTAAAATGA
*
23234727 CGAAACACCCCC-ATAGGGTAAAATGAC
1 CGAAATACCCCCGA-AGGGTAAAATGAC
23234754 TGATATACCC
Statistics
Matches: 323, Mismatches: 75, Indels: 13
0.79 0.18 0.03
Matches are distributed among these distances:
52 1 0.00
53 25 0.08
54 294 0.91
55 3 0.01
ACGTcount: A:0.45, C:0.21, G:0.16, T:0.18
Consensus pattern (53 bp):
CGAAATACCCCCGAAGGGTAAAATGACCAAAATACCCCCAAAAGGTAAAATGA
Found at i:23234423 original size:81 final size:81
Alignment explanation
Indices: 23234328--23234752 Score: 375
Period size: 81 Copynumber: 5.3 Consensus size: 81
23234318 ATTATCGAAA
* * *
23234328 TACCCCCGAAGGGTAAAATGATCGAAATACCCCCGAAGGGTAAAATGACCAAAATAACCCTAAAA
1 TACCCCTGAAGGGTAAAATGATCGAAATACCCCCGAAAGGTAAAATGACCAAAATACCCCTAAAA
*
23234393 GATAAAATGACTGAAT
66 GGTAAAATGACTGAAT
* * * * * * *
23234409 TACCCCTGAAGGGTAAAAT-AACTGAATTACCCCCAAAAGGTAAAATGATCGAATTACCCCCAAA
1 TACCCCTGAAGGGTAAAATGATC-GAAATACCCCCGAAAGGTAAAATGACCAAAATACCCCTAAA
* * *
23234473 GGGAAAAATGACCGAAT
65 AGGTAAAATGACTGAAT
* * * * *
23234490 TAACCCC-GAAGGGTAAAATGA-CCAAATTA-CCCCTAAAGGGTAAAATTACCGAATTACCTCC-
1 T-ACCCCTGAAGGGTAAAATGATCGAAA-TACCCCCGAAA-GGTAAAATGACCAAAATACC-CCT
23234551 AAAAGGTAAAATGACTGAAT
62 AAAAGGTAAAATGACTGAAT
* * * ** **
23234571 TACCCCCT-AAAGGTAAAATGACCAAAATACCCTTGAAAGGTAAAATGACTGAAATACCCCT-AA
1 TA-CCCCTGAAGGGTAAAATGATCGAAATACCCCCGAAAGGTAAAATGACCAAAATACCCCTAAA
* * *
23234634 AGTGTAAAATAACTAAAA
65 AG-GTAAAATGACTGAAT
* * *
23234652 TA-CCCTCGAAGGGTAAAATAATTGAAATACCCTCGAAAGGTAAAATGACCAAAATACCCCTAAA
1 TACCCCT-GAAGGGTAAAATGATCGAAATACCCCCGAAAGGTAAAATGACCAAAATACCCCTAAA
* *
23234716 GGGTAAAATGAC-GAAA
65 AGGTAAAATGACTGAAT
* *
23234732 CACCCC-CATAGGGTAAAATGA
1 TACCCCTGA-AGGGTAAAATGA
23234753 CTGATATACC
Statistics
Matches: 280, Mismatches: 47, Indels: 35
0.77 0.13 0.10
Matches are distributed among these distances:
79 5 0.02
80 33 0.12
81 222 0.79
82 20 0.07
ACGTcount: A:0.45, C:0.21, G:0.16, T:0.18
Consensus pattern (81 bp):
TACCCCTGAAGGGTAAAATGATCGAAATACCCCCGAAAGGTAAAATGACCAAAATACCCCTAAAA
GGTAAAATGACTGAAT
Found at i:23234763 original size:27 final size:26
Alignment explanation
Indices: 23234324--23234764 Score: 287
Period size: 27 Copynumber: 16.4 Consensus size: 26
23234314 TAAAATTATC
23234324 GAAATACCCCCGAAGGGTAAAATGA-T
1 GAAATACCCCC-AAGGGTAAAATGACT
*
23234350 CGAAATACCCCCGAAGGGTAAAATGACC
1 -GAAATACCCCC-AAGGGTAAAATGACT
* ** * *
23234378 AAAATAACCCTAAAAGATAAAATGACT
1 GAAAT-ACCCCCAAGGGTAAAATGACT
* * *
23234405 GAATTACCCCTGAAGGGTAAAATAACT
1 GAAATACCCC-CAAGGGTAAAATGACT
* *
23234432 GAATTACCCCCAAAAGGTAAAATGA-T
1 GAAATACCCCC-AAGGGTAAAATGACT
* * *
23234458 CGAATTACCCCCAAAGGGAAAAATGACC
1 -GAAATACCCCC-AAGGGTAAAATGACT
* *
23234486 GAATTAACCCCGAAGGGTAAAATGAC-
1 GAAAT-ACCCCCAAGGGTAAAATGACT
* * * *
23234512 CAAATTACCCCTAAAGGGTAAAATTACC
1 GAAA-TACCCC-CAAGGGTAAAATGACT
* * *
23234540 GAATTACCTCCAAAAGGTAAAATGACT
1 GAAATACC-CCCAAGGGTAAAATGACT
* * *
23234567 GAATTACCCCCTAAAGGTAAAATGACC
1 GAAATACCCCC-AAGGGTAAAATGACT
* ** *
23234594 AAAATACCCTTGAAAGGTAAAATGACT
1 GAAATACCC-CCAAGGGTAAAATGACT
* * *
23234621 GAAATACCCCTAAAGTGTAAAATAACT
1 GAAATACCCC-CAAGGGTAAAATGACT
* * * *
23234648 AAAATACCCTCGAAGGGTAAAATAATT
1 GAAATACCC-CCAAGGGTAAAATGACT
* * *
23234675 GAAATACCCTCGAAAGGTAAAATGACC
1 GAAATACCC-CCAAGGGTAAAATGACT
* *
23234702 AAAATACCCCTAAAGGGTAAAATGAC-
1 GAAATACCCC-CAAGGGTAAAATGACT
*
23234728 GAAACACCCCCATAGGGTAAAATGACT
1 GAAATACCCCCA-AGGGTAAAATGACT
*
23234755 GATATACCCC
1 GAAATACCCC
23234765 TAGGAGCCGA
Statistics
Matches: 335, Mismatches: 61, Indels: 36
0.78 0.14 0.08
Matches are distributed among these distances:
25 1 0.00
26 36 0.11
27 284 0.85
28 14 0.04
ACGTcount: A:0.45, C:0.21, G:0.16, T:0.18
Consensus pattern (26 bp):
GAAATACCCCCAAGGGTAAAATGACT
Found at i:23235166 original size:28 final size:28
Alignment explanation
Indices: 23235126--23235204 Score: 113
Period size: 28 Copynumber: 2.8 Consensus size: 28
23235116 TGCACTGTAT
*
23235126 TGTTACTATATTGGGCTAAGGCCCACAC
1 TGTTACTGTATTGGGCTAAGGCCCACAC
**
23235154 TGTTACTGTATTGGGCTAAGGTTCACAC
1 TGTTACTGTATTGGGCTAAGGCCCACAC
* *
23235182 TGTTACTGAAATGGGCTAAGGCC
1 TGTTACTGTATTGGGCTAAGGCC
23235205 AACATTCCAC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.30
Consensus pattern (28 bp):
TGTTACTGTATTGGGCTAAGGCCCACAC
Found at i:23242747 original size:30 final size:29
Alignment explanation
Indices: 23242686--23242791 Score: 88
Period size: 30 Copynumber: 3.6 Consensus size: 29
23242676 TGGTTGACAC
* * *
23242686 ATCCCTTTCCTTTATTCGATAATCGAGGCT
1 ATCCCTTTCCATAATTCGAT-ATCGAAGCT
*
23242716 ATCCCTTTCCATAATTCGATATGTGAAGCT
1 ATCCCTTTCCATAATTCGATAT-CGAAGCT
* * *
23242746 ATCGCTATT-CATAATTCGATAGCCAAGGCT
1 ATCCCT-TTCCATAATTCGATATCGAA-GCT
* *
23242776 ATCCGTTTTCATAATT
1 ATCCCTTTCCATAATT
23242792 TAGTGGTCGT
Statistics
Matches: 62, Mismatches: 10, Indels: 8
0.77 0.12 0.10
Matches are distributed among these distances:
29 6 0.10
30 54 0.87
31 2 0.03
ACGTcount: A:0.25, C:0.24, G:0.13, T:0.38
Consensus pattern (29 bp):
ATCCCTTTCCATAATTCGATATCGAAGCT
Found at i:23245756 original size:49 final size:49
Alignment explanation
Indices: 23245700--23245912 Score: 179
Period size: 49 Copynumber: 4.3 Consensus size: 49
23245690 TATTTCAATG
*
23245700 TTCTACCATCTCGAATGACTCAACAATGATGCCTTTCATTATTCCTACA
1 TTCTACCATCTCGGATGACTCAACAATGATGCCTTTCATTATTCCTACA
* * * * * *
23245749 TTTTACCATCTTGGGTG-GTCCGACAATGATG-GTTCTCA-TAGTT--TACTTA
1 TTCTACCATCTCGGATGACT-CAACAATGATGCCTT-TCATTA-TTCCTAC--A
* * * * * *
23245798 TTCTACCATCCCGGAT-AGCTCGACAATGATGGCATTCAATA-TCTCAACA
1 TTCTACCATCTCGGATGA-CTCAACAATGATGCCTTTCATTATTC-CTACA
23245847 TTCTACCATCTCGGATGACTCAACAATGATGCCTTTCATTATTCCTACA
1 TTCTACCATCTCGGATGACTCAACAATGATGCCTTTCATTATTCCTACA
* *
23245896 TTTTACCATCTTGGATG
1 TTCTACCATCTCGGATG
23245913 GTCCGACAAC
Statistics
Matches: 127, Mismatches: 23, Indels: 28
0.71 0.13 0.16
Matches are distributed among these distances:
47 3 0.02
48 6 0.05
49 109 0.86
50 7 0.06
51 2 0.02
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.35
Consensus pattern (49 bp):
TTCTACCATCTCGGATGACTCAACAATGATGCCTTTCATTATTCCTACA
Found at i:23245948 original size:98 final size:98
Alignment explanation
Indices: 23245846--23246024 Score: 218
Period size: 98 Copynumber: 1.8 Consensus size: 98
23245836 ATATCTCAAC
* * * * * * *
23245846 ATTCTACCATCTCGGAT-GACTCAACAATGATGCCTTTCATTAT-TCCTACATTTTACCATCTTG
1 ATTCTACCATCCCGAATAG-CTCAACAATGATGCCATTCAATATCT-CAACATTATACCATCTCG
* *
23245909 GATGGTCCGACAACGATGGTTCTCACAGTTTACTT
64 GATGGCCCGAAAACGATGGTTCTCACAGTTTACTT
** *
23245944 ATTCTACCATCCCGAATAGCTTGACAATGATGGCATTCAATATCTCAACATTATACCATCTCGGA
1 ATTCTACCATCCCGAATAGCTCAACAATGATGCCATTCAATATCTCAACATTATACCATCTCGGA
23246009 TGGCCCGAAAACGATG
66 TGGCCCGAAAACGATG
23246025 ATTTTTGCTA
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
98 65 0.97
99 2 0.03
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (98 bp):
ATTCTACCATCCCGAATAGCTCAACAATGATGCCATTCAATATCTCAACATTATACCATCTCGGA
TGGCCCGAAAACGATGGTTCTCACAGTTTACTT
Found at i:23246007 original size:147 final size:147
Alignment explanation
Indices: 23245703--23246010 Score: 553
Period size: 147 Copynumber: 2.1 Consensus size: 147
23245693 TTCAATGTTC
* *
23245703 TACCATCTCGAATGACTCAACAATGATGCCTTTCATTATTCCTACATTTTACCATCTTGGGTGGT
1 TACCATCTCGGATGACTCAACAATGATGCCTTTCATTATTCCTACATTTTACCATCTTGGATGGT
* * *
23245768 CCGACAATGATGGTTCTCATAGTTTACTTATTCTACCATCCCGGATAGCTCGACAATGATGGCAT
66 CCGACAACGATGGTTCTCACAGTTTACTTATTCTACCATCCCGAATAGCTCGACAATGATGGCAT
*
23245833 TCAATATCTCAACATTC
131 TCAATATCTCAACATTA
23245850 TACCATCTCGGATGACTCAACAATGATGCCTTTCATTATTCCTACATTTTACCATCTTGGATGGT
1 TACCATCTCGGATGACTCAACAATGATGCCTTTCATTATTCCTACATTTTACCATCTTGGATGGT
*
23245915 CCGACAACGATGGTTCTCACAGTTTACTTATTCTACCATCCCGAATAGCTTGACAATGATGGCAT
66 CCGACAACGATGGTTCTCACAGTTTACTTATTCTACCATCCCGAATAGCTCGACAATGATGGCAT
23245980 TCAATATCTCAACATTA
131 TCAATATCTCAACATTA
23245997 TACCATCTCGGATG
1 TACCATCTCGGATG
23246011 GCCCGAAAAC
Statistics
Matches: 154, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
147 154 1.00
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.33
Consensus pattern (147 bp):
TACCATCTCGGATGACTCAACAATGATGCCTTTCATTATTCCTACATTTTACCATCTTGGATGGT
CCGACAACGATGGTTCTCACAGTTTACTTATTCTACCATCCCGAATAGCTCGACAATGATGGCAT
TCAATATCTCAACATTA
Found at i:23246051 original size:147 final size:147
Alignment explanation
Indices: 23245703--23246073 Score: 451
Period size: 147 Copynumber: 2.5 Consensus size: 147
23245693 TTCAATGTTC
* * * * * * ** *
23245703 TACCATCTCGAATGACTCAACAATGATGCCTTTCATTATTCCTACATTTTACCATCTTGGGTGGT
1 TACCATCTCGGATGACCCAACAACGATGACTTTCACTATTACTACATTCAACCATCTTGGATGGT
* *
23245768 CCGACAATGATGGTTCTCATAGTTTACTTATTCTACCATCCCGGATAGCTCGACAATGATGGCAT
66 CCGACAATGATGGTTCTCACAGTTTACTTATTCTACCATCCCGAATAGCTCGACAATGATGGCAT
*
23245833 TCAATATCTCAACATTC
131 TCAATATCTCAACATTA
* * * * * **
23245850 TACCATCTCGGATGACTCAACAATGATGCCTTTCATTATTCCTACATTTTACCATCTTGGATGGT
1 TACCATCTCGGATGACCCAACAACGATGACTTTCACTATTACTACATTCAACCATCTTGGATGGT
* *
23245915 CCGACAACGATGGTTCTCACAGTTTACTTATTCTACCATCCCGAATAGCTTGACAATGATGGCAT
66 CCGACAATGATGGTTCTCACAGTTTACTTATTCTACCATCCCGAATAGCTCGACAATGATGGCAT
23245980 TCAATATCTCAACATTA
131 TCAATATCTCAACATTA
* * ** * *
23245997 TACCATCTCGGATGGCCCGAA-AACGATGATTTTTGCTATATAC-ACCTTCAACCATCCTGGATG
1 TACCATCTCGGATGACCC-AACAACGATGACTTTCACTAT-TACTACATTCAACCATCTTGGATG
23246060 G-CCTGACAATGATG
64 GTCC-GACAATGATG
23246074 ATTTTCAACC
Statistics
Matches: 200, Mismatches: 21, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
146 2 0.01
147 194 0.97
148 4 0.02
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.32
Consensus pattern (147 bp):
TACCATCTCGGATGACCCAACAACGATGACTTTCACTATTACTACATTCAACCATCTTGGATGGT
CCGACAATGATGGTTCTCACAGTTTACTTATTCTACCATCCCGAATAGCTCGACAATGATGGCAT
TCAATATCTCAACATTA
Found at i:23248780 original size:57 final size:58
Alignment explanation
Indices: 23248712--23248831 Score: 163
Period size: 57 Copynumber: 2.1 Consensus size: 58
23248702 AGGGCATTTT
* * *
23248712 CATTTTCATTTTCATTTTGGAGAAAACCACATTCATTTCCAAATGATTT-C-ATTTCTC
1 CATTTTCATTTTAATTTTGGAAAAAACCACAATCATTTCCAAATG-TTTCCTATTTCTC
* * *
23248769 CATTTTTATTTTAATTTTGGAAAAAACCATAATCATTTCTAAATGTTTCCTATTTCTC
1 CATTTTCATTTTAATTTTGGAAAAAACCACAATCATTTCCAAATGTTTCCTATTTCTC
23248827 CATTT
1 CATTT
23248832 CACCATTTCT
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
56 3 0.05
57 40 0.73
58 12 0.22
ACGTcount: A:0.29, C:0.18, G:0.06, T:0.47
Consensus pattern (58 bp):
CATTTTCATTTTAATTTTGGAAAAAACCACAATCATTTCCAAATGTTTCCTATTTCTC
Found at i:23257132 original size:18 final size:18
Alignment explanation
Indices: 23257091--23257125 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
23257081 AAATATCTCT
*
23257091 AATATTTTAATCAAATAA
1 AATAATTTAATCAAATAA
*
23257109 AATAATTTAATCTAATA
1 AATAATTTAATCAAATA
23257126 TTATAATAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (18 bp):
AATAATTTAATCAAATAA
Found at i:23276545 original size:38 final size:38
Alignment explanation
Indices: 23276503--23276577 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
23276493 TAAATCTTTG
* *
23276503 TTTAAAAATTTTAATGAAATTCTTTAAAAAATAATTAT
1 TTTAAAAATTTTAATGAAATTATTTAAAAAACAATTAT
23276541 TTTAAAAATTTTAATGAAATTATTTAAAAAACAATTA
1 TTTAAAAATTTTAATGAAATTATTTAAAAAACAATTA
23276578 ATGAATTGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.43
Consensus pattern (38 bp):
TTTAAAAATTTTAATGAAATTATTTAAAAAACAATTAT
Found at i:23277287 original size:37 final size:37
Alignment explanation
Indices: 23277208--23277289 Score: 112
Period size: 37 Copynumber: 2.2 Consensus size: 37
23277198 ATAAAAATAA
* *
23277208 ATAATTTAATCATATTTTAATATAATTATTATTAAAT
1 ATAATTTAATAACATTTTAATATAATTATTATTAAAT
* *
23277245 ATAATTTAATAACATTCTTAATATAATTATTTTTATAT
1 ATAATTTAATAACATT-TTAATATAATTATTATTAAAT
23277283 -TAATTTA
1 ATAATTTA
23277290 TATTAAAATG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
37 21 0.52
38 19 0.47
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (37 bp):
ATAATTTAATAACATTTTAATATAATTATTATTAAAT
Found at i:23277345 original size:33 final size:33
Alignment explanation
Indices: 23277275--23277364 Score: 85
Period size: 33 Copynumber: 2.8 Consensus size: 33
23277265 ATATAATTAT
* *** *
23277275 TTTTATATTAATTTATATTAAAATGTTTTTTAT
1 TTTTATATTAATTTATATTAAAATATTTAAAAA
23277308 TTTTATATTTAA-TTATATTAAAATATTTAAAAA
1 TTTTATA-TTAATTTATATTAAAATATTTAAAAA
* * *
23277341 TTTTAT-TTACTATATTTTAAAATA
1 TTTTATATTAATTTATATTAAAATA
23277365 GTACACTATT
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
31 3 0.06
32 11 0.23
33 29 0.62
34 4 0.09
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (33 bp):
TTTTATATTAATTTATATTAAAATATTTAAAAA
Found at i:23278299 original size:4 final size:4
Alignment explanation
Indices: 23278290--23278324 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
23278280 TTACCAAACT
23278290 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
23278325 TGTTACCTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:23280396 original size:22 final size:22
Alignment explanation
Indices: 23280362--23280403 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
23280352 TTTTTTATTT
*
23280362 ATAATAATAAATATTAAATTAA
1 ATAATAATAAATAATAAATTAA
23280384 ATAA-AATATAATAATAAATT
1 ATAATAATA-AATAATAAATT
23280404 TTAATATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
ATAATAATAAATAATAAATTAA
Found at i:23287858 original size:22 final size:23
Alignment explanation
Indices: 23287805--23287860 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
23287795 CCCATTTTTA
* * *
23287805 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
23287828 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
23287850 ATTAAAATTAA
1 ATTAAAATTAA
23287861 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:23287873 original size:16 final size:16
Alignment explanation
Indices: 23287836--23287875 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
23287826 TTAATAAAAT
* *
23287836 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
23287852 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
23287868 TAAAATTA
1 TAAAATTA
23287876 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:23287974 original size:77 final size:76
Alignment explanation
Indices: 23287882--23288044 Score: 310
Period size: 77 Copynumber: 2.1 Consensus size: 76
23287872 ATTATCAAAT
23287882 TATTAATTG-TTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAA
1 TATTAATTGTTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAA
23287946 ATTATTAATTG
66 ATTATTAATTG
23287957 TATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 TATTAATTGT-TTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
23288022 AATTATTAATTG
65 AATTATTAATTG
23288034 TATTAATTGTT
1 TATTAATTGTT
23288045 GTAACAAAAT
Statistics
Matches: 86, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
75 9 0.10
76 1 0.01
77 76 0.88
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (76 bp):
TATTAATTGTTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAA
ATTATTAATTG
Found at i:23287990 original size:9 final size:9
Alignment explanation
Indices: 23287948--23287984 Score: 74
Period size: 9 Copynumber: 4.1 Consensus size: 9
23287938 TTTATCAAAT
23287948 TATTAATTG
1 TATTAATTG
23287957 TATTAATTG
1 TATTAATTG
23287966 TATTAATTG
1 TATTAATTG
23287975 TATTAATTG
1 TATTAATTG
23287984 T
1 T
23287985 TGTAATAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:23294963 original size:7 final size:7
Alignment explanation
Indices: 23294951--23294977 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
23294941 TTTTGAATGA
23294951 ATGATTC
1 ATGATTC
23294958 ATGATTC
1 ATGATTC
23294965 ATGATTC
1 ATGATTC
23294972 ATGATT
1 ATGATT
23294978 GTTTAAAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.44
Consensus pattern (7 bp):
ATGATTC
Found at i:23296766 original size:67 final size:67
Alignment explanation
Indices: 23296658--23296819 Score: 198
Period size: 67 Copynumber: 2.4 Consensus size: 67
23296648 TCTGGTTTAC
* * * *** * *
23296658 ACATGTCACCCCATGTTTAATGTCTTGGTGGACTCCTCATGTGGTCATAATCGAACTAAGGTCTT
1 ACATGTAACCCTATGTTTAATGTCCTGGCAAACACCTCATGTGGCCATAATCGAACTAAGGTCTT
23296723 AA
66 AA
* * * * *
23296725 ACATGTAACCCTATGTTTAATGTTCTGGCAAACACCTCATGTTGCCATAGTTGAGCTAAGGTCTT
1 ACATGTAACCCTATGTTTAATGTCCTGGCAAACACCTCATGTGGCCATAATCGAACTAAGGTCTT
*
23296790 AC
66 AA
23296792 ACATGTAACCCTATGTTTAATGTCCTGG
1 ACATGTAACCCTATGTTTAATGTCCTGG
23296820 TGGACTACCC
Statistics
Matches: 80, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
67 80 1.00
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (67 bp):
ACATGTAACCCTATGTTTAATGTCCTGGCAAACACCTCATGTGGCCATAATCGAACTAAGGTCTT
AA
Found at i:23299136 original size:43 final size:43
Alignment explanation
Indices: 23299068--23299150 Score: 121
Period size: 43 Copynumber: 1.9 Consensus size: 43
23299058 AGGAATGTTA
* * *
23299068 TTTCCTAATTGTGGTTCTCTGTGTGTCCTAGGATGATGAGGGG
1 TTTCCTAATTGCGGTTCTCTATGTGTCCTAGGACGATGAGGGG
* *
23299111 TTTCCTAATTGCGGTTTTCTATGTGTTCTAGGACGATGAG
1 TTTCCTAATTGCGGTTCTCTATGTGTCCTAGGACGATGAG
23299151 AGGAATCACT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.16, C:0.14, G:0.29, T:0.41
Consensus pattern (43 bp):
TTTCCTAATTGCGGTTCTCTATGTGTCCTAGGACGATGAGGGG
Found at i:23299317 original size:61 final size:61
Alignment explanation
Indices: 23299208--23299368 Score: 209
Period size: 61 Copynumber: 2.6 Consensus size: 61
23299198 CCAGAAGAAT
** *
23299208 GAAAGCCTTTGTGGCAATACTTTAGACTGGAAAGCCTTTGTAGTGAGTACTAGATGTAAAG
1 GAAAGCCTTTGTGGCAATACTTTAGACAAGAAAGCCTTTGTAGCGAGTACTAGATGTAAAG
* * *
23299269 GAAAGCCTTTGTGGCAATACTTTGGACAAGAAAGACCTTT-TGGCGAGTACTAGATGTAAAT
1 GAAAGCCTTTGTGGCAATACTTTAGACAAGAAAG-CCTTTGTAGCGAGTACTAGATGTAAAG
* * *
23299330 GACAA-CCTTTGTGGCAATACTCTAGATACGAAAGCCTTT
1 GA-AAGCCTTTGTGGCAATACTTTAGACAAGAAAGCCTTT
23299369 ATACTGAGTG
Statistics
Matches: 88, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
60 5 0.06
61 76 0.86
62 7 0.08
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.29
Consensus pattern (61 bp):
GAAAGCCTTTGTGGCAATACTTTAGACAAGAAAGCCTTTGTAGCGAGTACTAGATGTAAAG
Found at i:23299390 original size:61 final size:60
Alignment explanation
Indices: 23299205--23299411 Score: 199
Period size: 61 Copynumber: 3.4 Consensus size: 60
23299195 TCACCAGAAG
* *
23299205 AATGAAAGCCTTTGTGGCAATACTTTAGACT-GGAAAGCCTTTGTAGTGAGTACTAGATGTA
1 AATGAAAGCCTTTGTGGCAATACTTTAGA-TAAGAAAGCCTTT-TACTGAGTACTAGATGTA
* * * *
23299266 AAGGAAAGCCTTTGTGGCAATACTTTGGACAAGAAAGACCTTTTGGC-GAGTACTAGATGTA
1 AATGAAAGCCTTTGTGGCAATACTTTAGATAAGAAAG-CCTTTT-ACTGAGTACTAGATGTA
* * * *
23299327 AATGACAA-CCTTTGTGGCAATACTCTAGATACGAAAGCCTTTATACTGAGT-GTAGGATATA
1 AATGA-AAGCCTTTGTGGCAATACTTTAGATAAGAAAGCCTTT-TACTGAGTACTA-GATGTA
* *
23299388 AATGACAA-CCTTTTTGGTAATACT
1 AATGA-AAGCCTTTGTGGCAATACT
23299412 GGATGTAAAG
Statistics
Matches: 123, Mismatches: 16, Indels: 14
0.80 0.10 0.09
Matches are distributed among these distances:
60 8 0.07
61 108 0.88
62 7 0.06
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (60 bp):
AATGAAAGCCTTTGTGGCAATACTTTAGATAAGAAAGCCTTTTACTGAGTACTAGATGTA
Found at i:23311001 original size:28 final size:28
Alignment explanation
Indices: 23310900--23311015 Score: 124
Period size: 30 Copynumber: 4.0 Consensus size: 28
23310890 CATGCAGAAT
* * * *
23310900 CAGTCTGGGCCTGAGCCCTATACAGTAG
1 CAGTGTGGGCCTTAGCCCAATACAGTAA
* *
23310928 CAGTGTGTGGGCCATAGCCCAAAACAGTAA
1 CA--GTGTGGGCCTTAGCCCAATACAGTAA
*
23310958 CAGAGTGTGGGCCTTAGCCCAATTCAGTAA
1 C--AGTGTGGGCCTTAGCCCAATACAGTAA
*
23310988 CAGTGTGGGCCTTAGCCCAAAACAGTAA
1 CAGTGTGGGCCTTAGCCCAATACAGTAA
23311016 TTACTACAAC
Statistics
Matches: 73, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
28 27 0.37
30 45 0.62
32 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.27, T:0.20
Consensus pattern (28 bp):
CAGTGTGGGCCTTAGCCCAATACAGTAA
Found at i:23311157 original size:26 final size:26
Alignment explanation
Indices: 23311127--23311203 Score: 109
Period size: 26 Copynumber: 3.0 Consensus size: 26
23311117 ACACCAATAT
*
23311127 CGCAGCAAAGCTGCCAGTAACAGTAA
1 CGCAGCAAAGCTACCAGTAACAGTAA
* * * *
23311153 TGCAGCAGAGCTACCAGTATCAATAA
1 CGCAGCAAAGCTACCAGTAACAGTAA
23311179 CGCAGCAAAGCTACCAGTAACAGTA
1 CGCAGCAAAGCTACCAGTAACAGTA
23311204 TTTGTGGCAA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.39, C:0.26, G:0.21, T:0.14
Consensus pattern (26 bp):
CGCAGCAAAGCTACCAGTAACAGTAA
Found at i:23311415 original size:27 final size:27
Alignment explanation
Indices: 23311385--23311578 Score: 255
Period size: 27 Copynumber: 7.2 Consensus size: 27
23311375 TATAACAGTT
23311385 ATTTTACCCTTCGAGGGTATTTCGATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
* *
23311412 ATTTTACCATT-TAGGGGTATTTCGATA
1 ATTTTACCCTTCGA-GGGTATTTCGATA
* * * *
23311439 ATTTTACCTTTCGAAGGTATTTTGGTA
1 ATTTTACCCTTCGAGGGTATTTCGATA
* * *
23311466 ATTTTATCCTTCGAGGTTATTTCAATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
*
23311493 ATTTTACCATTCGAGGGTATTTCGATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
23311520 ATTTTACCCTTCGAGGGTATTTCGATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
* * *
23311547 ATTTTACCCTTCAAGAGTATTTCAATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
23311574 ATTTT
1 ATTTT
23311579 CTGGCCCAAG
Statistics
Matches: 143, Mismatches: 22, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
26 1 0.01
27 141 0.99
28 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.44
Consensus pattern (27 bp):
ATTTTACCCTTCGAGGGTATTTCGATA
Found at i:23315336 original size:63 final size:62
Alignment explanation
Indices: 23315266--23315458 Score: 235
Period size: 63 Copynumber: 3.1 Consensus size: 62
23315256 CACGGCTTGG
* * *
23315266 ACACATGCCCATTTCTCTAGCTCGTGTGAACCTAATTCCAAAATAGTGAGTTACACGACCTGA
1 ACACATGCCCATGTCTCTAGCCCATGTGAACCTAATTCCAAAATAGTGAGTTACACGACCT-A
*
23315329 ACACATGCCCATGTCTCTAGCCCTTGTG-ACTCTAATTCCAAAATAGTGAGTTACACGACCTA
1 ACACATGCCCATGTCTCTAGCCCATGTGAAC-CTAATTCCAAAATAGTGAGTTACACGACCTA
* * ** * * * * *
23315391 GACATACGTTCGTGTCTCTGGCCCATGTGAACCTAATTCTAAAACAATGAGTTACACGACCTA
1 -ACACATGCCCATGTCTCTAGCCCATGTGAACCTAATTCCAAAATAGTGAGTTACACGACCTA
23315454 ACACA
1 ACACA
23315459 CGGCCGTATG
Statistics
Matches: 113, Mismatches: 14, Indels: 7
0.84 0.10 0.05
Matches are distributed among these distances:
62 7 0.06
63 104 0.92
64 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (62 bp):
ACACATGCCCATGTCTCTAGCCCATGTGAACCTAATTCCAAAATAGTGAGTTACACGACCTA
Found at i:23337441 original size:17 final size:18
Alignment explanation
Indices: 23337394--23337442 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 18
23337384 AAGATTTCTA
*
23337394 ATTTTCATATAAAGTAATTT
1 ATTTTCATA-AAA-TAATTC
23337414 ATTTT-ATAAAATAATTC
1 ATTTTCATAAAATAATTC
23337431 ATTTTCA-AAAAT
1 ATTTTCATAAAAT
23337443 TTCAATGAGC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 15 0.56
18 4 0.15
19 3 0.11
20 5 0.19
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (18 bp):
ATTTTCATAAAATAATTC
Found at i:23338507 original size:31 final size:31
Alignment explanation
Indices: 23338438--23338507 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
23338428 TAACGATGAG
*
23338438 TGACTAAAATGATAAATATATATAACGACAG
1 TGACTAAAATGATAAATATATATAACGACAA
* * *
23338469 TGACTAAAATGATTAAA-GTATGTAATGACAA
1 TGACTAAAATGA-TAAATATATATAACGACAA
*
23338500 TGTCTAAA
1 TGACTAAA
23338508 TTACAAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
31 29 0.88
32 4 0.12
ACGTcount: A:0.49, C:0.09, G:0.14, T:0.29
Consensus pattern (31 bp):
TGACTAAAATGATAAATATATATAACGACAA
Found at i:23342947 original size:6 final size:6
Alignment explanation
Indices: 23342936--23342960 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
23342926 ATTCTTTGTG
23342936 CTTTGC CTTTGC CTTTGC CTTTGC C
1 CTTTGC CTTTGC CTTTGC CTTTGC C
23342961 CTTTTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.36, G:0.16, T:0.48
Consensus pattern (6 bp):
CTTTGC
Found at i:23343014 original size:12 final size:12
Alignment explanation
Indices: 23342997--23343021 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
23342987 GAGTTGATCC
23342997 AAGAGAGAGAGA
1 AAGAGAGAGAGA
23343009 AAGAGAGAGAGA
1 AAGAGAGAGAGA
23343021 A
1 A
23343022 GGCAATGGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (12 bp):
AAGAGAGAGAGA
Found at i:23343505 original size:13 final size:13
Alignment explanation
Indices: 23343487--23343511 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23343477 ACTTCTGTCT
23343487 AAAATAATAACAC
1 AAAATAATAACAC
23343500 AAAATAATAACA
1 AAAATAATAACA
23343512 GGGTTCACTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.12, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAATAATAACAC
Found at i:23344328 original size:13 final size:13
Alignment explanation
Indices: 23344310--23344334 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
23344300 TTTAAATAAC
23344310 GAAAAAATTATGA
1 GAAAAAATTATGA
23344323 GAAAAAATTATG
1 GAAAAAATTATG
23344335 GAATGGATCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.16, T:0.24
Consensus pattern (13 bp):
GAAAAAATTATGA
Found at i:23347494 original size:15 final size:15
Alignment explanation
Indices: 23347474--23347504 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
23347464 ATGAGGTATG
*
23347474 ACGAAAGTGATGGTT
1 ACGAAAGGGATGGTT
23347489 ACGAAAGGGATGGTT
1 ACGAAAGGGATGGTT
23347504 A
1 A
23347505 TGAGGTATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.06, G:0.35, T:0.23
Consensus pattern (15 bp):
ACGAAAGGGATGGTT
Found at i:23350656 original size:43 final size:43
Alignment explanation
Indices: 23350606--23350691 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
23350596 TCATATCTCA
23350606 TTTCTCATATCATAATCATTTATCATATTTGCCATTTCAATAT
1 TTTCTCATATCATAATCATTTATCATATTTGCCATTTCAATAT
* * * * **
23350649 TTTCTCATCTCATATTCATTTCTCATCTTTTTCATTTCAATAT
1 TTTCTCATATCATAATCATTTATCATATTTGCCATTTCAATAT
23350692 CAATCACATA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.26, C:0.21, G:0.01, T:0.52
Consensus pattern (43 bp):
TTTCTCATATCATAATCATTTATCATATTTGCCATTTCAATAT
Found at i:23350684 original size:16 final size:17
Alignment explanation
Indices: 23350649--23350686 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
23350639 ATTTCAATAT
23350649 TTTCTCATCTCATATTCA
1 TTTCTCATCT-ATATTCA
*
23350667 TTTCTCATCT-TTTTCA
1 TTTCTCATCTATATTCA
23350683 TTTC
1 TTTC
23350687 AATATCAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 9 0.47
18 10 0.53
ACGTcount: A:0.16, C:0.26, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTCTCATCTATATTCA
Found at i:23358681 original size:40 final size:40
Alignment explanation
Indices: 23358453--23358674 Score: 274
Period size: 40 Copynumber: 5.6 Consensus size: 40
23358443 AATGATGTCT
* * * *
23358453 GGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCC
* * * *
23358493 GGACTAAGAT-CCGAAGGCTTTTGTGCGAGATACTAATTCC
1 GGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAATCC
*
23358533 GGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCC
23358572 GGG-TGAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCC
1 GGGCT-AAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCC
*
23358612 GGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATCC
*
23358652 GGGCTATGTCCCGAAGGCATTTG
1 GGGCTAAGTCCCGAAGGCATTTG
23358675 AACGAGTAGC
Statistics
Matches: 160, Mismatches: 15, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
38 1 0.01
39 32 0.20
40 116 0.73
41 11 0.07
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCC
Found at i:23365985 original size:40 final size:40
Alignment explanation
Indices: 23365754--23365978 Score: 280
Period size: 40 Copynumber: 5.7 Consensus size: 40
23365744 TTGAATGATG
* * * *
23365754 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * * *
23365794 TCCGGACTAAGAT-CCGAAGGCTTTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
23365834 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
23365873 TCCGGG-TGAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCT-AAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
23365913 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
23365954 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
23365979 AACGAGTAGC
Statistics
Matches: 163, Mismatches: 15, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
38 1 0.01
39 32 0.20
40 119 0.73
41 11 0.07
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:23377083 original size:21 final size:21
Alignment explanation
Indices: 23377054--23377106 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
23377044 ATTTCTCCTT
* *
23377054 ATGTTGCAATAAACTACTTGG
1 ATGTCGCAACAAACTACTTGG
*
23377075 ATGTCGCAACAAGCTACTTGG
1 ATGTCGCAACAAACTACTTGG
23377096 ATGTCGCAACA
1 ATGTCGCAACA
23377107 CGGCTTCTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (21 bp):
ATGTCGCAACAAACTACTTGG
Found at i:23386981 original size:21 final size:20
Alignment explanation
Indices: 23386933--23386982 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
23386923 CTTAAACATG
*
23386933 GCCGTGTGGCTACCCCACAC
1 GCCGTGTGGATACCCCACAC
* *
23386953 GCCTGTGTGGATACTCCGCAC
1 GCC-GTGTGGATACCCCACAC
23386974 GCTCGTGTG
1 GC-CGTGTG
23386983 CTTAGGCCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 3 0.12
21 21 0.84
22 1 0.04
ACGTcount: A:0.12, C:0.36, G:0.30, T:0.22
Consensus pattern (20 bp):
GCCGTGTGGATACCCCACAC
Found at i:23387937 original size:76 final size:75
Alignment explanation
Indices: 23387725--23387963 Score: 361
Period size: 75 Copynumber: 3.2 Consensus size: 75
23387715 TTGTCGGAAT
* *
23387725 AGTGCTGATTCCACCATATGTTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCTCGAATCATTG
1 AGTGCTGATTCCACCATATCTTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTG
*
23387790 GTGCTTGCTA
66 GTGGTTGCTA
* * * *
23387800 AGTGCTGATCCCACCGTATCTTAAATGTGAAAGGGGTTGCTAGGTGCTGATTCCCCTAATCATTG
1 AGTGCTGATTCCACCATATCTTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTG
*
23387865 GTGGTTTCTA
66 GTGGTTGCTA
* *
23387875 AGTGCTGATTCCACCATATCTTTGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGAATCACT
1 AGTGCTGATTCCACCATATC-TTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATT
23387940 GGTGGTTGCTA
65 GGTGGTTGCTA
* *
23387951 TGTGCTGAATCCA
1 AGTGCTGATTCCA
23387964 TCGATAATGG
Statistics
Matches: 146, Mismatches: 17, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
75 85 0.58
76 61 0.42
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.33
Consensus pattern (75 bp):
AGTGCTGATTCCACCATATCTTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTG
GTGGTTGCTA
Found at i:23399611 original size:41 final size:42
Alignment explanation
Indices: 23399554--23399634 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 42
23399544 CATGGCTTGT
* *
23399554 CACACGGGCGTGTGAGGCCATTT-TAGAGGTACACGGCCTCG
1 CACACGGGCGTGTGAGGCCATTTCGAAAGGTACACGGCCTCG
23399595 CACACGGGCGTGTGAGGCCATTTCGAAAGGTACACGGCCT
1 CACACGGGCGTGTGAGGCCATTTCGAAAGGTACACGGCCT
23399635 GGCTCACGAG
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
41 23 0.62
42 14 0.38
ACGTcount: A:0.21, C:0.27, G:0.33, T:0.19
Consensus pattern (42 bp):
CACACGGGCGTGTGAGGCCATTTCGAAAGGTACACGGCCTCG
Found at i:23403456 original size:18 final size:18
Alignment explanation
Indices: 23403435--23403472 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
23403425 CTTTCTCCTT
**
23403435 TTCAGCAACTTCTTCTTC
1 TTCAGCAACAACTTCTTC
23403453 TTCAGCAACAACTTCTTC
1 TTCAGCAACAACTTCTTC
23403471 TT
1 TT
23403473 TTGTAACATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.32, G:0.05, T:0.42
Consensus pattern (18 bp):
TTCAGCAACAACTTCTTC
Found at i:23410964 original size:18 final size:19
Alignment explanation
Indices: 23410943--23410978 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
23410933 ATAAAATGTA
23410943 AAAAAAAAACA-CAAACAC
1 AAAAAAAAACATCAAACAC
*
23410961 AAAAATAAACATCAAACA
1 AAAAAAAAACATCAAACA
23410979 AACGCCATCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.75, C:0.19, G:0.00, T:0.06
Consensus pattern (19 bp):
AAAAAAAAACATCAAACAC
Found at i:23415228 original size:26 final size:26
Alignment explanation
Indices: 23415193--23415261 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 26
23415183 TTTTTTATAT
* *
23415193 ATATGATTTATTTGAAGCTATTTTAC
1 ATATTATTTATTTAAAGCTATTTTAC
** * *
23415219 ATATTATTTATTTAAATTTCTTTTAT
1 ATATTATTTATTTAAAGCTATTTTAC
23415245 ATATTATTTATTATAAA
1 ATATTATTTATT-TAAA
23415262 CTTATATATA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
26 32 0.89
27 4 0.11
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (26 bp):
ATATTATTTATTTAAAGCTATTTTAC
Found at i:23415271 original size:26 final size:26
Alignment explanation
Indices: 23415219--23415272 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
23415209 GCTATTTTAC
* * *
23415219 ATATTATTTATTTAAATTTCTTTTAT
1 ATATTATTTATTTAAACTTCATATAT
23415245 ATATTATTTATTATAAACTT-ATATAT
1 ATATTATTTATT-TAAACTTCATATAT
23415271 AT
1 AT
23415273 CTTTAAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 18 0.75
27 6 0.25
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (26 bp):
ATATTATTTATTTAAACTTCATATAT
Found at i:23415287 original size:19 final size:21
Alignment explanation
Indices: 23415240--23415291 Score: 63
Period size: 19 Copynumber: 2.5 Consensus size: 21
23415230 TTAAATTTCT
*
23415240 TTTATATATTATTTATTATAAA
1 TTTATATA-TATCTATTATAAA
*
23415262 CTTATATATATCT-TTA-AAA
1 TTTATATATATCTATTATAAA
23415281 TTTATATATAT
1 TTTATATATAT
23415292 ATTTTAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 13 0.48
20 3 0.11
21 4 0.15
22 7 0.26
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTATATATATCTATTATAAA
Found at i:23415325 original size:15 final size:14
Alignment explanation
Indices: 23415303--23415372 Score: 53
Period size: 13 Copynumber: 5.2 Consensus size: 14
23415293 TTTTAAAAAC
23415303 TATTTTATAAGTTATT
1 TATTTTAT-A-TTATT
23415319 T-TTTTATATTATT
1 TATTTTATATTATT
23415332 TATTTTA-A--ATT
1 TATTTTATATTATT
*
23415343 T-TTTTATTGTTATT
1 TATTTTA-TATTATT
*
23415357 TATTTT-TATTTTT
1 TATTTTATATTATT
23415370 TAT
1 TAT
23415373 ATTTTGTTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 15
0.71 0.05 0.24
Matches are distributed among these distances:
10 5 0.11
11 4 0.09
13 15 0.33
14 10 0.22
15 10 0.22
16 1 0.02
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (14 bp):
TATTTTATATTATT
Found at i:23415343 original size:24 final size:24
Alignment explanation
Indices: 23415316--23415413 Score: 94
Period size: 24 Copynumber: 4.1 Consensus size: 24
23415306 TTTATAAGTT
*
23415316 ATTTTTTTATATTATTTATTTTAA
1 ATTTTTTTATATTATTTATTTTGA
* *
23415340 ATTTTTTTATTGTTATTTATTTT-T
1 ATTTTTTTA-TATTATTTATTTTGA
* * *
23415364 ATTTTTTATATTTTGTTTATTTGGA
1 ATTTTTT-TATATTATTTATTTTGA
*
23415389 A-CTTTTT-TATTATTTATTTTGA
1 ATTTTTTTATATTATTTATTTTGA
23415411 ATT
1 ATT
23415414 GTCATTATAA
Statistics
Matches: 59, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
22 13 0.22
23 1 0.02
24 30 0.51
25 15 0.25
ACGTcount: A:0.22, C:0.01, G:0.05, T:0.71
Consensus pattern (24 bp):
ATTTTTTTATATTATTTATTTTGA
Found at i:23415345 original size:25 final size:24
Alignment explanation
Indices: 23415317--23415407 Score: 69
Period size: 25 Copynumber: 3.6 Consensus size: 24
23415307 TTATAAGTTA
23415317 TTTTTTTATATTATTTATTTTAAA-
1 TTTTTTTAT-TTATTTATTTTAAAT
*
23415341 TTTTTTTATTGTTATTTATTTT-TAT
1 TTTTTTTA-T-TTATTTATTTTAAAT
* * * *
23415366 TTTTTATATTTTGTTTATTTGGAACT
1 TTTTTTTA-TTTATTTATTT-TAAAT
23415392 TTTTTATTATTTATTT
1 TTTTT-TTATTTATTT
23415408 TGAATTGTCA
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
24 18 0.34
25 21 0.40
26 12 0.23
27 2 0.04
ACGTcount: A:0.21, C:0.01, G:0.04, T:0.74
Consensus pattern (24 bp):
TTTTTTTATTTATTTATTTTAAAT
Found at i:23415359 original size:49 final size:49
Alignment explanation
Indices: 23415306--23415399 Score: 109
Period size: 49 Copynumber: 1.9 Consensus size: 49
23415296 TAAAAACTAT
* *
23415306 TTTATAAGTTATTTTTT-TATATTATTTATTTTAAATTTTTTTATTGTTA
1 TTTAT-AGTTATTTTTTATATATTATTTATTTGAAACTTTTTTATTGTTA
** * * *
23415355 TTTATTTTTATTTTTTATATTTTGTTTATTTGGAACTTTTTTATT
1 TTTATAGTTATTTTTTATATATTATTTATTTGAAACTTTTTTATT
23415400 ATTTATTTTG
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
48 9 0.24
49 28 0.76
ACGTcount: A:0.22, C:0.01, G:0.05, T:0.71
Consensus pattern (49 bp):
TTTATAGTTATTTTTTATATATTATTTATTTGAAACTTTTTTATTGTTA
Found at i:23415384 original size:9 final size:8
Alignment explanation
Indices: 23415314--23415385 Score: 51
Period size: 9 Copynumber: 8.8 Consensus size: 8
23415304 ATTTTATAAG
23415314 TTATTTTT
1 TTATTTTT
*
23415322 TTATATTAT
1 TTAT-TTTT
23415331 TTA-TTTT
1 TTATTTTT
**
23415338 AAATTTTT
1 TTATTTTT
23415346 TTATTGTTAT
1 TTATT-TT-T
23415356 TTA--TTT
1 TTATTTTT
23415362 TTATTTTT
1 TTATTTTT
23415370 TATATTTTGT
1 T-TATTTT-T
23415380 TTATTT
1 TTATTT
23415386 GGAACTTTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 15
0.70 0.08 0.21
Matches are distributed among these distances:
6 4 0.08
7 6 0.12
8 15 0.30
9 19 0.38
10 6 0.12
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (8 bp):
TTATTTTT
Found at i:23420010 original size:41 final size:41
Alignment explanation
Indices: 23419952--23420049 Score: 144
Period size: 41 Copynumber: 2.4 Consensus size: 41
23419942 GGATACTTGA
*
23419952 CAGCTTGTGTGAGCAGCATCGTGTAACTACATTACGACCAAT
1 CAGCTTGTGTGAGCAGCACCGTGTAACTACATTACGACC-AT
* * *
23419994 -AGCTTATGTGAGCAGCACCGTGTAACTACATTACTACCGT
1 CAGCTTGTGTGAGCAGCACCGTGTAACTACATTACGACCAT
23420034 CAGCTTGTGTGAGCAG
1 CAGCTTGTGTGAGCAG
23420050 ACCCACTTGT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
40 1 0.02
41 49 0.98
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (41 bp):
CAGCTTGTGTGAGCAGCACCGTGTAACTACATTACGACCAT
Found at i:23422303 original size:11 final size:11
Alignment explanation
Indices: 23422287--23422316 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
23422277 ATTAACCAAA
23422287 TAATTCAAACT
1 TAATTCAAACT
23422298 TAATTCAAACT
1 TAATTCAAACT
*
23422309 TGATTCAA
1 TAATTCAA
23422317 GCCTAACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.37
Consensus pattern (11 bp):
TAATTCAAACT
Found at i:23423492 original size:51 final size:51
Alignment explanation
Indices: 23423389--23423501 Score: 117
Period size: 51 Copynumber: 2.2 Consensus size: 51
23423379 ATTGATATAA
*
23423389 TAATAAATTTAGCTCATAAAATTTACACATATCATCAATTTACTCTTAATT
1 TAATAAATTTAGCTCATAAAATTTACACATATCATCAATTTACTCATAATT
* * * *
23423440 TAATAAATTTAG-TC-TGAAATATTTACACGT-TCTGTCAATTTAGTCATGATT
1 TAATAAATTTAGCTCAT-AAA-ATTTACACATATC-ATCAATTTACTCATAATT
23423491 T-ATCAAATTTA
1 TAAT-AAATTTA
23423502 ACTTGCAAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
49 1 0.02
50 9 0.17
51 43 0.81
ACGTcount: A:0.38, C:0.13, G:0.06, T:0.42
Consensus pattern (51 bp):
TAATAAATTTAGCTCATAAAATTTACACATATCATCAATTTACTCATAATT
Found at i:23426664 original size:31 final size:33
Alignment explanation
Indices: 23426622--23426686 Score: 91
Period size: 31 Copynumber: 2.0 Consensus size: 33
23426612 TATTTAATCG
23426622 AAAAAAGTATAAAT-TTAATT-TAA-AATATTTT
1 AAAAAAGTATAAATATT-ATTATAATAATATTTT
*
23426653 AAAAAATTATAAATATTATTATAATAATATTTT
1 AAAAAAGTATAAATATTATTATAATAATATTTT
23426686 A
1 A
23426687 TTTTTTATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 16 0.53
32 5 0.17
33 9 0.30
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (33 bp):
AAAAAAGTATAAATATTATTATAATAATATTTT
Found at i:23431137 original size:25 final size:25
Alignment explanation
Indices: 23431109--23431167 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
23431099 GGTTACCGAT
23431109 TTCAGCTCG-AGAGAGCTTACTGTTA
1 TTCAGCTCGCA-AGAGCTTACTGTTA
*
23431134 TTCAGCTCGCATGAGCTTACTGTTA
1 TTCAGCTCGCAAGAGCTTACTGTTA
*
23431159 CTCAGCTCG
1 TTCAGCTCG
23431168 TATGATCTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
25 30 0.97
26 1 0.03
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.32
Consensus pattern (25 bp):
TTCAGCTCGCAAGAGCTTACTGTTA
Found at i:23431172 original size:25 final size:26
Alignment explanation
Indices: 23431121--23431223 Score: 108
Period size: 25 Copynumber: 4.2 Consensus size: 26
23431111 CAGCTCGAGA
* *
23431121 GAGCTTACTG-TTATTCAGCTCGCAT
1 GAGCTTACTGATTACTCAGCTCGTAT
23431146 GAGCTTACTG-TTACTCAGCTCGTAT
1 GAGCTTACTGATTACTCAGCTCGTAT
* *
23431171 GATCTTACTGATTA--CAGCTCGTAC
1 GAGCTTACTGATTACTCAGCTCGTAT
* * *
23431195 GAGCATACAGATT-CTTAGCTCGTAT
1 GAGCTTACTGATTACTCAGCTCGTAT
23431220 GAGC
1 GAGC
23431224 ATACATGTAC
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
24 19 0.29
25 44 0.67
26 3 0.05
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.33
Consensus pattern (26 bp):
GAGCTTACTGATTACTCAGCTCGTAT
Found at i:23448798 original size:20 final size:20
Alignment explanation
Indices: 23448775--23448847 Score: 65
Period size: 20 Copynumber: 4.1 Consensus size: 20
23448765 TAAAGTGTAT
23448775 ACAAAGGCACCGAAGTGCAA
1 ACAAAGGCACCGAAGTGCAA
23448795 ACAAAGGCA-C----TG---
1 ACAAAGGCACCGAAGTGCAA
23448807 A-AAAGGCACCGAAGTGCAA
1 ACAAAGGCACCGAAGTGCAA
* *
23448826 ACAAAGGCACTGAAGTGAAA
1 ACAAAGGCACCGAAGTGCAA
23448846 AC
1 AC
23448848 CCCGTACAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 18
0.68 0.03 0.29
Matches are distributed among these distances:
11 7 0.17
12 2 0.05
15 2 0.05
16 2 0.05
19 2 0.05
20 27 0.64
ACGTcount: A:0.47, C:0.22, G:0.25, T:0.07
Consensus pattern (20 bp):
ACAAAGGCACCGAAGTGCAA
Found at i:23448815 original size:31 final size:31
Alignment explanation
Indices: 23448777--23448839 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
23448767 AAGTGTATAC
23448777 AAAGGCACCGAAGTGCAAACAAAGGCACTGA
1 AAAGGCACCGAAGTGCAAACAAAGGCACTGA
23448808 AAAGGCACCGAAGTGCAAACAAAGGCACTGA
1 AAAGGCACCGAAGTGCAAACAAAGGCACTGA
23448839 A
1 A
23448840 GTGAAAACCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.46, C:0.22, G:0.25, T:0.06
Consensus pattern (31 bp):
AAAGGCACCGAAGTGCAAACAAAGGCACTGA
Found at i:23453580 original size:56 final size:51
Alignment explanation
Indices: 23453505--23453641 Score: 168
Period size: 50 Copynumber: 2.6 Consensus size: 51
23453495 GAGATCCCAT
*
23453505 GTAAGACCATGTCTGGGACATGGCATTGGCATTATTGAGGTTATGAGAGGTCCCCC
1 GTAAGACCATGTCTGGGACATGGCATTGGCA--ATCGA-G--ATGAGAGGTCCCCC
* * *
23453561 GTAAGATCATGTCTAGGACATGGCGTTGGC-ATCGAGATGAGAGGTCCCCC
1 GTAAGACCATGTCTGGGACATGGCATTGGCAATCGAGATGAGAGGTCCCCC
* *
23453611 GTAAGACCATGTTTGGGACATGGCATGGGCA
1 GTAAGACCATGTCTGGGACATGGCATTGGCA
23453642 CCGATATGAG
Statistics
Matches: 71, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
50 39 0.55
52 1 0.01
53 4 0.06
56 27 0.38
ACGTcount: A:0.24, C:0.20, G:0.32, T:0.24
Consensus pattern (51 bp):
GTAAGACCATGTCTGGGACATGGCATTGGCAATCGAGATGAGAGGTCCCCC
Found at i:23453605 original size:50 final size:50
Alignment explanation
Indices: 23453547--23453652 Score: 149
Period size: 50 Copynumber: 2.1 Consensus size: 50
23453537 TATTGAGGTT
* * * *
23453547 ATGAGAGGTCCCCCGTAAGATCATGTCTAGGACATGGCGTTGGCATCGAG
1 ATGAGAGGTCCCCCGTAAGACCATGTCTAGGACATGGCATGGGCACCGAG
* * *
23453597 ATGAGAGGTCCCCCGTAAGACCATGTTTGGGACATGGCATGGGCACCGAT
1 ATGAGAGGTCCCCCGTAAGACCATGTCTAGGACATGGCATGGGCACCGAG
23453647 ATGAGA
1 ATGAGA
23453653 ATCTCTCATG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.25, C:0.22, G:0.32, T:0.21
Consensus pattern (50 bp):
ATGAGAGGTCCCCCGTAAGACCATGTCTAGGACATGGCATGGGCACCGAG
Found at i:23453941 original size:20 final size:20
Alignment explanation
Indices: 23453916--23453954 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
23453906 TGAGTTATTT
23453916 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAAG-AGAGTAAGTAAAC
23453936 AAGTAAGAGAGTAAGTAAA
1 AAGTAAGAGAGTAAGTAAA
23453955 GAAGAAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAC
Found at i:23456563 original size:130 final size:133
Alignment explanation
Indices: 23456325--23456563 Score: 403
Period size: 130 Copynumber: 1.8 Consensus size: 133
23456315 CCCCCTTATA
23456325 AAACATAAACAATTAAAGTTAACATTAAAAACAGAAATTAAAGTGAAAAATAAAAATTTTAAAAT
1 AAACATAAACAATTAAAGTTAACATTAAAAACAGAAATTAAAGTG--AAATAAAAATTTTAAAAT
23456390 TAATCAAAAAATTTCTTCTCAAAAGATTACATTAAATTAATGCCCAGGAGCGGTTGGAGGGGTCA
64 TAATCAAAAAATTTCTTCTCAAAAGATTACATTAAATTAATGCCCAGGAGCGGTTGGAGGGGTCA
23456455 ATATT
129 ATATT
* * *
23456460 AAACATAAACAATTAAAGTTAACATTAAATATAGAAGTTAAAGTG-AA-AAAAA-TTTAAAATTA
1 AAACATAAACAATTAAAGTTAACATTAAAAACAGAAATTAAAGTGAAATAAAAATTTTAAAATTA
*
23456522 ATCAGAAAATTTCTTCTCAAAAGATTACATTAAATTAATGCC
66 ATCAAAAAATTTCTTCTCAAAAGATTACATTAAATTAATGCC
23456564 TAGAAAAGGT
Statistics
Matches: 100, Mismatches: 4, Indels: 5
0.92 0.04 0.05
Matches are distributed among these distances:
130 51 0.51
131 5 0.05
132 2 0.02
135 42 0.42
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.28
Consensus pattern (133 bp):
AAACATAAACAATTAAAGTTAACATTAAAAACAGAAATTAAAGTGAAATAAAAATTTTAAAATTA
ATCAAAAAATTTCTTCTCAAAAGATTACATTAAATTAATGCCCAGGAGCGGTTGGAGGGGTCAAT
ATT
Found at i:23461806 original size:14 final size:14
Alignment explanation
Indices: 23461787--23461813 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
23461777 GTGGTCCAGT
23461787 TGAACTGAACCGAG
1 TGAACTGAACCGAG
23461801 TGAACTGAACCGA
1 TGAACTGAACCGA
23461814 CCAAGAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.22, G:0.26, T:0.15
Consensus pattern (14 bp):
TGAACTGAACCGAG
Found at i:23468356 original size:37 final size:37
Alignment explanation
Indices: 23468310--23468382 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
23468300 AAAGAGAAAT
23468310 AGATGCTTCAACTTAACAAGTTAGAAGAATTCTAAAC
1 AGATGCTTCAACTTAACAAGTTAGAAGAATTCTAAAC
* *
23468347 AGATTCTTCAACTTAACGAGTTAGAAGAATTCTAAA
1 AGATGCTTCAACTTAACAAGTTAGAAGAATTCTAAA
23468383 TGTCTTCATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (37 bp):
AGATGCTTCAACTTAACAAGTTAGAAGAATTCTAAAC
Found at i:23469124 original size:22 final size:19
Alignment explanation
Indices: 23469093--23469139 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 19
23469083 AAAGATGATA
23469093 ATTATTAATATATAATTATATCT
1 ATTA-TAATATAT-ATTA-AT-T
23469116 ATTATAATATATATTAATT
1 ATTATAATATATATTAATT
23469135 ATTAT
1 ATTAT
23469140 CAATTTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 2 0.08
21 4 0.17
22 8 0.33
23 4 0.17
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTATAATATATATTAATT
Found at i:23469135 original size:16 final size:15
Alignment explanation
Indices: 23469095--23469136 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
23469085 AGATGATAAT
23469095 TATTAATATATAATTA
1 TATTAAT-TATAATTA
23469111 TATCT-ATTATAATATA
1 TAT-TAATTATAAT-TA
23469127 TATTAATTAT
1 TATTAATTAT
23469137 TATCAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 7 0.30
16 15 0.65
17 1 0.04
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTAATTATAATTA
Found at i:23469756 original size:25 final size:25
Alignment explanation
Indices: 23469703--23469756 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
23469693 ATTTTGATTT
* *
23469703 AATTATCTAATTTTTCAATTTATTG
1 AATTATCTAATTTTTCAATTAATTA
23469728 AATTAT-TAATATTTT-ATATTAATTA
1 AATTATCTAAT-TTTTCA-ATTAATTA
23469753 AATT
1 AATT
23469757 TTTTAGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.56
Consensus pattern (25 bp):
AATTATCTAATTTTTCAATTAATTA
Found at i:23476211 original size:34 final size:33
Alignment explanation
Indices: 23476160--23476236 Score: 111
Period size: 34 Copynumber: 2.3 Consensus size: 33
23476150 AATAATAGTT
* *
23476160 CAGT-TCAGTTGGGCCTTAGCCCATTACGGTGA
1 CAGTATCAGTTGAGCCTTAGCCCATTACAGTGA
23476192 CAGTATCAGTGTGAGCCTTAGCCCATTACAGTGA
1 CAGTATCAGT-TGAGCCTTAGCCCATTACAGTGA
*
23476226 CAGTACCAGTT
1 CAGTATCAGTT
23476237 CAGACATGCA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
32 4 0.10
33 6 0.15
34 30 0.75
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.27
Consensus pattern (33 bp):
CAGTATCAGTTGAGCCTTAGCCCATTACAGTGA
Found at i:23476543 original size:27 final size:26
Alignment explanation
Indices: 23476505--23476604 Score: 155
Period size: 27 Copynumber: 3.8 Consensus size: 26
23476495 TAACATTAAA
*
23476505 CATACAGTCATTTTATAACATAAGGG
1 CATAAAGTCATTTTATAACATAAGGG
23476531 CATAATAGTCATTTTATAACATAAGGG
1 CATAA-AGTCATTTTATAACATAAGGG
*
23476558 CATAACAGTCATTTTATAACATAATGG
1 CATAA-AGTCATTTTATAACATAAGGG
*
23476585 CATAACGTCATTTTATAACA
1 CATAAAGTCATTTTATAACA
23476605 GTTTGGGGGT
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
26 18 0.26
27 51 0.74
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (26 bp):
CATAAAGTCATTTTATAACATAAGGG
Found at i:23484082 original size:27 final size:27
Alignment explanation
Indices: 23484042--23484170 Score: 190
Period size: 27 Copynumber: 4.8 Consensus size: 27
23484032 ATAACATTAA
* *
23484042 GCATAA-ATTCATTTTCTAACATAGGG
1 GCATAATAGTCATTTTATAACATAGGG
23484068 GCATAATAGTCATTTTATAACATAGGG
1 GCATAATAGTCATTTTATAACATAGGG
23484095 GCATAATAGTCATTTTATAACATAGGG
1 GCATAATAGTCATTTTATAACATAGGG
* *
23484122 GCATAACAATCATTTTATAACATAGGG
1 GCATAATAGTCATTTTATAACATAGGG
*
23484149 GCATAACCA-TCATTTTATAACA
1 GCATAA-TAGTCATTTTATAACA
23484171 GTTTGGGGGT
Statistics
Matches: 97, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
26 6 0.06
27 89 0.92
28 2 0.02
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33
Consensus pattern (27 bp):
GCATAATAGTCATTTTATAACATAGGG
Found at i:23484894 original size:30 final size:31
Alignment explanation
Indices: 23484849--23484910 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
23484839 CTAAAGGCAG
*
23484849 AAGAAGAAAGAAATATTGATTTGCATAAAGA
1 AAGAAGAAAGAAATATTGATTCGCATAAAGA
* *
23484880 AAGAA-AAATAAATATTGATTCGCTTAAAGA
1 AAGAAGAAAGAAATATTGATTCGCATAAAGA
23484910 A
1 A
23484911 CTTACCGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 23 0.82
31 5 0.18
ACGTcount: A:0.55, C:0.05, G:0.16, T:0.24
Consensus pattern (31 bp):
AAGAAGAAAGAAATATTGATTCGCATAAAGA
Found at i:23486465 original size:50 final size:50
Alignment explanation
Indices: 23486352--23486554 Score: 282
Period size: 50 Copynumber: 4.1 Consensus size: 50
23486342 CTTAGGATGT
* * * * * **
23486352 TCTCATATCAATGCCCATGCCATGTCCCAGACATGGTCTTA-GGGGGACC
1 TCTCATCTCAGTGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACC
* * *
23486401 TCTCATCTCAGTGCCAACGCCATGTCCGAGACATGGTTTTACATGGGACC
1 TCTCATCTCAGTGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACC
* *
23486451 TCTCATCTCGGTGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACC
1 TCTCATCTCAGTGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACC
*
23486501 TCTCATCTCAGTGCCAACGCCATGTCCCAAACATGGTCTTACATGAGACC
1 TCTCATCTCAGTGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACC
23486551 TCTC
1 TCTC
23486555 TACCCAAATG
Statistics
Matches: 137, Mismatches: 16, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
49 35 0.26
50 102 0.74
ACGTcount: A:0.23, C:0.32, G:0.20, T:0.26
Consensus pattern (50 bp):
TCTCATCTCAGTGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACC
Found at i:23496301 original size:50 final size:50
Alignment explanation
Indices: 23496188--23496472 Score: 367
Period size: 50 Copynumber: 5.7 Consensus size: 50
23496178 ATGCCAAAGT
* ** * * **
23496188 CATGTCCCTGACATGGTCTTACATGGGATGTTCTCATACT-AGTGCCCATGC
1 CATGTCCCAGACATGGTCTTACATGGGA-CCTCTCAT-CTCGGTGCCAACAC
** *
23496239 CATGTCCCAGACATGGTCTTACGGGGGACCTCTAATCTCGGTGCCAACAC
1 CATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACAC
* * **
23496289 AATGTCCGAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAGGC
1 CATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACAC
* * * *
23496339 CATGTCCCAAACATGGTCTTACATGGGACTTCTCATCTCGGTGACAACGC
1 CATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACAC
23496389 CATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGA-
1 CATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAC-AC
23496439 CATGTCCCAGACATGGTCTTACATGGGACCTCTC
1 CATGTCCCAGACATGGTCTTACATGGGACCTCTC
23496473 TACCCAAATG
Statistics
Matches: 205, Mismatches: 27, Indels: 5
0.86 0.11 0.02
Matches are distributed among these distances:
49 2 0.01
50 178 0.87
51 25 0.12
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.26
Consensus pattern (50 bp):
CATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACAC
Found at i:23496451 original size:150 final size:151
Alignment explanation
Indices: 23496179--23496472 Score: 432
Period size: 150 Copynumber: 2.0 Consensus size: 151
23496169 GATCATAACA
* ** * * * *
23496179 TGCCAAAGTCATGTCCCTGACATGGTCTTACATGGGATGTTCTCATACTAGTGCCCATGCCATGT
1 TGCCAAAGCCATGTCCCAAACATGGTCTTACATGGGATCTTCTCATACTAGTGACAACGCCATGT
* *
23496244 CCCAGACATGGTCTTACGGGGGACCTCTAATCTCGGTGCCAACACAATGTCCGAGACATGGTCTT
66 CCCAGACATGGTCTTACAGGGGACCTCTAATCTCGGTGCCAACACAATGTCCCAGACATGGTCTT
23496309 ACATGGGACCTCTCATCTCGG
131 ACATGGGACCTCTCATCTCGG
* *
23496330 TGCCAAGGCCATGTCCCAAACATGGTCTTACATGGGA-CTTCTCAT-CTCGGTGACAACGCCATG
1 TGCCAAAGCCATGTCCCAAACATGGTCTTACATGGGATCTTCTCATACT-AGTGACAACGCCATG
* *
23496393 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGAC-ATGTCCCAGACATGGTC
65 TCCCAGACATGGTCTTACAGGGGACCTCTAATCTCGGTGCCAAC-ACAATGTCCCAGACATGGTC
23496457 TTACATGGGACCTCTC
129 TTACATGGGACCTCTC
23496473 TACCCAAATG
Statistics
Matches: 128, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
149 2 0.02
150 91 0.71
151 35 0.27
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.26
Consensus pattern (151 bp):
TGCCAAAGCCATGTCCCAAACATGGTCTTACATGGGATCTTCTCATACTAGTGACAACGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTAATCTCGGTGCCAACACAATGTCCCAGACATGGTCTT
ACATGGGACCTCTCATCTCGG
Found at i:23497795 original size:32 final size:33
Alignment explanation
Indices: 23497744--23497850 Score: 137
Period size: 33 Copynumber: 3.3 Consensus size: 33
23497734 AGACAAAAAC
*
23497744 AATATTCAGCAAACACAATGAATGGGGAGAAG-
1 AATATTCGGCAAACACAATGAATGGGGAGAAGT
* * *
23497776 AGGT-TTCGGCAAACGCAATGAATGGAGAGAAGT
1 A-ATATTCGGCAAACACAATGAATGGGGAGAAGT
* *
23497809 AATATTCGACAAACTCAATGAATGGGGAGAAGT
1 AATATTCGGCAAACACAATGAATGGGGAGAAGT
23497842 AATATTCGG
1 AATATTCGG
23497851 GAAAGGGAAC
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
32 27 0.43
33 36 0.57
ACGTcount: A:0.41, C:0.12, G:0.27, T:0.20
Consensus pattern (33 bp):
AATATTCGGCAAACACAATGAATGGGGAGAAGT
Found at i:23501123 original size:12 final size:13
Alignment explanation
Indices: 23501106--23501134 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
23501096 AGATGAGCAA
23501106 AATTTGGC-TTTT
1 AATTTGGCTTTTT
23501118 AATTTGGCTTTTT
1 AATTTGGCTTTTT
23501131 AATT
1 AATT
23501135 CATTTAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.21, C:0.07, G:0.14, T:0.59
Consensus pattern (13 bp):
AATTTGGCTTTTT
Found at i:23502392 original size:17 final size:17
Alignment explanation
Indices: 23502359--23502393 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
23502349 CTACAGGGGT
* *
23502359 CACACAGCCGTGTGACA
1 CACACAGCCGGGAGACA
23502376 CACACAGCCGGGAGACA
1 CACACAGCCGGGAGACA
23502393 C
1 C
23502394 GCCCGTGTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.31, C:0.37, G:0.26, T:0.06
Consensus pattern (17 bp):
CACACAGCCGGGAGACA
Found at i:23503804 original size:25 final size:25
Alignment explanation
Indices: 23503720--23503834 Score: 74
Period size: 25 Copynumber: 4.6 Consensus size: 25
23503710 GTACATGTAT
* **
23503720 GCTCATACGAGCTGTA-AATGGTAA
1 GCTCATACGAGCTGAATAACCGTAA
* * * **
23503744 GCTCTTCCGAGATGAATAACATTAA
1 GCTCATACGAGCTGAATAACCGTAA
* * *
23503769 ACTCCTCCGAGCTGAATAACCGTAA
1 GCTCATACGAGCTGAATAACCGTAA
*
23503794 GCTCATACGAGCT-AAGT-ATCGATAA
1 GCTCATACGAGCTGAA-TAACCG-TAA
*
23503819 GCTCATATGAGCTGAA
1 GCTCATACGAGCTGAA
23503835 ATCGATAACA
Statistics
Matches: 70, Mismatches: 17, Indels: 6
0.75 0.18 0.06
Matches are distributed among these distances:
24 17 0.24
25 51 0.73
26 2 0.03
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (25 bp):
GCTCATACGAGCTGAATAACCGTAA
Found at i:23505362 original size:45 final size:44
Alignment explanation
Indices: 23505249--23505377 Score: 186
Period size: 44 Copynumber: 2.9 Consensus size: 44
23505239 CGCCTAAATG
* * * *
23505249 AATGAGTAAGACCATAGTTGAAAGACGTTATGGCATCAGGATAA
1 AATGAGTAAGACCATAGCTGAAAGATGCTATGGCATCATGATAA
*
23505293 AATGAGTAAGACCATAACTGAAAGATGCTATGGCATCATGATAGA
1 AATGAGTAAGACCATAGCTGAAAGATGCTATGGCATCATGATA-A
* *
23505338 AATGAGTAAGACCATGGCTAAAAGATGCTATGGCATCATG
1 AATGAGTAAGACCATAGCTGAAAGATGCTATGGCATCATG
23505378 GTACTTAGGA
Statistics
Matches: 76, Mismatches: 8, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
44 38 0.50
45 38 0.50
ACGTcount: A:0.40, C:0.13, G:0.24, T:0.22
Consensus pattern (44 bp):
AATGAGTAAGACCATAGCTGAAAGATGCTATGGCATCATGATAA
Found at i:23505407 original size:45 final size:45
Alignment explanation
Indices: 23505255--23505394 Score: 129
Period size: 45 Copynumber: 3.1 Consensus size: 45
23505245 AATGAATGAG
* * * * * * *
23505255 TAAGACCATAGTTGAAAGACGTTATGGCATCAGGATA-AAATGAG
1 TAAGACCATGGCTGAAAGATGCTATGGCATCATGATACAAAGGAC
** * * *
23505299 TAAGACCATAACTGAAAGATGCTATGGCATCATGATAGAAATGAG
1 TAAGACCATGGCTGAAAGATGCTATGGCATCATGATACAAAGGAC
* * **
23505344 TAAGACCATGGCTAAAAGATGCTATGGCATCATGGTACTTAGGAC
1 TAAGACCATGGCTGAAAGATGCTATGGCATCATGATACAAAGGAC
23505389 TAAGAC
1 TAAGAC
23505395 TATTGTTGAA
Statistics
Matches: 81, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
44 32 0.40
45 49 0.60
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.23
Consensus pattern (45 bp):
TAAGACCATGGCTGAAAGATGCTATGGCATCATGATACAAAGGAC
Found at i:23507612 original size:46 final size:46
Alignment explanation
Indices: 23507557--23507706 Score: 140
Period size: 46 Copynumber: 3.3 Consensus size: 46
23507547 ATGTGTTACG
* *
23507557 GACTCAAGAATACATGAATAGTTTTCGAA-CTCTTACATATGTTGCA
1 GACTCAAGAATACATGAATAG-GTTCGAAGCTCTTACATATATTGCA
* * * * *
23507603 GATTCAAGAATAGAGGAATAGGTTCTAAGCTCTTGCATATATTGCA
1 GACTCAAGAATACATGAATAGGTTCGAAGCTCTTACATATATTGCA
* * * * * * * *
23507649 GACTCGAGAATACATGAATATGTTCTAAGCCCCTGCATATGTTGCG
1 GACTCAAGAATACATGAATAGGTTCGAAGCTCTTACATATATTGCA
*
23507695 GACTCGAGAATA
1 GACTCAAGAATA
23507707 TAGGAATATT
Statistics
Matches: 87, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
45 5 0.06
46 82 0.94
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.29
Consensus pattern (46 bp):
GACTCAAGAATACATGAATAGGTTCGAAGCTCTTACATATATTGCA
Found at i:23507714 original size:46 final size:46
Alignment explanation
Indices: 23507592--23507715 Score: 158
Period size: 46 Copynumber: 2.7 Consensus size: 46
23507582 CGAACTCTTA
* * * * * *
23507592 CATATGTTGCAGATTCAAGAATAGAGGAATAGGTTCTAAGCTCTTG
1 CATATGTTGCAGACTCGAGAATACAGGAATATGTTCTAAGCCCCTG
* *
23507638 CATATATTGCAGACTCGAGAATACATGAATATGTTCTAAGCCCCTG
1 CATATGTTGCAGACTCGAGAATACAGGAATATGTTCTAAGCCCCTG
* *
23507684 CATATGTTGCGGACTCGAGAATATAGGAATAT
1 CATATGTTGCAGACTCGAGAATACAGGAATAT
23507716 TAAGCCCTAG
Statistics
Matches: 66, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
46 66 1.00
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (46 bp):
CATATGTTGCAGACTCGAGAATACAGGAATATGTTCTAAGCCCCTG
Found at i:23511276 original size:30 final size:29
Alignment explanation
Indices: 23511242--23511321 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 29
23511232 GAGAATGTAA
23511242 TGCTCACACAAGCTGACAGTATTTCAAT-G-T
1 TGCTCACACAAGCTGACA-T-TTT-AATGGAT
*
23511272 TGCTCAGACAAGCTGACATTTTAATGGAAT
1 TGCTCACACAAGCTGACATTTTAATGG-AT
*
23511302 TGCTCACACAAGTTGACATT
1 TGCTCACACAAGCTGACATT
23511322 GTATCGAGGT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
27 3 0.07
28 4 0.09
29 1 0.02
30 36 0.82
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.30
Consensus pattern (29 bp):
TGCTCACACAAGCTGACATTTTAATGGAT
Found at i:23513692 original size:21 final size:21
Alignment explanation
Indices: 23513668--23513741 Score: 62
Period size: 21 Copynumber: 3.5 Consensus size: 21
23513658 CAATAAACTA
23513668 TAAACATTAAACCTCAAACCC
1 TAAACATTAAACCTCAAACCC
* **
23513689 TAAA-ATCAAAACCTCAAACAT
1 TAAACAT-TAAACCTCAAACCC
* *
23513710 TAAAAAATAAACCT-ATAACCC
1 TAAACATTAAACCTCA-AACCC
23513731 TAAACCATTAA
1 TAAA-CATTAA
23513742 CCATAAATTT
Statistics
Matches: 40, Mismatches: 9, Indels: 7
0.71 0.16 0.12
Matches are distributed among these distances:
20 3 0.08
21 32 0.80
22 5 0.12
ACGTcount: A:0.54, C:0.26, G:0.00, T:0.20
Consensus pattern (21 bp):
TAAACATTAAACCTCAAACCC
Found at i:23515499 original size:40 final size:40
Alignment explanation
Indices: 23515434--23515544 Score: 111
Period size: 40 Copynumber: 2.8 Consensus size: 40
23515424 TTGCACAATT
**
23515434 GTGCCCCTGTTTGCATTTC-GATGCCCCTGTAT-ACACTTTG
1 GTGCCCCTGTTTGCACGTCAG-TGCCCCTGT-TCACACTTTG
* *
23515474 GTGTCCCTGTTTGCACGTCAGTGCCCCTGTTCGCACTTTG
1 GTGCCCCTGTTTGCACGTCAGTGCCCCTGTTCACACTTTG
* **
23515514 GTGCCCCAGACTGCACGT-ATGTGCCCCTGTT
1 GTGCCCCTGTTTGCACGTCA-GTGCCCCTGTT
23515545 TTGCATCTAC
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
39 2 0.03
40 57 0.95
41 1 0.02
ACGTcount: A:0.11, C:0.32, G:0.23, T:0.33
Consensus pattern (40 bp):
GTGCCCCTGTTTGCACGTCAGTGCCCCTGTTCACACTTTG
Found at i:23515501 original size:20 final size:19
Alignment explanation
Indices: 23515478--23515545 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 19
23515468 ACTTTGGTGT
23515478 CCCTGTTTGCACGTCAGTGC
1 CCCTGTTTGCACGT-AGTGC
* * *
23515498 CCCTGTTCGCACTTTGGTGC
1 CCCTGTTTGCAC-GTAGTGC
* **
23515518 CCCAGACTGCACGTATGTGC
1 CCCTGTTTGCACGTA-GTGC
23515538 CCCTGTTT
1 CCCTGTTT
23515546 TGCATCTACG
Statistics
Matches: 34, Mismatches: 12, Indels: 4
0.68 0.24 0.08
Matches are distributed among these distances:
19 1 0.03
20 32 0.94
21 1 0.03
ACGTcount: A:0.10, C:0.35, G:0.24, T:0.31
Consensus pattern (19 bp):
CCCTGTTTGCACGTAGTGC
Found at i:23519483 original size:3 final size:3
Alignment explanation
Indices: 23519477--23519522 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
23519467 GTGGCTTGTT
23519477 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
23519523 GTTTTGGTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:23527341 original size:14 final size:14
Alignment explanation
Indices: 23527322--23527350 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
23527312 ATTTTGCTTC
23527322 ATGCATCTGTAAGT
1 ATGCATCTGTAAGT
23527336 ATGCATCTGTAAGT
1 ATGCATCTGTAAGT
23527350 A
1 A
23527351 AGATGTGTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.34
Consensus pattern (14 bp):
ATGCATCTGTAAGT
Found at i:23527502 original size:48 final size:46
Alignment explanation
Indices: 23527416--23527521 Score: 122
Period size: 48 Copynumber: 2.2 Consensus size: 46
23527406 TTTGCATGTA
* * * * *
23527416 TATATATTCTTTCTTTCTATCTGTTTGTGTATATATATATTTTCTTT
1 TATATATTCTTCCTTTCTATCTATATGTGTATACATATACTTT-TTT
* *
23527463 TCATATATTCTTCCTTTCTATCTATATGTGTGTGCATATACTTTTTT
1 T-ATATATTCTTCCTTTCTATCTATATGTGTATACATATACTTTTTT
23527510 TATATAATTCTT
1 TATAT-ATTCTT
23527522 TCTATCTTCC
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
46 4 0.08
47 11 0.22
48 35 0.70
ACGTcount: A:0.21, C:0.13, G:0.07, T:0.59
Consensus pattern (46 bp):
TATATATTCTTCCTTTCTATCTATATGTGTATACATATACTTTTTT
Found at i:23532824 original size:19 final size:19
Alignment explanation
Indices: 23532800--23532853 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
23532790 AATCTTCAAG
* *
23532800 GATATGCAATCTTTGATAT
1 GATATGCAATCTTAGATAA
23532819 GATATGCAATCTTAGATAA
1 GATATGCAATCTTAGATAA
23532838 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
23532854 AGATAAGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAA
Found at i:23532879 original size:22 final size:22
Alignment explanation
Indices: 23532814--23532876 Score: 69
Period size: 19 Copynumber: 3.0 Consensus size: 22
23532804 TGCAATCTTT
*
23532814 GATATGATATGCAATCTT---A
1 GATAAGATATGCAATCTTAGAA
23532833 GATAAGATATGCAATCTTAGAA
1 GATAAGATATGCAATCTTAGAA
* *
23532855 GATAAGATTTTGTAATCTTAGA
1 GATAAGA-TATGCAATCTTAGA
23532877 GATTTAATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
19 17 0.46
22 8 0.22
23 12 0.32
ACGTcount: A:0.40, C:0.08, G:0.17, T:0.35
Consensus pattern (22 bp):
GATAAGATATGCAATCTTAGAA
Found at i:23533822 original size:25 final size:24
Alignment explanation
Indices: 23533783--23533833 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
23533773 CATCGTAACA
*
23533783 TTATTTTAAATTTATCATGT-ATAT
1 TTATTTTAAACTTATCAT-TAATAT
23533807 TTATTTTAAAACTTATCATTAATAT
1 TTATTTT-AAACTTATCATTAATAT
23533832 TT
1 TT
23533834 TAAATTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 8 0.33
25 16 0.67
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.57
Consensus pattern (24 bp):
TTATTTTAAACTTATCATTAATAT
Found at i:23539971 original size:24 final size:24
Alignment explanation
Indices: 23539943--23539993 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
23539933 TTTCAAGAAG
* *
23539943 ATTTAATATTTATGAGTATAATAT
1 ATTTAACATTTATGAGCATAATAT
* *
23539967 ATTTAGCATTTATTAGCATAATAT
1 ATTTAACATTTATGAGCATAATAT
23539991 ATT
1 ATT
23539994 CGACTTTGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.39, C:0.04, G:0.08, T:0.49
Consensus pattern (24 bp):
ATTTAACATTTATGAGCATAATAT
Found at i:23544164 original size:14 final size:14
Alignment explanation
Indices: 23544145--23544172 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
23544135 ATAAATCTTA
23544145 AAAAAATATTTTAT
1 AAAAAATATTTTAT
23544159 AAAAAATATTTTAT
1 AAAAAATATTTTAT
23544173 GTGTATTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AAAAAATATTTTAT
Found at i:23544401 original size:14 final size:15
Alignment explanation
Indices: 23544368--23544409 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 15
23544358 GATCTGGGTT
23544368 CAAATAATTTTTGTAC
1 CAAA-AATTTTTGTAC
23544384 CAAAAATTTTTGTA-
1 CAAAAATTTTTGTAC
23544398 CAAAAAGTTTTT
1 CAAAAA-TTTTT
23544410 TTTTGTACCA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.24
15 15 0.60
16 4 0.16
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (15 bp):
CAAAAATTTTTGTAC
Found at i:23545259 original size:25 final size:24
Alignment explanation
Indices: 23545206--23545260 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
23545196 AATCATTTTA
* *
23545206 TTTTTTAAATTTGCTTTATTTCTT
1 TTTTTTAAATTTGCTTTAGTTATT
*
23545230 CTTTTTAGAATTT-CTTTTAGTTATT
1 TTTTTTA-AATTTGC-TTTAGTTATT
23545255 TTTTTT
1 TTTTTT
23545261 CAATAAAAGG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
24 7 0.28
25 18 0.72
ACGTcount: A:0.16, C:0.07, G:0.05, T:0.71
Consensus pattern (24 bp):
TTTTTTAAATTTGCTTTAGTTATT
Found at i:23559507 original size:16 final size:17
Alignment explanation
Indices: 23559475--23559518 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
23559465 TTAATCACTT
23559475 TAATATTAAATTTAATC
1 TAATATTAAATTTAATC
*
23559492 TAATATTATA-TTAATC
1 TAATATTAAATTTAATC
*
23559508 TAATATAAAAT
1 TAATATTAAAT
23559519 ATTATATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (17 bp):
TAATATTAAATTTAATC
Found at i:23559546 original size:28 final size:23
Alignment explanation
Indices: 23559477--23559574 Score: 92
Period size: 23 Copynumber: 4.1 Consensus size: 23
23559467 AATCACTTTA
*
23559477 ATATTAAATTTAATCT--AATATT
1 ATATT-AATTTAATATAAAATATT
*
23559499 ATATTAATCTAATATAAAATATT
1 ATATTAATTTAATATAAAATATT
23559522 ATATTAATTTAATCACTTGATAAATATT
1 ATATTAATTTAAT-A--T-A-AAATATT
* *
23559550 ATATTAATTTAATATTAAATCTT
1 ATATTAATTTAATATAAAATATT
23559573 AT
1 AT
23559575 TAAAATAATA
Statistics
Matches: 64, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
21 8 0.12
22 5 0.08
23 26 0.41
24 1 0.02
25 1 0.02
26 1 0.02
27 2 0.03
28 20 0.31
ACGTcount: A:0.46, C:0.05, G:0.01, T:0.48
Consensus pattern (23 bp):
ATATTAATTTAATATAAAATATT
Found at i:23559946 original size:19 final size:19
Alignment explanation
Indices: 23559906--23559946 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
23559896 TTTTGGGCTC
*
23559906 TCAGGCCCAATTTACAATT
1 TCAGGCCCAATTTACAAGT
* *
23559925 TCAGGTCCAATTTTCAAGT
1 TCAGGCCCAATTTACAAGT
23559944 TCA
1 TCA
23559947 ATTACCCATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.34
Consensus pattern (19 bp):
TCAGGCCCAATTTACAAGT
Found at i:23565278 original size:26 final size:26
Alignment explanation
Indices: 23565248--23565316 Score: 129
Period size: 26 Copynumber: 2.7 Consensus size: 26
23565238 CTCATTTGTG
*
23565248 AGTCATCTTGAGACAATCTCTCTGAA
1 AGTCATCTTGGGACAATCTCTCTGAA
23565274 AGTCATCTTGGGACAATCTCTCTGAA
1 AGTCATCTTGGGACAATCTCTCTGAA
23565300 AGTCATCTTGGGACAAT
1 AGTCATCTTGGGACAAT
23565317 GCATGACTAG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (26 bp):
AGTCATCTTGGGACAATCTCTCTGAA
Found at i:23566895 original size:20 final size:20
Alignment explanation
Indices: 23566872--23566911 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
23566862 TAATTACTTT
*
23566872 AATATTAAATTAATATAATA
1 AATACTAAATTAATATAATA
* *
23566892 AATACTATATTAATTTAATA
1 AATACTAAATTAATATAATA
23566912 TTAAATCTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (20 bp):
AATACTAAATTAATATAATA
Found at i:23567059 original size:17 final size:16
Alignment explanation
Indices: 23567014--23567061 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
23567004 ACTACTAAGA
23567014 TAAATATTAAATTAA-AT
1 TAAATATTAAA--AATAT
23567031 TAAATATT-AAAATAT
1 TAAATATTAAAAATAT
23567046 TAAAATATTAAAAATA
1 T-AAATATTAAAAATA
23567062 ATATTATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
14 2 0.07
15 3 0.11
16 9 0.32
17 14 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAATATTAAAAATAT
Done.