Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr6
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: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 58 of 136
Found at i:19181920 original size:63 final size:63
Alignment explanation
Indices: 19181818--19181950 Score: 212
Period size: 63 Copynumber: 2.1 Consensus size: 63
19181808 TTTTTAAAAA
* *
19181818 CACTTCTCAAAAGCAATACTAAACTAGCCCTAAATATATTGACTAGAGAATACTCTCATAGCT
1 CACTTCTCAAAAGCAACACTAAACTAGCCCTAAACATATTGACTAGAGAATACTCTCATAGCT
* * * *
19181881 CACTTCTCAAAGGTAACGCTAAACTAGCCCTAAGCATATTGACTAGAGAATACTCTCATAGCT
1 CACTTCTCAAAAGCAACACTAAACTAGCCCTAAACATATTGACTAGAGAATACTCTCATAGCT
19181944 CACTTCT
1 CACTTCT
19181951 TTGCTATTTT
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.36, C:0.26, G:0.11, T:0.27
Consensus pattern (63 bp):
CACTTCTCAAAAGCAACACTAAACTAGCCCTAAACATATTGACTAGAGAATACTCTCATAGCT
Found at i:19182034 original size:68 final size:67
Alignment explanation
Indices: 19181924--19182116 Score: 287
Period size: 68 Copynumber: 2.8 Consensus size: 67
19181914 GCATATTGAC
* *
19181924 TAGAGAATACTCTCATAGCTCACTTCTTTGCTATTTTCATTAAAAAGTTAATTTTAATCCCACAT
1 TAGAGAATACTC-CATAACTCACTTCTTTACTATTTTCATTAAAAA-TTAATTTTAATCCCACAT
*
19181989 TAAT
64 CAAT
* * *
19181993 TAGAGAATACTCCACAACTCACTTCTTCACTATTTTCATTAAAAAATTAATTTTAATCTCACATC
1 TAGAGAATACTCCATAACTCACTTCTTTACTATTTTCATT-AAAAATTAATTTTAATCCCACATC
*
19182058 GAT
65 AAT
*
19182061 TAGAGAATACTCCATAACTCACTTCTTTACTATTTTCATTAAAAAATAATTTTAAT
1 TAGAGAATACTCCATAACTCACTTCTTTACTATTTTCATTAAAAATTAATTTTAAT
19182117 AATATAAAAA
Statistics
Matches: 113, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
67 15 0.13
68 81 0.72
69 17 0.15
ACGTcount: A:0.36, C:0.19, G:0.05, T:0.39
Consensus pattern (67 bp):
TAGAGAATACTCCATAACTCACTTCTTTACTATTTTCATTAAAAATTAATTTTAATCCCACATCA
AT
Found at i:19182964 original size:12 final size:12
Alignment explanation
Indices: 19182949--19182974 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
19182939 GTTGTTTTAT
19182949 TATTATAATCAA
1 TATTATAATCAA
19182961 TATTATAATCAA
1 TATTATAATCAA
19182973 TA
1 TA
19182975 GCATCATCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (12 bp):
TATTATAATCAA
Found at i:19183030 original size:15 final size:16
Alignment explanation
Indices: 19183003--19183032 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
19182993 AAATTATTTA
19183003 AATTTACTTATTAAAT
1 AATTTACTTATTAAAT
19183019 AATTTA-TTATTAAA
1 AATTTACTTATTAAA
19183033 CTTAAATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
AATTTACTTATTAAAT
Found at i:19183184 original size:19 final size:18
Alignment explanation
Indices: 19183130--19183185 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 18
19183120 TAGTTTTGTA
19183130 ATAATTTTCTAAT-ATTTT
1 ATAATTTT-TAATCATTTT
*
19183148 ATAA-ATTTATATCAATTTT
1 ATAATTTTTA-ATC-ATTTT
19183167 CATAATTTTTAATCATTTT
1 -ATAATTTTTAATCATTTT
19183186 TATGGGAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
16 2 0.06
17 4 0.13
18 4 0.13
19 10 0.32
20 7 0.23
21 4 0.13
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (18 bp):
ATAATTTTTAATCATTTT
Found at i:19189780 original size:170 final size:168
Alignment explanation
Indices: 19189496--19189824 Score: 518
Period size: 170 Copynumber: 1.9 Consensus size: 168
19189486 AATTTGTATG
19189496 CTAACATTAAATTATTTTGAGGTATTGTTGTTTTGGATTATGCAACATCCAAGCTATTTTCAATA
1 CTAACATTAAATTATTTTGAGGTATTGTTGTTTTGGATTATGCAACATCCAAGCTATTTTCAATA
* * *
19189561 TCTTCTATTCACACTTGACTTTTTAGGCACTATTAGTTTGTTGATAATCCAACACTGAAGGGCTG
66 TCTTCTATGCACACTTGACCTTTTAGGCACTATTAGTTGGTTGATAATCCAACACTGAAGGGCTG
*
19189626 TTATCTCATATTCCAGGAATATCATGGCAATTTATAAA
131 TTATCTCACATTCCAGGAATATCATGGCAATTTATAAA
* * *
19189664 CTAA-ATTAAA-TAGTTTTGAGGTATTGTTGTTTCTGGATTGTGCAACATACCCATGCTGTTTTC
1 CTAACATTAAATTA-TTTTGAGGTATTGTTGTTT-TGGATTATGCAACAT--CCAAGCTATTTTC
* *
19189727 AGTATCTTCTATGCACACTTGACCTTTTAGGCACTATTAGTTGGTTGATAATCCCACACTGAAGG
62 AATATCTTCTATGCACACTTGACCTTTTAGGCACTATTAGTTGGTTGATAATCCAACACTGAAGG
*
19189792 GCTGTTATCTCACATTCCAGGAATATCTTGGCA
127 GCTGTTATCTCACATTCCAGGAATATCATGGCA
19189825 TCATTTCGGC
Statistics
Matches: 147, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
166 2 0.01
167 25 0.17
168 18 0.12
170 102 0.69
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (168 bp):
CTAACATTAAATTATTTTGAGGTATTGTTGTTTTGGATTATGCAACATCCAAGCTATTTTCAATA
TCTTCTATGCACACTTGACCTTTTAGGCACTATTAGTTGGTTGATAATCCAACACTGAAGGGCTG
TTATCTCACATTCCAGGAATATCATGGCAATTTATAAA
Found at i:19195441 original size:62 final size:63
Alignment explanation
Indices: 19195365--19195484 Score: 233
Period size: 62 Copynumber: 1.9 Consensus size: 63
19195355 TGTATCACGC
19195365 TTCATAGCTTAATTTAATCTTTACAAAATGTGAGGGG-CAACTCTGTAAGTATTGGGTCACAT
1 TTCATAGCTTAATTTAATCTTTACAAAATGTGAGGGGACAACTCTGTAAGTATTGGGTCACAT
19195427 TTCATAGCTTAATTTAATCTTTACAAAATGTGAGGGGACAACTCTGTAAGTATTGGGT
1 TTCATAGCTTAATTTAATCTTTACAAAATGTGAGGGGACAACTCTGTAAGTATTGGGT
19195485 TGAATGGTAA
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
62 37 0.65
63 20 0.35
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (63 bp):
TTCATAGCTTAATTTAATCTTTACAAAATGTGAGGGGACAACTCTGTAAGTATTGGGTCACAT
Found at i:19200142 original size:30 final size:29
Alignment explanation
Indices: 19200075--19200146 Score: 81
Period size: 31 Copynumber: 2.4 Consensus size: 29
19200065 TCAATTTGAT
* * *
19200075 AAATTTTAGTTTTTGTATTTTTTGAATTA
1 AAATTTTAATTTTTATATTTTTTAAATTA
*
19200104 ATTTATTTTAATTTTTATATTTTTTAAATTTA
1 A--AATTTTAATTTTTATATTTTTTAAA-TTA
19200136 AAATTTTAATT
1 AAATTTTAATT
19200147 CTAACTAAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
29 1 0.03
30 9 0.26
31 21 0.60
32 4 0.11
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (29 bp):
AAATTTTAATTTTTATATTTTTTAAATTA
Found at i:19200894 original size:5 final size:5
Alignment explanation
Indices: 19200884--19200953 Score: 140
Period size: 5 Copynumber: 14.0 Consensus size: 5
19200874 TGAGTTGACT
19200884 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
19200934 ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA
19200954 GTGGTTCTGG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 65 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:19202666 original size:26 final size:25
Alignment explanation
Indices: 19202610--19202671 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
19202600 NNNNNNNNNN
* *
19202610 TAAATTAAAATATTAAACTTATATTA
1 TAAATTAAAA-ATAAAACTTAAATTA
* *
19202636 TAAATTAAAAATAAAATTTAAATTT
1 TAAATTAAAAATAAAACTTAAATTA
*
19202661 TAAAATAAAAA
1 TAAATTAAAAA
19202672 ATTATTTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
25 21 0.68
26 10 0.32
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (25 bp):
TAAATTAAAAATAAAACTTAAATTA
Found at i:19202693 original size:20 final size:21
Alignment explanation
Indices: 19202668--19202711 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
19202658 TTTTAAAATA
*
19202668 AAAAATTA-TTTA-AATATTAT
1 AAAAATAACTTTACAAT-TTAT
19202688 AAAAATAACTTTACAATTTAT
1 AAAAATAACTTTACAATTTAT
19202709 AAA
1 AAA
19202712 TAACAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 7 0.33
21 11 0.52
22 3 0.14
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (21 bp):
AAAAATAACTTTACAATTTAT
Found at i:19203104 original size:13 final size:13
Alignment explanation
Indices: 19203086--19203114 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
19203076 TGAGGTGGTA
19203086 GTTCATTTATTTG
1 GTTCATTTATTTG
19203099 GTTCATTTATTTG
1 GTTCATTTATTTG
19203112 GTT
1 GTT
19203115 ATCAATTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.14, C:0.07, G:0.17, T:0.62
Consensus pattern (13 bp):
GTTCATTTATTTG
Found at i:19203245 original size:16 final size:16
Alignment explanation
Indices: 19203224--19203269 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
19203214 CGTTTGGTTC
19203224 ACTGTAATGGAATAGA
1 ACTGTAATGGAATAGA
19203240 ACTGTAACT-GAATAGA
1 ACTGTAA-TGGAATAGA
*
19203256 GCTGTAATGGAATA
1 ACTGTAATGGAATA
19203270 AAGCTATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 1 0.04
16 25 0.93
17 1 0.04
ACGTcount: A:0.41, C:0.09, G:0.24, T:0.26
Consensus pattern (16 bp):
ACTGTAATGGAATAGA
Found at i:19203274 original size:16 final size:16
Alignment explanation
Indices: 19203225--19203279 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
19203215 GTTTGGTTCA
19203225 CTGTAATGGAATAGAA-
1 CTGTAATGGAATA-AAG
*
19203241 CTGTAACT-GAATAGAG
1 CTGTAA-TGGAATAAAG
19203257 CTGTAATGGAATAAAG
1 CTGTAATGGAATAAAG
*
19203273 CTATAAT
1 CTGTAAT
19203280 CAATAATTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
15 2 0.06
16 30 0.91
17 1 0.03
ACGTcount: A:0.42, C:0.09, G:0.22, T:0.27
Consensus pattern (16 bp):
CTGTAATGGAATAAAG
Found at i:19203518 original size:58 final size:58
Alignment explanation
Indices: 19203448--19203579 Score: 169
Period size: 58 Copynumber: 2.3 Consensus size: 58
19203438 TTATTAAATT
* * * *
19203448 TTAATA-ATATTATTATTAAATATATTTTAATAAAAATAATAAATAATTTAATCATATT-
1 TTAATATA-ATTATTATTAAATACAATTTAAT-AAAATAATAAATAATTTAATAACATTC
* *
19203506 TTTATATAATTATTATTAAATACAATTTAATAAAATAATATATAATTTAATAACATTC
1 TTAATATAATTATTATTAAATACAATTTAATAAAATAATAAATAATTTAATAACATTC
*
19203564 TTAATGTAATTATTAT
1 TTAATATAATTATTAT
19203580 AATATGAATT
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
57 23 0.36
58 40 0.62
59 1 0.02
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (58 bp):
TTAATATAATTATTATTAAATACAATTTAATAAAATAATAAATAATTTAATAACATTC
Found at i:19207628 original size:16 final size:18
Alignment explanation
Indices: 19207602--19207634 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
19207592 TTAATTTAAA
19207602 TAAATTAA-TTTCTCAAT
1 TAAATTAATTTTCTCAAT
19207619 TAAA-TAATTTTCTCAA
1 TAAATTAATTTTCTCAA
19207635 CTCAATTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAATTAATTTTCTCAAT
Found at i:19208572 original size:24 final size:22
Alignment explanation
Indices: 19208544--19208599 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 22
19208534 CAACTCTTTC
19208544 CAGCAGATTTCAACTCTTTCACTT
1 CAGCAGATTTC--CTCTTTCACTT
*
19208568 CAGCAGAATT-CTCTTTCACTT
1 CAGCAGATTTCCTCTTTCACTT
*
19208589 CAGTAGATTTC
1 CAGCAGATTTC
19208600 TTCCTCGACA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 19 0.68
24 9 0.32
ACGTcount: A:0.25, C:0.27, G:0.11, T:0.38
Consensus pattern (22 bp):
CAGCAGATTTCCTCTTTCACTT
Found at i:19208583 original size:21 final size:21
Alignment explanation
Indices: 19208557--19208600 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
19208547 CAGATTTCAA
19208557 CTCTTTCACTTCAGCAGAATT
1 CTCTTTCACTTCAGCAGAATT
* *
19208578 CTCTTTCACTTCAGTAGATTT
1 CTCTTTCACTTCAGCAGAATT
19208599 CT
1 CT
19208601 TCCTCGACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.27, G:0.09, T:0.43
Consensus pattern (21 bp):
CTCTTTCACTTCAGCAGAATT
Found at i:19210646 original size:185 final size:184
Alignment explanation
Indices: 19210332--19210889 Score: 823
Period size: 185 Copynumber: 3.0 Consensus size: 184
19210322 ACTATGTTTA
* * * *
19210332 TAGTGTAAA-TTGAGACTAAAATTCTCTCTTTTCTTCATGTATGAGTATATTTGATAAGATGTGA
1 TAGTGTAAACTT-AGACCAAAA-T-TCTCTATTCTTTATGTATGATTATATTTGATAAGATGTGA
*
19210396 CATTCTTGTAATTGTATGCATGTTTCGAGAAATGTATGCGAATGAATGTATGTAATTAATTTATT
63 CATTCTTGTAATTGTATGCATGTTTCGAGGAATGTATGCGAATGAATGTATGTAATTAATTTATT
* *
19210461 GCTATGGATGATAAAGTAATTTTTCCGAATTTGTGATTCATTGAAAATAAATGTAATT
128 GCTATGGATGATAAAGTAAATTTTCCAAATTTGTGATTC-TTGAAAATAAATGTAATT
* *
19210519 TAGTGTAAACTTAGACCAAAATTCTCTATTCTTTATGTATGATTATATTTGATAAAATGTAACAT
1 TAGTGTAAACTTAGACCAAAATTCTCTATTCTTTATGTATGATTATATTTGATAAGATGTGACAT
* * *
19210584 TCTTGTAATTGTATACATGTTTCGAGGAATGTATGAGAATGAATGTATGTAATTAGTTTATTGCT
66 TCTTGTAATTGTATGCATGTTTCGAGGAATGTATGCGAATGAATGTATGTAATTAATTTATTGCT
* * * *
19210649 ATGGATGATAAAGTAAAATTTCCAAATTTATGATTCCTAGAGAATAAATGTAATT
131 ATGGATGATAAAGTAAATTTTCCAAATTTGTGATT-CTTGAAAATAAATGTAATT
* * *
19210704 TAGTGTAAACTGAGACCAAAATTCTCTCTTCTTTATGTTTGATTATATTTGATAAGATGTGACAT
1 TAGTGTAAACTTAGACCAAAATTCTCTATTCTTTATGTATGATTATATTTGATAAGATGTGACAT
* * *
19210769 TCTTGTAATTGTATGCATGTTTCGAGGAATGCATGCGAATGAATGTATGTAATTATTTTATTGCC
66 TCTTGTAATTGTATGCATGTTTCGAGGAATGTATGCGAATGAATGTATGTAATTAATTTATTGCT
* * *
19210834 GTGGATGATAAAGTAAATTTTCCAAAATTGTGATT-TTTAGAAATAAATGTAATT
131 ATGGATGATAAAGTAAATTTTCCAAATTTGTGATTCTTGA-AAATAAATGTAATT
19210888 TA
1 TA
19210890 TTATTATCTC
Statistics
Matches: 335, Mismatches: 33, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
183 2 0.01
184 15 0.04
185 297 0.89
186 2 0.01
187 17 0.05
188 2 0.01
ACGTcount: A:0.34, C:0.08, G:0.17, T:0.41
Consensus pattern (184 bp):
TAGTGTAAACTTAGACCAAAATTCTCTATTCTTTATGTATGATTATATTTGATAAGATGTGACAT
TCTTGTAATTGTATGCATGTTTCGAGGAATGTATGCGAATGAATGTATGTAATTAATTTATTGCT
ATGGATGATAAAGTAAATTTTCCAAATTTGTGATTCTTGAAAATAAATGTAATT
Found at i:19211421 original size:22 final size:22
Alignment explanation
Indices: 19211389--19211431 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
19211379 ATGTTCACGC
19211389 ATATATAAGGAAA-ACATGCCAT
1 ATATATAAGGAAAGA-ATGCCAT
*
19211411 ATATATTAGGAAAGAATGCCA
1 ATATATAAGGAAAGAATGCCA
19211432 CATGCACTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.49, C:0.12, G:0.16, T:0.23
Consensus pattern (22 bp):
ATATATAAGGAAAGAATGCCAT
Found at i:19221202 original size:101 final size:102
Alignment explanation
Indices: 19221082--19221266 Score: 266
Period size: 101 Copynumber: 1.8 Consensus size: 102
19221072 AAAGTGATGG
* * * *
19221082 TCACGTGTGTAGTAGTATGTGCAGGCTACTACGTGTACCGGAATGAT-A-GGTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGATACCACGTGTACCGG-ATGATAATGGTCACATGTGTAGT
*
19221145 AATTTGTGCAGGCTACTATGCGTACCAGATAGTTTCGA
65 AATATGTGCAGGCTACTATGCGTACCAGATAGTTTCGA
* * *
19221183 TCACGTGTGTAGTACTATGTGCAGTATACCACGTGTATCGGATGGTAATGGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGATACCACGTGTACCGGATGATAATGGTCACATGTGTAGTA
*
19221248 CTATGTGCAGGCTACTATG
66 ATATGTGCAGGCTACTATG
19221267 TGAACCGAAC
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
100 4 0.05
101 37 0.51
102 32 0.44
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAGGATACCACGTGTACCGGATGATAATGGTCACATGTGTAGTA
ATATGTGCAGGCTACTATGCGTACCAGATAGTTTCGA
Found at i:19221321 original size:45 final size:45
Alignment explanation
Indices: 19221270--19221364 Score: 172
Period size: 45 Copynumber: 2.1 Consensus size: 45
19221260 TACTATGTGA
* *
19221270 ACCGAACATCATTGATTAGTAAGGTGGTTGCTATGTGCTGATTCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
19221315 ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
1 ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
19221360 ACCGA
1 ACCGA
19221365 GTATCTGTTA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (45 bp):
ACCGAACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCC
Found at i:19223329 original size:16 final size:17
Alignment explanation
Indices: 19223300--19223332 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
19223290 AATAAGCAGC
*
19223300 AAAATCAGAGAAAGAGA
1 AAAAACAGAGAAAGAGA
19223317 AAAAACAGA-AAAGAGA
1 AAAAACAGAGAAAGAGA
19223333 GAGGAATAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.70, C:0.06, G:0.21, T:0.03
Consensus pattern (17 bp):
AAAAACAGAGAAAGAGA
Found at i:19224184 original size:3 final size:3
Alignment explanation
Indices: 19224166--19224222 Score: 71
Period size: 3 Copynumber: 19.0 Consensus size: 3
19224156 TATTTAGTTA
* *
19224166 ATT ATT -TT AGT ATT ATT ATT ATT ATT ATT ATT ACT ATT AATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT
*
19224211 ATT ACT ATT ATT
1 ATT ATT ATT ATT
19224223 TTTTTATTTA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
2 2 0.04
3 41 0.89
4 3 0.07
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:19227680 original size:21 final size:22
Alignment explanation
Indices: 19227644--19227685 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
19227634 ATTTGAGGTT
19227644 TTTAAAATCAATTTAAAATCAA
1 TTTAAAATCAATTTAAAATCAA
19227666 TTTAAAATC-ATTTAAAATCA
1 TTTAAAATCAATTTAAAATCA
19227686 TTTTTTGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (22 bp):
TTTAAAATCAATTTAAAATCAA
Found at i:19227688 original size:10 final size:11
Alignment explanation
Indices: 19227644--19227685 Score: 77
Period size: 11 Copynumber: 3.9 Consensus size: 11
19227634 ATTTGAGGTT
19227644 TTTAAAATCAA
1 TTTAAAATCAA
19227655 TTTAAAATCAA
1 TTTAAAATCAA
19227666 TTTAAAATC-A
1 TTTAAAATCAA
19227676 TTTAAAATCA
1 TTTAAAATCA
19227686 TTTTTTGGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
10 10 0.33
11 20 0.67
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (11 bp):
TTTAAAATCAA
Found at i:19233111 original size:45 final size:45
Alignment explanation
Indices: 19233046--19233144 Score: 123
Period size: 45 Copynumber: 2.2 Consensus size: 45
19233036 TTATTTTCAT
* *
19233046 TTCCA-TT-TCCATTTTGAGAAAACCACATTCATTTCTAAATG-A
1 TTCCATTTCTCCATATTGAGAAAACCACAATCATTTCTAAATGTA
* * *
19233088 TTCCATTTCTCCATATTGAAGAAAATCATAATCATTTCTAAATGTT
1 TTCCATTTCTCCATATTG-AGAAAACCACAATCATTTCTAAATGTA
19233134 TTCCATTTCTC
1 TTCCATTTCTC
19233145 TATTTTTATT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
42 5 0.10
43 2 0.04
44 8 0.17
45 22 0.46
46 11 0.23
ACGTcount: A:0.31, C:0.21, G:0.06, T:0.41
Consensus pattern (45 bp):
TTCCATTTCTCCATATTGAGAAAACCACAATCATTTCTAAATGTA
Found at i:19238867 original size:29 final size:29
Alignment explanation
Indices: 19238835--19238905 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 29
19238825 ATAATGCCTA
19238835 ATAAATATAACACCGATACAAAGTACCTG
1 ATAAATATAACACCGATACAAAGTACCTG
** *
19238864 AT-AATATGGTCACCGATACATAGTACCTG
1 ATAAATAT-AACACCGATACAAAGTACCTG
19238893 ATAAATATAACAC
1 ATAAATATAACAC
19238906 TAGCACATAG
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 5 0.14
29 25 0.71
30 5 0.14
ACGTcount: A:0.45, C:0.20, G:0.11, T:0.24
Consensus pattern (29 bp):
ATAAATATAACACCGATACAAAGTACCTG
Found at i:19238913 original size:29 final size:29
Alignment explanation
Indices: 19238797--19238926 Score: 95
Period size: 29 Copynumber: 4.5 Consensus size: 29
19238787 ACATAGTACC
*
19238797 TAGTACCTAATAAATATAACACTAG-CACA
1 TAGTACCTGATAAATATAACAC-AGACACA
* * * * *
19238826 TAATGCCTAATAAATATAACACCGATACA
1 TAGTACCTGATAAATATAACACAGACACA
* ** * *
19238855 AAGTACCTGAT-AATATGGTCACCGATACA
1 TAGTACCTGATAAATAT-AACACAGACACA
19238884 TAGTACCTGATAAATATAACACTAG-CACA
1 TAGTACCTGATAAATATAACAC-AGACACA
* *
19238913 TAGTGCTTGATAAA
1 TAGTACCTGATAAA
19238927 CTCTAATGAC
Statistics
Matches: 80, Mismatches: 17, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
28 6 0.08
29 68 0.85
30 6 0.08
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.25
Consensus pattern (29 bp):
TAGTACCTGATAAATATAACACAGACACA
Found at i:19240734 original size:27 final size:26
Alignment explanation
Indices: 19240673--19240734 Score: 61
Period size: 27 Copynumber: 2.3 Consensus size: 26
19240663 CGATAAACTG
* *
19240673 AAAGAAACGCCTTTGTGGCGTACTCT
1 AAAGAAATGCCTTTGTGGCGTACCCT
* * * *
19240699 GAAGGAATGGCTTTCGTGGTGTACCCT
1 AAAGAAATGCCTTT-GTGGCGTACCCT
19240726 AAAGAAATG
1 AAAGAAATG
19240735 TTTCTTGTGG
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
26 10 0.37
27 17 0.63
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.26
Consensus pattern (26 bp):
AAAGAAATGCCTTTGTGGCGTACCCT
Found at i:19242103 original size:10 final size:10
Alignment explanation
Indices: 19242090--19242114 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
19242080 TAATTACAAA
19242090 AAATTCATAT
1 AAATTCATAT
19242100 AAATTCATAT
1 AAATTCATAT
19242110 AAATT
1 AAATT
19242115 TTGACATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (10 bp):
AAATTCATAT
Found at i:19243397 original size:10 final size:10
Alignment explanation
Indices: 19243382--19243420 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
19243372 TACCTTAAAA
19243382 TGTGTAGTTT
1 TGTGTAGTTT
19243392 TGTGTAG-TT
1 TGTGTAGTTT
19243401 TGTGTAGTGTT
1 TGTGTAGT-TT
19243412 T-TGTAGTTT
1 TGTGTAGTTT
19243421 AATGTTTCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 11 0.41
10 13 0.48
11 3 0.11
ACGTcount: A:0.10, C:0.00, G:0.31, T:0.59
Consensus pattern (10 bp):
TGTGTAGTTT
Found at i:19243406 original size:19 final size:19
Alignment explanation
Indices: 19243382--19243420 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
19243372 TACCTTAAAA
19243382 TGTGTAGT-TTTGTGTAGTT
1 TGTGTAGTGTTT-TGTAGTT
19243401 TGTGTAGTGTTTTGTAGTT
1 TGTGTAGTGTTTTGTAGTT
19243420 T
1 T
19243421 AATGTTTCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 16 0.84
20 3 0.16
ACGTcount: A:0.10, C:0.00, G:0.31, T:0.59
Consensus pattern (19 bp):
TGTGTAGTGTTTTGTAGTT
Found at i:19248258 original size:17 final size:18
Alignment explanation
Indices: 19248238--19248283 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 18
19248228 TTTCTTTTGA
19248238 ATCACTCTTTTTT-TTTT
1 ATCACTCTTTTTTGTTTT
19248255 ATCACTCATCTTTTTGTTTT
1 ATCACTC-T-TTTTTGTTTT
19248275 -TC-CTCTTTT
1 ATCACTCTTTT
19248284 CTCCACTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
16 3 0.12
17 8 0.31
18 4 0.15
19 7 0.27
20 4 0.15
ACGTcount: A:0.11, C:0.22, G:0.02, T:0.65
Consensus pattern (18 bp):
ATCACTCTTTTTTGTTTT
Found at i:19251511 original size:27 final size:27
Alignment explanation
Indices: 19251481--19251535 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
19251471 TCTTCAAATT
*
19251481 CGGCTGCACCTAAATAAAACAAATGAA
1 CGGCTGCACCTAAATAAAACAAACGAA
19251508 CGGCTGCACCTAAATAAAACAAACGAA
1 CGGCTGCACCTAAATAAAACAAACGAA
19251535 C
1 C
19251536 TTCATTAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.47, C:0.25, G:0.15, T:0.13
Consensus pattern (27 bp):
CGGCTGCACCTAAATAAAACAAACGAA
Found at i:19259903 original size:21 final size:22
Alignment explanation
Indices: 19259861--19259910 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
19259851 AAGGTGGAAG
*
19259861 TTATGTGACAGTTTATCTGCAA
1 TTATGTGACAGTTTATCGGCAA
*
19259883 TTATGTGACTG-TTATCGGCAA
1 TTATGTGACAGTTTATCGGCAA
*
19259904 ATATGTG
1 TTATGTG
19259911 GTGGTTTGTC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 15 0.60
22 10 0.40
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.40
Consensus pattern (22 bp):
TTATGTGACAGTTTATCGGCAA
Found at i:19259936 original size:47 final size:47
Alignment explanation
Indices: 19259883--19259972 Score: 110
Period size: 47 Copynumber: 1.9 Consensus size: 47
19259873 TTATCTGCAA
* * *
19259883 TTATGT-GACTGTTATCGGCAAATATGTGGTGGTTTGTCCACAATGTG
1 TTATGTGGACAGTTA-CAGCAAATATGTGGTGGCTTGTCCACAATGTG
* **
19259930 TTATGTGGCCAGTTACAGCATTTATGTGGTGGCTTGTCCACAA
1 TTATGTGGACAGTTACAGCAAATATGTGGTGGCTTGTCCACAA
19259973 ATGGTGTGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
47 30 0.83
48 6 0.17
ACGTcount: A:0.21, C:0.16, G:0.27, T:0.37
Consensus pattern (47 bp):
TTATGTGGACAGTTACAGCAAATATGTGGTGGCTTGTCCACAATGTG
Found at i:19260150 original size:22 final size:22
Alignment explanation
Indices: 19260122--19260166 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
19260112 ATTATGATGA
19260122 TTGATATG-ATGAGATTGATATT
1 TTGATATGTATGAGATT-ATATT
*
19260144 TTGATATGTATGTGATTATATT
1 TTGATATGTATGAGATTATATT
19260166 T
1 T
19260167 GTGTTGATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.51
Consensus pattern (22 bp):
TTGATATGTATGAGATTATATT
Found at i:19264937 original size:17 final size:17
Alignment explanation
Indices: 19264911--19264943 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
19264901 TAAGAGAATA
19264911 GAATAGAATAAAATAAT
1 GAATAGAATAAAATAAT
*
19264928 GAATATAATAAAATAA
1 GAATAGAATAAAATAA
19264944 AAACAAATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (17 bp):
GAATAGAATAAAATAAT
Found at i:19267884 original size:29 final size:29
Alignment explanation
Indices: 19267852--19268088 Score: 93
Period size: 29 Copynumber: 8.4 Consensus size: 29
19267842 GTCGTAATTG
19267852 TCCCTTTTCATATTCGATGGTCCAAACCA
1 TCCCTTTTCATATTCGATGGTCCAAACCA
* * *
19267881 TCCCATTTCA-A-T--A--G-CCGAAGCTA
1 TCCCTTTTCATATTCGATGGTCC-AAACCA
* * * *
19267904 TCCCATTTCATATTCGATAG-CCGAAGCTA
1 TCCCTTTTCATATTCGATGGTCC-AAACCA
* ***
19267933 TCCCTTTTCATATTCAATGGTCGTCACCA
1 TCCCTTTTCATATTCGATGGTCCAAACCA
* ***
19267962 TCCTTTTTCATAGTT-GATGGTCGTCACCA
1 TCCCTTTTCATA-TTCGATGGTCCAAACCA
* * *
19267991 TCCCTTTTCAAAGTT-TATGGT-CATCACCA
1 TCCCTTTTCATA-TTCGATGGTCCA-AACCA
* * * **
19268020 TCCCTTTTTATAATCGAT-GACCAAAGTTA
1 TCCCTTTTCATATTCGATGGTCCAAA-CCA
* * * *
19268049 TCCCTTTTCATATTCGATAGTCGAAGCTA
1 TCCCTTTTCATATTCGATGGTCCAAACCA
19268078 TCCCTTTTCAT
1 TCCCTTTTCAT
19268089 TGGTCGATGA
Statistics
Matches: 162, Mismatches: 32, Indels: 28
0.73 0.14 0.13
Matches are distributed among these distances:
22 2 0.01
23 15 0.09
24 1 0.01
25 2 0.01
27 2 0.01
28 4 0.02
29 129 0.80
30 7 0.04
ACGTcount: A:0.24, C:0.27, G:0.12, T:0.37
Consensus pattern (29 bp):
TCCCTTTTCATATTCGATGGTCCAAACCA
Found at i:19280522 original size:26 final size:27
Alignment explanation
Indices: 19280493--19280545 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
19280483 ATGACCGTAA
19280493 TGCCCCTAAAGGGTAAATGACT-ATTT
1 TGCCCCTAAAGGGTAAATGACTGATTT
**
19280519 TGCCCCTCGAGGGTAAATGACTGATTT
1 TGCCCCTAAAGGGTAAATGACTGATTT
19280546 GTACTATAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 20 0.83
27 4 0.17
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (27 bp):
TGCCCCTAAAGGGTAAATGACTGATTT
Found at i:19286390 original size:29 final size:29
Alignment explanation
Indices: 19286335--19286396 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
19286325 CATAATTTAA
* *
19286335 CATAAAAAGTCCCAAATGGAAATAAAGTT
1 CATAAAAAGTCCCAAATGCAAATAAAGTC
19286364 CATAAAAA-T-CCAAATGACAAATAAAAGTC
1 CATAAAAAGTCCCAAATG-CAAAT-AAAGTC
19286393 CATA
1 CATA
19286397 TTTATGTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 7 0.24
28 5 0.17
29 17 0.59
ACGTcount: A:0.55, C:0.16, G:0.10, T:0.19
Consensus pattern (29 bp):
CATAAAAAGTCCCAAATGCAAATAAAGTC
Found at i:19286796 original size:49 final size:49
Alignment explanation
Indices: 19286718--19286853 Score: 200
Period size: 49 Copynumber: 2.8 Consensus size: 49
19286708 ACACCATTTG
*
19286718 TGGACAAGCCACCACTGATATGCAAATATACTGCCACTGATAAATTTTA
1 TGGACAAGCCACCACTGATTTGCAAATATACTGCCACTGATAAATTTTA
* * * * * *
19286767 TGGACAAGCCACCATTGATTTGTATATATATTGCCATTGATAAATTTTG
1 TGGACAAGCCACCACTGATTTGCAAATATACTGCCACTGATAAATTTTA
*
19286816 TGGACAAGCCACCACTGATTTGCAGATATACTGCCACT
1 TGGACAAGCCACCACTGATTTGCAAATATACTGCCACT
19286854 ACTTTGACCT
Statistics
Matches: 75, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
49 75 1.00
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.30
Consensus pattern (49 bp):
TGGACAAGCCACCACTGATTTGCAAATATACTGCCACTGATAAATTTTA
Found at i:19303754 original size:25 final size:25
Alignment explanation
Indices: 19303694--19303754 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
19303684 CTCCTAAATT
19303694 TTAATTGAATTATCTAATTTTTCAA
1 TTAATTGAATTATCTAATTTTTCAA
*
19303719 TTTATTGAATTAT-TAATATTTT-ATA
1 TTAATTGAATTATCTAAT-TTTTCA-A
*
19303744 TTAATTAAATT
1 TTAATTGAATT
19303755 TTTTAGAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
24 5 0.16
25 26 0.84
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (25 bp):
TTAATTGAATTATCTAATTTTTCAA
Found at i:19305622 original size:41 final size:42
Alignment explanation
Indices: 19305518--19305624 Score: 121
Period size: 43 Copynumber: 2.5 Consensus size: 42
19305508 TCCATAGTTA
* *
19305518 GGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTGTGAAAG
1 GGGTTGCTAAGTGCTGATTCCACCGTATCCTTGAATAT-AAAG
* *
19305561 GGGTTGTTATGTGCTGATTCC-CCGTATCAC-TGAATAT-AAG
1 GGGTTGCTAAGTGCTGATTCCACCGTATC-CTTGAATATAAAG
*
19305601 GTGGTTGCTAAGTGCTCATTCCAC
1 G-GGTTGCTAAGTGCTGATTCCAC
19305625 TTAGTAACAG
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
40 4 0.07
41 17 0.31
42 13 0.24
43 20 0.37
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.34
Consensus pattern (42 bp):
GGGTTGCTAAGTGCTGATTCCACCGTATCCTTGAATATAAAG
Found at i:19319206 original size:28 final size:28
Alignment explanation
Indices: 19319165--19319263 Score: 153
Period size: 28 Copynumber: 3.5 Consensus size: 28
19319155 AGGGAGATTG
*
19319165 GCACTAAGTATGCGAGTTTAATTGTAAA
1 GCACTAAGTGTGCGAGTTTAATTGTAAA
*
19319193 GCACTAAGTGTGCGAGTTTAATGGTAAA
1 GCACTAAGTGTGCGAGTTTAATTGTAAA
* * *
19319221 GCACTAAGTGTGCGAGTTTGATTATTAA
1 GCACTAAGTGTGCGAGTTTAATTGTAAA
19319249 GCACTAAGTGTGCGA
1 GCACTAAGTGTGCGA
19319264 ACTTATTAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 65 1.00
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTAATTGTAAA
Found at i:19326493 original size:22 final size:22
Alignment explanation
Indices: 19326450--19326496 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
19326440 ATTAGGTACC
* *
19326450 ATTGTTGACGCACTTGCGCTTT
1 ATTGTCGACGCACTTGCACTTT
19326472 ATTGTCGACGCACTTTG-ACTTT
1 ATTGTCGACGCAC-TTGCACTTT
19326494 ATT
1 ATT
19326497 TTTAATACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.43
Consensus pattern (22 bp):
ATTGTCGACGCACTTGCACTTT
Found at i:19328646 original size:17 final size:17
Alignment explanation
Indices: 19328624--19328656 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
19328614 GTTAGTGCAC
*
19328624 ATTGTCGTTGCATTTTT
1 ATTGTCATTGCATTTTT
19328641 ATTGTCATTGCATTTT
1 ATTGTCATTGCATTTT
19328657 AATGTTAGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.12, G:0.15, T:0.58
Consensus pattern (17 bp):
ATTGTCATTGCATTTTT
Found at i:19334514 original size:19 final size:17
Alignment explanation
Indices: 19334465--19334515 Score: 50
Period size: 19 Copynumber: 2.8 Consensus size: 17
19334455 TTTTAATGGT
19334465 TAAA-TAAGTAAATTAG
1 TAAATTAAGTAAATTAG
*
19334481 TAAATAAATGATAAATTAAG
1 TAAATTAA-G-TAAATT-AG
19334501 TAAAATTAAGTAAAT
1 T-AAATTAAGTAAAT
19334516 GTATCATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
16 4 0.14
17 2 0.07
18 1 0.04
19 11 0.39
20 4 0.14
21 6 0.21
ACGTcount: A:0.59, C:0.00, G:0.10, T:0.31
Consensus pattern (17 bp):
TAAATTAAGTAAATTAG
Found at i:19335402 original size:42 final size:43
Alignment explanation
Indices: 19335355--19335458 Score: 111
Period size: 42 Copynumber: 2.4 Consensus size: 43
19335345 TCCTGCGGTG
* * *
19335355 TGATTTCATCTAAGACCATGTATGGGAAATTGGCATC-ATATA
1 TGATTTCATGTAAGACCATGCATGGGAAAGTGGCATCGATATA
* * * *
19335397 TGATTTCTTGTAAGACCCTGCCTGGGACAGTGGCATCGATATA
1 TGATTTCATGTAAGACCATGCATGGGAAAGTGGCATCGATATA
* **
19335440 TTATAACATGTAAGACCAT
1 TGATTTCATGTAAGACCAT
19335459 ATTTGGGATA
Statistics
Matches: 49, Mismatches: 12, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
42 30 0.61
43 19 0.39
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (43 bp):
TGATTTCATGTAAGACCATGCATGGGAAAGTGGCATCGATATA
Found at i:19336105 original size:48 final size:48
Alignment explanation
Indices: 19336010--19336110 Score: 123
Period size: 48 Copynumber: 2.1 Consensus size: 48
19336000 GATATGATGC
* * * *
19336010 TGTCAAAATTGGTGCTTAATTGCTGTCCACTTTTGAGTATATTAATGT
1 TGTCAAAATTGGTGCTTAAGTGCTGTCCACTTTTGAGCAAATCAATGT
* **
19336058 TGTCCAAATTGGTGCTTAAGTGCTGTCCTTTTTTGTA-CAAATCAATGT
1 TGTCAAAATTGGTGCTTAAGTGCTGTCCACTTTTG-AGCAAATCAATGT
19336106 TGTCA
1 TGTCA
19336111 GAATGTTCTT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
48 43 0.98
49 1 0.02
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.43
Consensus pattern (48 bp):
TGTCAAAATTGGTGCTTAAGTGCTGTCCACTTTTGAGCAAATCAATGT
Found at i:19338762 original size:50 final size:50
Alignment explanation
Indices: 19338700--19338959 Score: 394
Period size: 50 Copynumber: 5.2 Consensus size: 50
19338690 CATTTGGGTA
* * *
19338700 AAGAGGTTCCATGTAAGACAATGTCTGGGACATGGCGTTGGCACCAAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
* *
19338750 AAGAGATCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
*
19338800 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
* * * *
19338850 GAGAGGTCCCATGTAAGACCATGTTTGAGACATGGCGTTGGAACCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
* * *
19338900 AAGAGGTCTCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
*
19338950 GAGAGGTCCC
1 AAGAGGTCCC
19338960 NNNNNNNNNN
Statistics
Matches: 190, Mismatches: 20, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 190 1.00
ACGTcount: A:0.27, C:0.20, G:0.32, T:0.22
Consensus pattern (50 bp):
AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
Found at i:19344580 original size:90 final size:91
Alignment explanation
Indices: 19344462--19344643 Score: 357
Period size: 90 Copynumber: 2.0 Consensus size: 91
19344452 AAGTTAGGAC
19344462 ACGATGTCTCGAATTCCCGATACGCGAATAAAAATGCTTATTTAAAAAATATTTGGCTATCTCGG
1 ACGATGTCTCGAATTCCCGATACGCGAATAAAAATGCTTATTTAAAAAATATTTGGCTATCTCGG
19344527 ATTTAAAAGGGAGATCACGACCAGTA
66 ATTTAAAAGGGAGATCACGACCAGTA
19344553 ACGATGTCTC-AATTCCCGATACGCGAATAAAAATGCTTATTTAAAAAATATTTGGCTATCTCGG
1 ACGATGTCTCGAATTCCCGATACGCGAATAAAAATGCTTATTTAAAAAATATTTGGCTATCTCGG
19344617 ATTTAAAAGGGAGATCACGACCAGTA
66 ATTTAAAAGGGAGATCACGACCAGTA
19344643 A
1 A
19344644 GTTAGGACGC
Statistics
Matches: 91, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
90 81 0.89
91 10 0.11
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (91 bp):
ACGATGTCTCGAATTCCCGATACGCGAATAAAAATGCTTATTTAAAAAATATTTGGCTATCTCGG
ATTTAAAAGGGAGATCACGACCAGTA
Found at i:19348080 original size:18 final size:18
Alignment explanation
Indices: 19348057--19348093 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
19348047 GACTAACCCA
19348057 CCGAAGCTGAAAAACGAC
1 CCGAAGCTGAAAAACGAC
19348075 CCGAAGCTGAAAAACGAC
1 CCGAAGCTGAAAAACGAC
19348093 C
1 C
19348094 ATGATATTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.43, C:0.30, G:0.22, T:0.05
Consensus pattern (18 bp):
CCGAAGCTGAAAAACGAC
Found at i:19349698 original size:51 final size:51
Alignment explanation
Indices: 19349579--19349719 Score: 178
Period size: 51 Copynumber: 2.8 Consensus size: 51
19349569 TGAAAGTGAA
* *
19349579 AGTGATGGTCACGTGTGTAGTACTATGTGCAGGCTACGATGCGTACCGAAT
1 AGTGATGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTACCGAAT
* * * *
19349630 AGCT--TCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAT
1 AG-TGAT-GGTCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTACCGAAT
* *
19349681 AGTGATGGTCACATGTGTAGTACTATGTGCAGACTACTA
1 AGTGATGGTCACGTGTGTAGTACTATGTGCAGGCTACTA
19349720 TGTGAACCGG
Statistics
Matches: 77, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
50 2 0.03
51 73 0.95
52 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (51 bp):
AGTGATGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTACCGAAT
Found at i:19356469 original size:32 final size:32
Alignment explanation
Indices: 19356413--19356486 Score: 80
Period size: 32 Copynumber: 2.3 Consensus size: 32
19356403 CAGCTGCCTT
* *
19356413 TGTTCACACCCGATGGACCATCCAACTTC-TGA
1 TGTTCACACCCGAAGGACCATCCAACTCCAT-A
* *
19356445 TGTTCACACCC-AAGGAACCTTCCAAGTCCATA
1 TGTTCACACCCGAAGG-ACCATCCAACTCCATA
19356477 TGTTCACACC
1 TGTTCACACC
19356487 AAAGACTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
31 3 0.08
32 32 0.89
33 1 0.03
ACGTcount: A:0.27, C:0.35, G:0.14, T:0.24
Consensus pattern (32 bp):
TGTTCACACCCGAAGGACCATCCAACTCCATA
Found at i:19359103 original size:50 final size:50
Alignment explanation
Indices: 19359047--19359240 Score: 185
Period size: 50 Copynumber: 3.9 Consensus size: 50
19359037 CATTGAGGTT
* *
19359047 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAC
** * *
19359097 ATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGAT
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAC
** ** * * * *
19359147 ATGAGAACTCTTATGTAAGACCATATCTGGGATATAGCATTGGTA--GTAC
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AC
* * ** * *
19359196 AAGAAACATCCCATGTAAGACCATGTCTAGGACATGGCTTTGGCA
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
19359241 TGTTATTATC
Statistics
Matches: 114, Mismatches: 29, Indels: 3
0.78 0.20 0.02
Matches are distributed among these distances:
48 1 0.01
49 34 0.30
50 79 0.69
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAC
Found at i:19367571 original size:175 final size:176
Alignment explanation
Indices: 19367260--19367614 Score: 498
Period size: 175 Copynumber: 2.0 Consensus size: 176
19367250 CTTCAATTAT
* * * * *
19367260 TCAATAATGGTAACATTCTCAAACTATAACAGTACCAAAAATTACGACATGGATCGGCTAGTTTA
1 TCAAAAATGGTAACATTCTCAAAATATAACAGTACAAAAAATTACGACATGGATCAGCTAGCTTA
* *
19367325 AGTTTCCAACATTTTGAAAAACATAAAAATTTCAAGAAAAGGAATAAATTAAACTAACCAAATTG
66 AGTTTCCAACATTCTGAAAAACATAAAAATTTCAAAAAAAGGAATAAATTAAACTAACCAAATTG
* * *
19367390 AAGCTTGAAAAATTGGAGCCCTAGCCATGCTTTGAGAGTTTCTCCC
131 AAGCTTGAAAAATTAGAGCCCTAGCCATGCGTCGAGAGTTTCTCCC
*
19367436 TCAAAAATGGTAACATTCTCAAAATTTAACAGTACAAAAAATTACGACATAGG-TCAGCTAGCTT
1 TCAAAAATGGTAACATTCTCAAAATATAACAGTACAAAAAATTACGACAT-GGATCAGCTAGCTT
* ** * ** * *
19367500 AATTTTCCAGGATTCTG-AAATCATAATGATTTCAAAAAAAGGACTAAATTAAACTAGCCAAATT
65 AAGTTTCCAACATTCTGAAAAACATAAAAATTTCAAAAAAAGGAATAAATTAAACTAACCAAATT
* *
19367564 GAAGCTTGAAAATTTAGAGCCCTAGCCGTGCGTCGAGAGTTTCTCCC
130 GAAGCTTGAAAAATTAGAGCCCTAGCCATGCGTCGAGAGTTTCTCCC
19367611 TCAA
1 TCAA
19367615 TGGTTTCGAT
Statistics
Matches: 157, Mismatches: 21, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
175 87 0.55
176 68 0.43
177 2 0.01
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (176 bp):
TCAAAAATGGTAACATTCTCAAAATATAACAGTACAAAAAATTACGACATGGATCAGCTAGCTTA
AGTTTCCAACATTCTGAAAAACATAAAAATTTCAAAAAAAGGAATAAATTAAACTAACCAAATTG
AAGCTTGAAAAATTAGAGCCCTAGCCATGCGTCGAGAGTTTCTCCC
Found at i:19368257 original size:28 final size:28
Alignment explanation
Indices: 19368217--19368276 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
19368207 CTCGGATCGT
* *
19368217 ACATATGTAGATTACGAAGTCAGTTTGC
1 ACATAAGTAGATTACGAAGTCAGTTTAC
*
19368245 ACATAAGTAGATTACGGAGTCAGTTTAC
1 ACATAAGTAGATTACGAAGTCAGTTTAC
19368273 ACAT
1 ACAT
19368277 GGATGCTTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (28 bp):
ACATAAGTAGATTACGAAGTCAGTTTAC
Found at i:19368548 original size:52 final size:52
Alignment explanation
Indices: 19368492--19368635 Score: 173
Period size: 52 Copynumber: 2.8 Consensus size: 52
19368482 ACAATTCACA
* **
19368492 CATTCAATACAATGACAACTCACATATACATTTCATCACAAAA-TAGTTCAAG
1 CATTCAATACAATGAAAACTTGCATATACATTTCATCACAAAACT-GTTCAAG
* * * * ** *
19368544 CATTCGATGCAAAGAAAATTTGTGTATACATTTCATCACAAAACTGTTCATG
1 CATTCAATACAATGAAAACTTGCATATACATTTCATCACAAAACTGTTCAAG
*
19368596 CATTTAATACAATGAAAACTTGCATATACATTTCATCACA
1 CATTCAATACAATGAAAACTTGCATATACATTTCATCACA
19368636 CAAAAAATTT
Statistics
Matches: 74, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
52 73 0.99
53 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (52 bp):
CATTCAATACAATGAAAACTTGCATATACATTTCATCACAAAACTGTTCAAG
Found at i:19376291 original size:20 final size:20
Alignment explanation
Indices: 19376268--19376308 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
19376258 GAAAGCTAAA
*
19376268 TTGAGCTCGAATGAGCTGAT
1 TTGAGCTCAAATGAGCTGAT
19376288 TTGAGCTCAAATGAGCTGAT
1 TTGAGCTCAAATGAGCTGAT
19376308 T
1 T
19376309 GGGGCTGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.32
Consensus pattern (20 bp):
TTGAGCTCAAATGAGCTGAT
Found at i:19376323 original size:20 final size:20
Alignment explanation
Indices: 19376270--19376324 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 20
19376260 AAGCTAAATT
* * *
19376270 GAGCTCGAATGAGCTGATTT
1 GAGCTCAAACGAGCTGATTG
*
19376290 GAGCTCAAATGAGCTGATTG
1 GAGCTCAAACGAGCTGATTG
* *
19376310 GGGCTGAAACGAGCT
1 GAGCTCAAACGAGCT
19376325 AAAGGAGCTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.27, C:0.16, G:0.33, T:0.24
Consensus pattern (20 bp):
GAGCTCAAACGAGCTGATTG
Found at i:19387057 original size:4 final size:4
Alignment explanation
Indices: 19387048--19387097 Score: 91
Period size: 4 Copynumber: 12.5 Consensus size: 4
19387038 CAAATAATTT
*
19387048 CATA CATA CATA CACA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
19387096 CA
1 CA
19387098 CATACAGTGT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.22
Consensus pattern (4 bp):
CATA
Found at i:19396160 original size:14 final size:14
Alignment explanation
Indices: 19396141--19396170 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
19396131 ATAGATTTTA
19396141 TTTTATTTCTATTT
1 TTTTATTTCTATTT
*
19396155 TTTTATTTTTATTT
1 TTTTATTTCTATTT
19396169 TT
1 TT
19396171 CCCAAAAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTATTTCTATTT
Found at i:19400603 original size:13 final size:13
Alignment explanation
Indices: 19400585--19400612 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
19400575 TACTTTTACC
19400585 ATTATTATATATA
1 ATTATTATATATA
19400598 ATTATTATATATA
1 ATTATTATATATA
19400611 AT
1 AT
19400613 CATGTGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATTATTATATATA
Found at i:19403098 original size:18 final size:18
Alignment explanation
Indices: 19403075--19403109 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
19403065 TGATAAAATT
19403075 ATTGAAAATTTTCATTTG
1 ATTGAAAATTTTCATTTG
19403093 ATTGAAAATTTTCATTT
1 ATTGAAAATTTTCATTT
19403110 CAGCATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.06, G:0.09, T:0.51
Consensus pattern (18 bp):
ATTGAAAATTTTCATTTG
Found at i:19404199 original size:13 final size:15
Alignment explanation
Indices: 19404175--19404206 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
19404165 TTTAAGTGGA
19404175 AATATGTTAATTA-T
1 AATATGTTAATTAGT
19404189 AATAT-TTAATTAGT
1 AATATGTTAATTAGT
19404203 AATA
1 AATA
19404207 AAATAAGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (15 bp):
AATATGTTAATTAGT
Found at i:19411016 original size:20 final size:20
Alignment explanation
Indices: 19410979--19411017 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
19410969 CCCGCAGTTC
* * *
19410979 AAATTTTCCAACTTTTTCCT
1 AAATGTTCCAAATATTTCCT
19410999 AAATGTTCCAAATATTTCC
1 AAATGTTCCAAATATTTCC
19411018 AATTTAGTCC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.23, G:0.03, T:0.44
Consensus pattern (20 bp):
AAATGTTCCAAATATTTCCT
Found at i:19411017 original size:30 final size:29
Alignment explanation
Indices: 19410978--19411035 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
19410968 CCCCGCAGTT
*
19410978 CAAATTTTCCAACTTT-TTCCTAAATGTTC
1 CAAATTTTCCAA-TTTAGTCCTAAATGTTC
19411007 CAAATATTTCCAATTTAGTCCTAAATGTT
1 CAAAT-TTTCCAATTTAGTCCTAAATGTT
19411036 TCTAAAGTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 8 0.31
30 18 0.69
ACGTcount: A:0.31, C:0.21, G:0.05, T:0.43
Consensus pattern (29 bp):
CAAATTTTCCAATTTAGTCCTAAATGTTC
Found at i:19415944 original size:20 final size:20
Alignment explanation
Indices: 19415904--19415961 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
19415894 CCCTAGTTTG
* **
19415904 CACTTCGGTGCCCTTACTCA
1 CACTTCAGTGCCCTTGTTCA
19415924 CACTTCAGTGCCCTTGTTCA
1 CACTTCAGTGCCCTTGTTCA
* * *
19415944 CACATCAATGCCCCTGTT
1 CACTTCAGTGCCCTTGTT
19415962 TGCACTTTGG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.17, C:0.38, G:0.14, T:0.31
Consensus pattern (20 bp):
CACTTCAGTGCCCTTGTTCA
Found at i:19416367 original size:24 final size:24
Alignment explanation
Indices: 19416332--19416386 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
19416322 AAGATCGAAC
19416332 ATGA-GTTAAATAAAATTGTTTGA
1 ATGATGTTAAATAAAATTGTTTGA
*
19416355 ATGATGTTAAATAAACTTGTTTGA
1 ATGATGTTAAATAAAATTGTTTGA
19416379 ATGATGTT
1 ATGATGTT
19416387 GAAAAACGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 4 0.13
24 26 0.87
ACGTcount: A:0.38, C:0.02, G:0.18, T:0.42
Consensus pattern (24 bp):
ATGATGTTAAATAAAATTGTTTGA
Found at i:19416587 original size:275 final size:275
Alignment explanation
Indices: 19416096--19416617 Score: 1017
Period size: 275 Copynumber: 1.9 Consensus size: 275
19416086 ATTAACAAAA
*
19416096 TTGTTTGAATGATGTTGAAAACCGAATCTAAATTGGATAAATGACAGTGGAATGCCATAAATGTT
1 TTGTTTGAATGATGTTGAAAAACGAATCTAAATTGGATAAATGACAGTGGAATGCCATAAATGTT
19416161 ATATGATTCGTGTGTGAAAAACTCACCTGTTGCTGTGAAATTCTGATAGCAGGGATTTGTATAGT
66 ATATGATTCGTGTGTGAAAAACTCACCTGTTGCTGTGAAATTCTGATAGCAGGGATTTGTATAGT
19416226 AGCTAGTTCATTTGTTTAAATATGAACTGAGGTGAATTATATTGTTTAAAATGTGAATGATAATG
131 AGCTAGTTCATTTGTTTAAATATGAACTGAGGTGAATTATATTGTTTAAAATGTGAATGATAATG
19416291 GAACAAAATGACTTGAGTTATAAATGGTCAAAAGATCGAACATGAGTTAAATAAAATTGTTTGAA
196 GAACAAAATGACTTGAGTTATAAATGGTCAAAAGATCGAACATGAGTTAAATAAAATTGTTTGAA
19416356 TGATGTTAAATAAAC
261 TGATGTTAAATAAAC
*
19416371 TTGTTTGAATGATGTTGAAAAACGAATCTGAATTGGATAAATGACAGTGGAATGCCATAAATGTT
1 TTGTTTGAATGATGTTGAAAAACGAATCTAAATTGGATAAATGACAGTGGAATGCCATAAATGTT
*
19416436 ATATGATTCGTGTGTGAAAAACTCACCTGTTGCTGTGAAATTTTGATAGCAGGGATTTGTATAGT
66 ATATGATTCGTGTGTGAAAAACTCACCTGTTGCTGTGAAATTCTGATAGCAGGGATTTGTATAGT
19416501 AGCTAGTTCATTTGTTTAAATATGAACTGAGGTGAATTATATTGTTTAAAATGTGAATGATAATG
131 AGCTAGTTCATTTGTTTAAATATGAACTGAGGTGAATTATATTGTTTAAAATGTGAATGATAATG
19416566 GAACAAAATGACTTGAGTTATAAATGGTCAAAAGATCGAACATGAGTTAAAT
196 GAACAAAATGACTTGAGTTATAAATGGTCAAAAGATCGAACATGAGTTAAAT
19416618 GGTTATGTTA
Statistics
Matches: 244, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
275 244 1.00
ACGTcount: A:0.37, C:0.08, G:0.21, T:0.34
Consensus pattern (275 bp):
TTGTTTGAATGATGTTGAAAAACGAATCTAAATTGGATAAATGACAGTGGAATGCCATAAATGTT
ATATGATTCGTGTGTGAAAAACTCACCTGTTGCTGTGAAATTCTGATAGCAGGGATTTGTATAGT
AGCTAGTTCATTTGTTTAAATATGAACTGAGGTGAATTATATTGTTTAAAATGTGAATGATAATG
GAACAAAATGACTTGAGTTATAAATGGTCAAAAGATCGAACATGAGTTAAATAAAATTGTTTGAA
TGATGTTAAATAAAC
Found at i:19425961 original size:367 final size:367
Alignment explanation
Indices: 19425288--19426022 Score: 1470
Period size: 367 Copynumber: 2.0 Consensus size: 367
19425278 AAAGAGTTAT
19425288 GCGTAAATGCACTAGCTTGTGGTTATGGTCAATGTTTATGCTTATGTATTGTGTGTTATGCCAAT
1 GCGTAAATGCACTAGCTTGTGGTTATGGTCAATGTTTATGCTTATGTATTGTGTGTTATGCCAAT
19425353 GAAATGAGTGAGAATAGACAATGAAATGATAAGTTCATAGATGAGACGAAATATGATGAAATAAA
66 GAAATGAGTGAGAATAGACAATGAAATGATAAGTTCATAGATGAGACGAAATATGATGAAATAAA
19425418 AAGGATTGTTGAGTTAAAGGACATACTTGTAAGGAAGGAATTTACTTATGATATATGTGAGTTTA
131 AAGGATTGTTGAGTTAAAGGACATACTTGTAAGGAAGGAATTTACTTATGATATATGTGAGTTTA
19425483 CTTATGTCATGAATAAATACACTAATTCATGAATTGATAATGTAATTAAGCTTATGCTAAGTAAA
196 CTTATGTCATGAATAAATACACTAATTCATGAATTGATAATGTAATTAAGCTTATGCTAAGTAAA
19425548 TGGAATGATAAATAAGTAAATGAAATGGTTCACCATTTTAAGAAAAGGTTGATGATGATCTAATT
261 TGGAATGATAAATAAGTAAATGAAATGGTTCACCATTTTAAGAAAAGGTTGATGATGATCTAATT
19425613 TAGCTTATAAGACCTTATTATGTTATAAATGGAAAGTATTCA
326 TAGCTTATAAGACCTTATTATGTTATAAATGGAAAGTATTCA
19425655 GCGTAAATGCACTAGCTTGTGGTTATGGTCAATGTTTATGCTTATGTATTGTGTGTTATGCCAAT
1 GCGTAAATGCACTAGCTTGTGGTTATGGTCAATGTTTATGCTTATGTATTGTGTGTTATGCCAAT
19425720 GAAATGAGTGAGAATAGACAATGAAATGATAAGTTCATAGATGAGACGAAATATGATGAAATAAA
66 GAAATGAGTGAGAATAGACAATGAAATGATAAGTTCATAGATGAGACGAAATATGATGAAATAAA
19425785 AAGGATTGTTGAGTTAAAGGACATACTTGTAAGGAAGGAATTTACTTATGATATATGTGAGTTTA
131 AAGGATTGTTGAGTTAAAGGACATACTTGTAAGGAAGGAATTTACTTATGATATATGTGAGTTTA
19425850 CTTATGTCATGAATAAATACACTAATTCATGAATTGATAATGTAATTAAGCTTATGCTAAGTAAA
196 CTTATGTCATGAATAAATACACTAATTCATGAATTGATAATGTAATTAAGCTTATGCTAAGTAAA
19425915 TGGAATGATAAATAAGTAAATGAAATGGTTCACCATTTTAAGAAAAGGTTGATGATGATCTAATT
261 TGGAATGATAAATAAGTAAATGAAATGGTTCACCATTTTAAGAAAAGGTTGATGATGATCTAATT
19425980 TAGCTTATAAGACCTTATTATGTTATAAATGGAAAGTATTCA
326 TAGCTTATAAGACCTTATTATGTTATAAATGGAAAGTATTCA
19426022 G
1 G
19426023 GATGTTAATG
Statistics
Matches: 368, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
367 368 1.00
ACGTcount: A:0.38, C:0.08, G:0.20, T:0.34
Consensus pattern (367 bp):
GCGTAAATGCACTAGCTTGTGGTTATGGTCAATGTTTATGCTTATGTATTGTGTGTTATGCCAAT
GAAATGAGTGAGAATAGACAATGAAATGATAAGTTCATAGATGAGACGAAATATGATGAAATAAA
AAGGATTGTTGAGTTAAAGGACATACTTGTAAGGAAGGAATTTACTTATGATATATGTGAGTTTA
CTTATGTCATGAATAAATACACTAATTCATGAATTGATAATGTAATTAAGCTTATGCTAAGTAAA
TGGAATGATAAATAAGTAAATGAAATGGTTCACCATTTTAAGAAAAGGTTGATGATGATCTAATT
TAGCTTATAAGACCTTATTATGTTATAAATGGAAAGTATTCA
Found at i:19432301 original size:11 final size:11
Alignment explanation
Indices: 19432282--19432311 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
19432272 AGAATGATGA
*
19432282 ATGAGTGAGGG
1 ATGATTGAGGG
19432293 ATGATTGAGGG
1 ATGATTGAGGG
19432304 ATGATTGA
1 ATGATTGA
19432312 AAAAGTGAGA
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:0.30, C:0.00, G:0.43, T:0.27
Consensus pattern (11 bp):
ATGATTGAGGG
Found at i:19433561 original size:46 final size:46
Alignment explanation
Indices: 19433509--19433603 Score: 163
Period size: 46 Copynumber: 2.1 Consensus size: 46
19433499 ACAAAGAAAA
* *
19433509 AACCTCGACCCACTATCAAGAATGATAGGAACCTTGGTATATGATG
1 AACCTCGACCCACTATAAAGAATGATAGGAACCTTAGTATATGATG
*
19433555 AACCTCGACCCACTATAAAGGATGATAGGAACCTTAGTATATGATG
1 AACCTCGACCCACTATAAAGAATGATAGGAACCTTAGTATATGATG
19433601 AAC
1 AAC
19433604 GCCACACTAT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (46 bp):
AACCTCGACCCACTATAAAGAATGATAGGAACCTTAGTATATGATG
Found at i:19436046 original size:33 final size:31
Alignment explanation
Indices: 19435985--19436048 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 31
19435975 ATGGCAGTGT
* *
19435985 TTATATGAAAGACCATAGCTGGGCTATGGCA
1 TTATATGAAAGACCATAACTGAGCTATGGCA
*
19436016 TTATGATGATAAGACCATAACTGAGTTATGGCA
1 TTAT-ATGA-AAGACCATAACTGAGCTATGGCA
19436049 CTACGAATGC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 4 0.14
32 4 0.14
33 20 0.71
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.28
Consensus pattern (31 bp):
TTATATGAAAGACCATAACTGAGCTATGGCA
Found at i:19441367 original size:101 final size:102
Alignment explanation
Indices: 19441252--19441436 Score: 277
Period size: 101 Copynumber: 1.8 Consensus size: 102
19441242 AAAGTGATGG
* * *
19441252 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACC-AGA-A-TGATAGGTCGCATGTGTAC
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGA-ATAGTGAT-GGTCACAAGTGTAC
*
19441314 TACTATGTGTAGGCTACTATGCGTACAGGATAGCTTCGA
64 TACTATGTGCAGGCTACTATGCGTACAGGATAGCTTCGA
* *
19441353 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATCGAATAGTGATGGTCACAAGTGTAGTA
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAATAGTGATGGTCACAAGTGTACTA
19441418 CTATGTGCAGGCTACTATG
66 CTATGTGCAGGCTACTATG
19441437 TGAACCGGTA
Statistics
Matches: 75, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
101 38 0.51
102 33 0.44
103 4 0.05
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.30
Consensus pattern (102 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGAATAGTGATGGTCACAAGTGTACTA
CTATGTGCAGGCTACTATGCGTACAGGATAGCTTCGA
Found at i:19441372 original size:51 final size:50
Alignment explanation
Indices: 19441249--19441434 Score: 207
Period size: 51 Copynumber: 3.7 Consensus size: 50
19441239 GTGAAAGTGA
*
19441249 TGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAAT-GAT
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAATAG-T
* * * * * * *
19441299 AGGTCGCATGTGTACTACTATGTGTAGGCTACTATGCGTA-CAGGATAGCT
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAATAG-T
* *
19441349 TCGATCACATGTGTAGTACTATGTGCAGGCTACTACGTGTATC-GAATAGT
1 T-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAATAGT
*
19441399 GATGGTCACAAGTGTAGTACTATGTGCAGGCTACTA
1 --TGGTCACATGTGTAGTACTATGTGCAGGCTACTA
19441435 TGTGAACCGG
Statistics
Matches: 112, Mismatches: 19, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
49 5 0.04
50 36 0.32
51 69 0.62
52 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (50 bp):
TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAATAGT
Found at i:19441683 original size:16 final size:16
Alignment explanation
Indices: 19441662--19441693 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
19441652 TGATTGAAAG
*
19441662 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
19441678 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
19441694 GCAACAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:19449530 original size:18 final size:19
Alignment explanation
Indices: 19449488--19449532 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
19449478 TCAAGATCTT
19449488 AAATTAATGTGGTCCAAAG
1 AAATTAATGTGGTCCAAAG
19449507 AAATTAATGTGGTCCAAA-
1 AAATTAATGTGGTCCAAAG
19449525 AAATTAAT
1 AAATTAAT
19449533 TAGTACATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 8 0.31
19 18 0.69
ACGTcount: A:0.47, C:0.09, G:0.16, T:0.29
Consensus pattern (19 bp):
AAATTAATGTGGTCCAAAG
Found at i:19452954 original size:3 final size:3
Alignment explanation
Indices: 19452948--19453036 Score: 58
Period size: 3 Copynumber: 29.7 Consensus size: 3
19452938 CTTATATCTT
* * * *
19452948 TAA TAA TAA TAA TAA TAA TAC TTA TAA TATT TAA TAA TAA T-A CAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA
* * * *
19452993 TAA TAA TACC T-A TAA TATT TAA TAA TAA T-A CAA TAA TAA AAA TA
1 TAA TAA TA-A TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TA
19453037 TGTTTAACAA
Statistics
Matches: 64, Mismatches: 16, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
2 3 0.05
3 56 0.88
4 5 0.08
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:19452995 original size:33 final size:33
Alignment explanation
Indices: 19452928--19453031 Score: 169
Period size: 33 Copynumber: 3.2 Consensus size: 33
19452918 AAATATGTTG
*
19452928 AATAATAATACTTAT-ATCTTTAATAATAAT--
1 AATAATAATACTTATAATATTTAATAATAATAC
19452958 AATAATAATACTTATAATATTTAATAATAATAC
1 AATAATAATACTTATAATATTTAATAATAATAC
*
19452991 AATAATAATACCTATAATATTTAATAATAATAC
1 AATAATAATACTTATAATATTTAATAATAATAC
19453024 AATAATAA
1 AATAATAA
19453032 AAATATGTTT
Statistics
Matches: 69, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
30 15 0.22
31 14 0.20
33 40 0.58
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (33 bp):
AATAATAATACTTATAATATTTAATAATAATAC
Found at i:19454039 original size:26 final size:26
Alignment explanation
Indices: 19454005--19454064 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
19453995 AATTAATAAT
19454005 ATTATAAAAATATAAAGAT-TAAATTAA
1 ATTA-AAAAATA-AAAGATATAAATTAA
* *
19454032 ATTAAAAATTAAAATATATAAATTAA
1 ATTAAAAAATAAAAGATATAAATTAA
*
19454058 ATCAAAA
1 ATTAAAA
19454065 CTAAAATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 5 0.17
26 20 0.69
27 4 0.14
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (26 bp):
ATTAAAAAATAAAAGATATAAATTAA
Found at i:19454072 original size:31 final size:31
Alignment explanation
Indices: 19454011--19454070 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
19454001 TAATATTATA
* *
19454011 AAAATATAAAGATTAAATTAAATTAAAAATT
1 AAAATATAAAGATTAAATAAAACTAAAAATT
19454042 AAAATATATAA-ATTAAATCAAAACTAAAA
1 AAAATATA-AAGATTAAAT-AAAACTAAAA
19454071 TTTATTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 15 0.60
32 10 0.40
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (31 bp):
AAAATATAAAGATTAAATAAAACTAAAAATT
Found at i:19455484 original size:50 final size:49
Alignment explanation
Indices: 19455421--19455524 Score: 140
Period size: 49 Copynumber: 2.1 Consensus size: 49
19455411 GTGTTCTACA
*
19455421 TTTAATTAAGTCATGCA-TA-AAAACATCTTATATGTTAATTAAGTTTGTAT
1 TTTAATTAAGTCATGCATTATAAAAC-TC--ATATGTTAAATAAGTTTGTAT
* *
19455471 TTTAATTATGTCATGCATTATGAAACTCATATGTTAAATAAGTTTGTAT
1 TTTAATTAAGTCATGCATTATAAAACTCATATGTTAAATAAGTTTGTAT
19455520 TTTAA
1 TTTAA
19455525 GACGTGCATT
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
49 25 0.51
50 16 0.33
51 4 0.08
52 4 0.08
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.45
Consensus pattern (49 bp):
TTTAATTAAGTCATGCATTATAAAACTCATATGTTAAATAAGTTTGTAT
Found at i:19455559 original size:46 final size:47
Alignment explanation
Indices: 19455444--19455560 Score: 139
Period size: 49 Copynumber: 2.5 Consensus size: 47
19455434 TGCATAAAAA
* *
19455444 CATCTTATATGTTAATTAAGTTTGTATTTTAATTATGTCATGCATTATG
1 CATCTTATATGTTAATTAAGTTTGTATTTTAATGACGTCAT--ATTATG
* * * *
19455493 AAACTCATATGTTAAATAAGTTTGTATTTTAA-GACGTGCAT-TTATG
1 CATCTTATATGTTAATTAAGTTTGTATTTTAATGACGT-CATATTATG
19455539 CATCTTATATGTTAATTAAGTT
1 CATCTTATATGTTAATTAAGTT
19455561 CAAGCATAAG
Statistics
Matches: 57, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
46 23 0.40
48 3 0.05
49 31 0.54
ACGTcount: A:0.32, C:0.09, G:0.13, T:0.47
Consensus pattern (47 bp):
CATCTTATATGTTAATTAAGTTTGTATTTTAATGACGTCATATTATG
Found at i:19455936 original size:37 final size:37
Alignment explanation
Indices: 19455895--19455989 Score: 127
Period size: 37 Copynumber: 2.6 Consensus size: 37
19455885 CATCAAGCAT
* *
19455895 AGAGACATGACTATTCAAATACACATAGATCAAGTGA
1 AGAGACATGACTTTTCAAATACACATAGAACAAGTGA
* * * *
19455932 AGAGACATGGCTTTTCAACTAGACATGGAACAAGTGA
1 AGAGACATGACTTTTCAAATACACATAGAACAAGTGA
*
19455969 AGAAACATGACTTTTCAAATA
1 AGAGACATGACTTTTCAAATA
19455990 TCTTTCATTC
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.43, C:0.16, G:0.18, T:0.23
Consensus pattern (37 bp):
AGAGACATGACTTTTCAAATACACATAGAACAAGTGA
Found at i:19459853 original size:99 final size:101
Alignment explanation
Indices: 19459725--19459945 Score: 250
Period size: 99 Copynumber: 2.2 Consensus size: 101
19459715 TATCCTATAT
** * * * * *
19459725 ATGGTCTTACATGGGAGTTCTCATATCGGTG-TCCATGCGATGTCCCAGACATGGTCTTACGGGG
1 ATGGTCTTACATGGGACCTCTAATATCGGTGCT-AACGCCATGTCCCAGACATGGTCTTACAGGG
*
19459789 GACCTCTC-TCT-TGGTGCCAACGCCATGTCCCAGAC
65 GACCTCTCATCTATGATGCCAACGCCATGTCCCAGAC
* * *
19459824 ATGGTCTTATATGGGACCTCTAATCTCGGTGCTAACGCCATGTCCCAGACATGGTCTTACATGGG
1 ATGGTCTTACATGGGACCTCTAATATCGGTGCTAACGCCATGTCCCAGACATGGTCTTACAGGGG
*
19459889 ACCTCTCATAATCTCAATGATGCCAATGCCATGTCCCAGAC
66 ACCTCTC---ATCT--ATGATGCCAACGCCATGTCCCAGAC
*
19459930 ATGCTCTTACATGGGA
1 ATGGTCTTACATGGGA
19459946 TCTCATTCAC
Statistics
Matches: 100, Mismatches: 14, Indels: 9
0.81 0.11 0.07
Matches are distributed among these distances:
99 60 0.60
100 1 0.01
103 3 0.03
106 36 0.36
ACGTcount: A:0.22, C:0.28, G:0.23, T:0.28
Consensus pattern (101 bp):
ATGGTCTTACATGGGACCTCTAATATCGGTGCTAACGCCATGTCCCAGACATGGTCTTACAGGGG
ACCTCTCATCTATGATGCCAACGCCATGTCCCAGAC
Found at i:19459876 original size:50 final size:50
Alignment explanation
Indices: 19459725--19459945 Score: 230
Period size: 50 Copynumber: 4.3 Consensus size: 50
19459715 TATCCTATAT
** * * * *
19459725 ATGGTCTTACATGGGAGTTCTCATATCGGTGTCC-ATGCGATGTCCCAGAC
1 ATGGTCTTACATGGGACCTCTAATCTCGGTG-CCAACGCCATGTCCCAGAC
** * *
19459775 ATGGTCTTACGGGGGACCTCT-CTCTTGGTGCCAACGCCATGTCCCAGAC
1 ATGGTCTTACATGGGACCTCTAATCTCGGTGCCAACGCCATGTCCCAGAC
* *
19459824 ATGGTCTTATATGGGACCTCTAATCTCGGTGCTAACGCCATGTCCCAGAC
1 ATGGTCTTACATGGGACCTCTAATCTCGGTGCCAACGCCATGTCCCAGAC
* *
19459874 ATGGTCTTACATGGGACCTCTCATAATCTCAATGATGCCAATGCCATGTCCCAGAC
1 ATGGTCTTACATGGGA-C-CTC-TAATCTC---GGTGCCAACGCCATGTCCCAGAC
*
19459930 ATGCTCTTACATGGGA
1 ATGGTCTTACATGGGA
19459946 TCTCATTCAC
Statistics
Matches: 143, Mismatches: 20, Indels: 10
0.83 0.12 0.06
Matches are distributed among these distances:
48 2 0.01
49 38 0.27
50 57 0.40
51 1 0.01
52 3 0.02
53 7 0.05
56 35 0.24
ACGTcount: A:0.22, C:0.28, G:0.23, T:0.28
Consensus pattern (50 bp):
ATGGTCTTACATGGGACCTCTAATCTCGGTGCCAACGCCATGTCCCAGAC
Found at i:19460789 original size:21 final size:21
Alignment explanation
Indices: 19460763--19460804 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
19460753 AATGAAGAAG
19460763 ATGAGCATATTTTGCCATCTT
1 ATGAGCATATTTTGCCATCTT
19460784 ATGAGCATATTTTGCCATCTT
1 ATGAGCATATTTTGCCATCTT
19460805 TTCCCCTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.43
Consensus pattern (21 bp):
ATGAGCATATTTTGCCATCTT
Found at i:19464265 original size:50 final size:51
Alignment explanation
Indices: 19464206--19464336 Score: 140
Period size: 50 Copynumber: 2.6 Consensus size: 51
19464196 TATTGAGGTT
*** * *
19464206 ATGAGAGGTCCCACGTAAGACCATATCTAGGG-CATGGTGTTGGCACTGAG
1 ATGAGAGGTCCCACGTAAGACCATATCTAGGGACATGACATGGGCACCGAG
* * * *
19464256 ATGAGAGGTCCCCCATAAGACCATGTCT-GGGACATGACATGGGCACCGAT
1 ATGAGAGGTCCCACGTAAGACCATATCTAGGGACATGACATGGGCACCGAG
** *
19464306 ATGAGAACTCCCATGTAAGACCATATCTAGG
1 ATGAGAGGTCCCACGTAAGACCATATCTAGG
19464337 ATATGGCATT
Statistics
Matches: 64, Mismatches: 15, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
49 3 0.05
50 59 0.92
51 2 0.03
ACGTcount: A:0.29, C:0.23, G:0.27, T:0.21
Consensus pattern (51 bp):
ATGAGAGGTCCCACGTAAGACCATATCTAGGGACATGACATGGGCACCGAG
Found at i:19477608 original size:16 final size:15
Alignment explanation
Indices: 19477589--19477622 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
19477579 AAATGACTTG
19477589 AAAAGAAAATAAAAAT
1 AAAAGAAAAT-AAAAT
*
19477605 AAAAGCAAATAAAAT
1 AAAAGAAAATAAAAT
19477620 AAA
1 AAA
19477623 TAAATATCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.79, C:0.03, G:0.06, T:0.12
Consensus pattern (15 bp):
AAAAGAAAATAAAAT
Found at i:19482395 original size:113 final size:112
Alignment explanation
Indices: 19482213--19482415 Score: 397
Period size: 113 Copynumber: 1.8 Consensus size: 112
19482203 ACAAAAGCGA
19482213 AATCACCCCCTATCAGTAAAATGTTACAATGAAATTTGTAAGATTTTGGTTTAATAAGCTTATGA
1 AATCACCCCCTATCAGTAAAATGTTACAATGAAATTTGTAAGATTTTGGTTTAATAAGCTTATGA
19482278 GTGTAGTGTTACAAAAGTTTGTGTAAGATAATTTGAGGCTTTACTAC
66 GTGTAGTGTTACAAAAGTTTGTGTAAGATAATTTGAGGCTTTACTAC
19482325 AATCACCCCCATATCAGTAAAATGTTACAATGAAATTTGTAAGATTTTGGTTTAATAAGCTTATG
1 AATCACCCCC-TATCAGTAAAATGTTACAATGAAATTTGTAAGATTTTGGTTTAATAAGCTTATG
19482390 AGTGTAGTGTTACAAAAGTTTGTGTA
65 AGTGTAGTGTTACAAAAGTTTGTGTA
19482416 CGGGAGAATA
Statistics
Matches: 90, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
112 10 0.11
113 80 0.89
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.36
Consensus pattern (112 bp):
AATCACCCCCTATCAGTAAAATGTTACAATGAAATTTGTAAGATTTTGGTTTAATAAGCTTATGA
GTGTAGTGTTACAAAAGTTTGTGTAAGATAATTTGAGGCTTTACTAC
Found at i:19484407 original size:49 final size:49
Alignment explanation
Indices: 19484335--19484520 Score: 180
Period size: 51 Copynumber: 3.7 Consensus size: 49
19484325 GTGAAGTTGC
* *
19484335 TAGGTCACGTGTGTAGTACTATGTGTAGGCTACTACAGTACCGGAAT-GA
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTACAGTACC-GAATAGA
* *
19484384 TAGGTCATATGTGTAGTACTATGTGCAGGCTACTATGC-GTACCGAATAGCT
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTA--CAGTACCGAATAG-A
* * * * * *
19484435 TCGATCACATGTGTAGTAGTATGTGCAGGCTACTACGAGTGTCTG-ATAAA
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTAC-AGT-ACCGAATAGA
* *
19484485 AATGGTCACATGTGTAGTACTATGTGTAGGCTACTA
1 TA-GGTCACATGTGTAGTACTATGTGCAGGCTACTA
19484521 TGTGAACTGA
Statistics
Matches: 112, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
49 37 0.33
50 6 0.05
51 67 0.60
52 2 0.02
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (49 bp):
TAGGTCACATGTGTAGTACTATGTGCAGGCTACTACAGTACCGAATAGA
Found at i:19488635 original size:20 final size:20
Alignment explanation
Indices: 19488572--19488636 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 20
19488562 TTGCAATGGC
19488572 ATTTCGTGTCTTCTAGATAG
1 ATTTCGTGTCTTCTAGATAG
* * *
19488592 ATTTC--CTATTCTTG-TCAGG
1 ATTTCGTGTCTTCTAGAT-A-G
19488611 CATTTCGTGTCTTCTAGATAG
1 -ATTTCGTGTCTTCTAGATAG
19488632 ATTTC
1 ATTTC
19488637 CTATTCTCTG
Statistics
Matches: 33, Mismatches: 6, Indels: 12
0.65 0.12 0.24
Matches are distributed among these distances:
17 1 0.03
18 7 0.21
19 1 0.03
20 15 0.45
21 1 0.03
22 7 0.21
23 1 0.03
ACGTcount: A:0.18, C:0.18, G:0.17, T:0.46
Consensus pattern (20 bp):
ATTTCGTGTCTTCTAGATAG
Found at i:19497268 original size:42 final size:42
Alignment explanation
Indices: 19497209--19497292 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
19497199 TGTACCTCAA
*
19497209 TGTCACACGACATCGGTCTTTCACATAGCCTGGCGACATGGT
1 TGTCACACGACATCGGTCTTTCACATAGCCCGGCGACATGGT
19497251 TGTCACACGACATCGGTCTTTCACATAGCCCGGCGACATGGT
1 TGTCACACGACATCGGTCTTTCACATAGCCCGGCGACATGGT
19497293 CGTGTGATCT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.21, C:0.30, G:0.24, T:0.25
Consensus pattern (42 bp):
TGTCACACGACATCGGTCTTTCACATAGCCCGGCGACATGGT
Found at i:19498313 original size:28 final size:28
Alignment explanation
Indices: 19498281--19498377 Score: 140
Period size: 28 Copynumber: 3.5 Consensus size: 28
19498271 AAACAATAGG
* *
19498281 CAATGGAAGCCTTTGTGGCAATCGATGA
1 CAATGGAAGCCTTTGTGGTAATCTATGA
*
19498309 CAATGGAAGCCTTTGTGGTAATCTATAA
1 CAATGGAAGCCTTTGTGGTAATCTATGA
* *
19498337 CAATGGAAGCCTTTGTGGTGATCTAAGA
1 CAATGGAAGCCTTTGTGGTAATCTATGA
*
19498365 AAATGGAAGCCTT
1 CAATGGAAGCCTT
19498378 CGTGACAAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 62 1.00
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (28 bp):
CAATGGAAGCCTTTGTGGTAATCTATGA
Found at i:19514555 original size:44 final size:44
Alignment explanation
Indices: 19514507--19514715 Score: 138
Period size: 44 Copynumber: 4.8 Consensus size: 44
19514497 CCTCGGTTGC
* *
19514507 AGTGGAGCAGGTTAAAGATAGCAGATCTTATCTCCCTAAGCAGT
1 AGTGGAGCAGATTAAAGACAGCAGATCTTATCTCCCTAAGCAGT
* * * * *
19514551 AGTGGAGCAGATCAAAGACGGAAAATCTTATCTTTCC-AAG-A-T
1 AGTGGAGCAGATTAAAGACAGCAGATCTTATC-TCCCTAAGCAGT
* * * * * *
19514593 AGTGGGAAGCAGATTTAAGCCA-CCGAACCTTGTCTCCCTAAGCAGC
1 AGT-GG-AGCAGATTAAAGACAGCAG-ATCTTATCTCCCTAAGCAGT
* * * * ** *
19514639 AGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGT
1 AGTGGAGCAGATTAAAGACAGCAGATCTTATCTCCCTAAGCAGT
* * * *
19514683 AGTGGAGCAGATCAAAGACGGAAAATCTTATCT
1 AGTGGAGCAGATTAAAGACAGCAGATCTTATCT
19514716 TTCCAAGATA
Statistics
Matches: 118, Mismatches: 39, Indels: 16
0.68 0.23 0.09
Matches are distributed among these distances:
42 4 0.03
43 6 0.05
44 99 0.84
45 7 0.06
46 2 0.02
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (44 bp):
AGTGGAGCAGATTAAAGACAGCAGATCTTATCTCCCTAAGCAGT
Found at i:19514725 original size:132 final size:132
Alignment explanation
Indices: 19514505--19514804 Score: 462
Period size: 132 Copynumber: 2.3 Consensus size: 132
19514495 TCCCTCGGTT
*
19514505 GCAGTGGAGCAGGTTAAAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
1 GCAGTGGAGTAGGTTAAAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
19514570 GGAAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCGAA-CCTTGTCTCCCTAA
66 GGAAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACC-AAGCCTTGTCTCCCTAA
19514634 GCA
130 GCA
* * * *
19514637 GCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
1 GCAGTGGAGTAGGTTAAAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
* *
19514702 GGAAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTTTCCCTGAG
66 GGAAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTAAG
19514767 CA
131 CA
** *
19514769 ATAGTGGAGTAGGTTTAAA-ATTA-CAGGTCTTATCTC
1 GCAGTGGAGTAGG-TTAAAGA-TAGCAGATCTTATCTC
19514805 TCTGAAGTTG
Statistics
Matches: 151, Mismatches: 14, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
131 2 0.01
132 144 0.95
133 5 0.03
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.25
Consensus pattern (132 bp):
GCAGTGGAGTAGGTTAAAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGAC
GGAAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTAAG
CA
Found at i:19532816 original size:47 final size:48
Alignment explanation
Indices: 19532762--19532861 Score: 168
Period size: 48 Copynumber: 2.1 Consensus size: 48
19532752 CATGTTCGAC
19532762 TTTACCAATTCACA-ACAT-TTTAGGGTGTTTTCACTTATTAAAACTTA
1 TTTACCAATTCACATA-ATATTTAGGGTGTTTTCACTTATTAAAACTTA
*
19532809 TTTACCAATTCACATAATATTTTGGGTGTTTTCACTTATTAAAACTTA
1 TTTACCAATTCACATAATATTTAGGGTGTTTTCACTTATTAAAACTTA
19532857 TTTAC
1 TTTAC
19532862 TCATGGAATG
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
47 16 0.32
48 34 0.68
ACGTcount: A:0.31, C:0.16, G:0.08, T:0.45
Consensus pattern (48 bp):
TTTACCAATTCACATAATATTTAGGGTGTTTTCACTTATTAAAACTTA
Found at i:19537724 original size:19 final size:20
Alignment explanation
Indices: 19537687--19537724 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
19537677 TAGAATTTAT
* *
19537687 TGATGAGTTTTTTATAAAAC
1 TGATGAATTTTTTACAAAAC
19537707 TGATGAATTTTTT-CAAAA
1 TGATGAATTTTTTACAAAA
19537725 TACATCACTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.45
Consensus pattern (20 bp):
TGATGAATTTTTTACAAAAC
Found at i:19537842 original size:23 final size:23
Alignment explanation
Indices: 19537812--19537935 Score: 101
Period size: 23 Copynumber: 5.5 Consensus size: 23
19537802 TAGACATGTA
19537812 TAAAAACCCTAACCTAATTAAAT
1 TAAAAACCCTAACCTAATTAAAT
* *
19537835 TAAAAACCCTAACCTAGTTTAAT
1 TAAAAACCCTAACCTAATTAAAT
********* *
19537858 TAAAAA---TCNNNNNNNNAACT
1 TAAAAACCCTAACCTAATTAAAT
19537878 TAAAAACCCTAACCTAATTAAAT
1 TAAAAACCCTAACCTAATTAAAT
*
19537901 TAAAAATCCTAACCTAATTAAAT
1 TAAAAACCCTAACCTAATTAAAT
*
19537924 TAAAAACTCTAA
1 TAAAAACCCTAA
19537936 ACTTAAAAAC
Statistics
Matches: 72, Mismatches: 26, Indels: 6
0.69 0.25 0.06
Matches are distributed among these distances:
20 9 0.12
23 63 0.88
ACGTcount: A:0.48, C:0.19, G:0.01, T:0.26
Consensus pattern (23 bp):
TAAAAACCCTAACCTAATTAAAT
Found at i:19537935 original size:18 final size:20
Alignment explanation
Indices: 19537877--19538038 Score: 55
Period size: 23 Copynumber: 7.5 Consensus size: 20
19537867 NNNNNNNAAC
19537877 TTAAAAACCCTAACCTAATTAAA
1 TTAAAAA-CCT-A-CTAATTAAA
19537900 TTAAAAATCCTAACCTAATTAAA
1 TTAAAAA-CCT-A-CTAATTAAA
*
19537923 TTAAAAA-CT-CT-A--AAC
1 TTAAAAACCTACTAATTAAA
*** *
19537938 TTAAAAACCCTAACCCCTTTAAC
1 TTAAAAA-CCT-A-CTAATTAAA
*
19537961 TTAAAAACCCTAACCTAATTAAC
1 TTAAAAA-CCT-A-CTAATTAAA
19537984 TTAAAAACTCTAACCTAATTAAA
1 TTAAAAAC-CT-A-CTAATTAAA
* *
19538007 TTAAAAATCCTAACCAAATTTAA
1 TTAAAAA-CCT-A-CTAATTAAA
19538030 TTAAAAACC
1 TTAAAAACC
19538039 CTAAACCCTA
Statistics
Matches: 119, Mismatches: 10, Indels: 21
0.79 0.07 0.14
Matches are distributed among these distances:
15 9 0.08
17 3 0.03
18 2 0.02
20 1 0.01
21 2 0.02
22 3 0.03
23 98 0.82
24 1 0.01
ACGTcount: A:0.50, C:0.22, G:0.00, T:0.28
Consensus pattern (20 bp):
TTAAAAACCTACTAATTAAA
Found at i:19537939 original size:61 final size:61
Alignment explanation
Indices: 19537812--19537996 Score: 219
Period size: 61 Copynumber: 3.0 Consensus size: 61
19537802 TAGACATGTA
* * **
19537812 TAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAGTTTAATTAAAAA-TCNNNNNNNNAA
1 TAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACTC------TAAA
19537876 CT
60 CT
*
19537878 TAAAAACCCTAACCTAATTAAATTAAAAATCCTAACCTAATTAAATTAAAAACTCTAAACT
1 TAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACTCTAAACT
*** * *
19537939 TAAAAACCCTAACCCCTTTAACTTAAAAACCCTAACCTAATTAACTTAAAAACTCTAA
1 TAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACTCTAA
19537997 CCTAATTAAA
Statistics
Matches: 107, Mismatches: 11, Indels: 7
0.86 0.09 0.06
Matches are distributed among these distances:
61 56 0.52
66 49 0.46
67 2 0.02
ACGTcount: A:0.48, C:0.22, G:0.01, T:0.26
Consensus pattern (61 bp):
TAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACTCTAAACT
Found at i:19537965 original size:38 final size:37
Alignment explanation
Indices: 19537896--19537973 Score: 93
Period size: 38 Copynumber: 2.1 Consensus size: 37
19537886 CTAACCTAAT
* * *
19537896 TAAATTAAAAATCCTAACCTAATTAAATTAAAAACTC
1 TAAATTAAAAACCCTAACCCAATTAAATTAAAAACCC
** *
19537933 TAAACTTAAAAACCCTAACCCCTTTAACTTAAAAACCC
1 TAAA-TTAAAAACCCTAACCCAATTAAATTAAAAACCC
19537971 TAA
1 TAA
19537974 CCTAATTAAC
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
37 4 0.12
38 30 0.88
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (37 bp):
TAAATTAAAAACCCTAACCCAATTAAATTAAAAACCC
Found at i:19537988 original size:46 final size:45
Alignment explanation
Indices: 19537938--19538087 Score: 194
Period size: 46 Copynumber: 3.3 Consensus size: 45
19537928 AACTCTAAAC
19537938 TTAAAAACCCTAACCCCTTTAACTTAAAAACCCTAACCTAA-TTAA
1 TTAAAAACCCTAACCCC-TTAACTTAAAAACCCTAACCTAATTTAA
* ** * * *
19537983 CTTAAAAACTCTAACCTAATTAAATTAAAAATCCTAACCAAATTTAA
1 -TTAAAAACCCTAACC-CCTTAACTTAAAAACCCTAACCTAATTTAA
* *
19538030 TTAAAAACCCTAAACCCTAAACTTAAAAACCCTAACCTAATTTAA
1 TTAAAAACCCTAACCCCTTAACTTAAAAACCCTAACCTAATTTAA
19538075 TTAAAAACCCTAA
1 TTAAAAACCCTAA
19538088 ACTAAATTAA
Statistics
Matches: 88, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
45 37 0.42
46 47 0.53
47 4 0.05
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.27
Consensus pattern (45 bp):
TTAAAAACCCTAACCCCTTAACTTAAAAACCCTAACCTAATTTAA
Found at i:19538003 original size:107 final size:110
Alignment explanation
Indices: 19537874--19538097 Score: 312
Period size: 107 Copynumber: 2.0 Consensus size: 110
19537864 TCNNNNNNNN
*
19537874 AACTTAAAAACCCTAACCTAATTAAATTAAAAATCCTAACCTAATTAAATTAAAAA-CT-CTAAA
1 AACTTAAAAACCCTAACCTAATTAAATTAAAAATCCTAACCAAATTAAATTAAAAACCTACTAAA
** *
19537937 CTTAAAAACCCTAACC-CCTTTAACTTAAAAACCCTAACCT-AATT
66 CTTAAAAACCCTAACCTAATTTAA-TTAAAAACCCTAAACTAAATT
* *
19537981 AACTTAAAAACTCTAACCTAATTAAATTAAAAATCCTAACCAAATTTAATTAAAAACCCTAAACC
1 AACTTAAAAACCCTAACCTAATTAAATTAAAAATCCTAACCAAATTAAATTAAAAA-CCT--A--
19538046 CTAAACTTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACTAAATT
61 CTAAACTTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACTAAATT
19538096 AA
1 AA
19538098 TAATTTTACT
Statistics
Matches: 102, Mismatches: 6, Indels: 10
0.86 0.05 0.08
Matches are distributed among these distances:
107 53 0.52
109 2 0.02
114 36 0.35
115 11 0.11
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (110 bp):
AACTTAAAAACCCTAACCTAATTAAATTAAAAATCCTAACCAAATTAAATTAAAAACCTACTAAA
CTTAAAAACCCTAACCTAATTTAATTAAAAACCCTAAACTAAATT
Found at i:19538072 original size:45 final size:45
Alignment explanation
Indices: 19537938--19538089 Score: 184
Period size: 45 Copynumber: 3.3 Consensus size: 45
19537928 AACTCTAAAC
* *
19537938 TTAAAAACCCTAACCCCTTTAACTTAAAAACCCTAACCTAA-TTAA
1 TTAAAAACCCTAAACCC-TAAACTTAAAAACCCTAACCTAATTTAA
* * * *
19537983 CTTAAAAACTCT-AA-CCTAATTAAATTAAAAATCCTAACCAAATTTAA
1 -TTAAAAACCCTAAACCCT-A--AACTTAAAAACCCTAACCTAATTTAA
19538030 TTAAAAACCCTAAACCCTAAACTTAAAAACCCTAACCTAATTTAA
1 TTAAAAACCCTAAACCCTAAACTTAAAAACCCTAACCTAATTTAA
19538075 TTAAAAACCCTAAAC
1 TTAAAAACCCTAAAC
19538090 TAAATTAATA
Statistics
Matches: 90, Mismatches: 10, Indels: 13
0.80 0.09 0.12
Matches are distributed among these distances:
43 1 0.01
44 2 0.02
45 39 0.43
46 38 0.42
47 7 0.08
48 3 0.03
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.26
Consensus pattern (45 bp):
TTAAAAACCCTAAACCCTAAACTTAAAAACCCTAACCTAATTTAA
Found at i:19538092 original size:23 final size:23
Alignment explanation
Indices: 19537938--19538098 Score: 170
Period size: 23 Copynumber: 7.0 Consensus size: 23
19537928 AACTCTAAAC
**
19537938 TTAAAAACCCTAACC-CCTTTAA
1 TTAAAAACCCTAACCTAATTTAA
19537960 CTTAAAAACCCTAACCTAA-TTAA
1 -TTAAAAACCCTAACCTAATTTAA
* *
19537983 CTTAAAAACTCTAACCTAATTAAA
1 -TTAAAAACCCTAACCTAATTTAA
* *
19538007 TTAAAAATCCTAACCAAATTTAA
1 TTAAAAACCCTAACCTAATTTAA
*
19538030 TTAAAAACCCTAAACCCTAA---AC
1 TTAAAAACCCT-AA-CCTAATTTAA
19538052 TTAAAAACCCTAACCTAATTTAA
1 TTAAAAACCCTAACCTAATTTAA
* *
19538075 TTAAAAACCCTAAACTAAATTAA
1 TTAAAAACCCTAACCTAATTTAA
19538098 T
1 T
19538099 AATTTTACTT
Statistics
Matches: 117, Mismatches: 14, Indels: 14
0.81 0.10 0.10
Matches are distributed among these distances:
20 5 0.04
21 2 0.02
22 12 0.10
23 89 0.76
24 5 0.04
25 4 0.03
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (23 bp):
TTAAAAACCCTAACCTAATTTAA
Found at i:19538098 original size:68 final size:68
Alignment explanation
Indices: 19537933--19538087 Score: 199
Period size: 68 Copynumber: 2.2 Consensus size: 68
19537923 TTAAAAACTC
** *
19537933 TAAACTTAAAAACCCTAACC-CCTTTAACTTAAAAACCCTAACCTAATTAACTTAAAAACTCTAA
1 TAAA-TTAAAAACCCTAACCAAATTTAA-TTAAAAACCCTAACCTAA-TAACTTAAAAACCCTAA
19537997 CCTAAT
63 CCTAAT
*
19538003 TAAATTAAAAATCCTAACCAAATTTAATTAAAAACCCTAAACCCT-A-AACTTAAAAACCCTAAC
1 TAAATTAAAAACCCTAACCAAATTTAATTAAAAACCCT-AA-CCTAATAACTTAAAAACCCTAAC
19538066 CTAAT
64 CTAAT
*
19538071 TTAATTAAAAACCCTAA
1 TAAATTAAAAACCCTAA
19538088 ACTAAATTAA
Statistics
Matches: 76, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
68 36 0.47
69 25 0.33
70 12 0.16
71 3 0.04
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.26
Consensus pattern (68 bp):
TAAATTAAAAACCCTAACCAAATTTAATTAAAAACCCTAACCTAATAACTTAAAAACCCTAACCT
AAT
Found at i:19542175 original size:13 final size:13
Alignment explanation
Indices: 19542157--19542189 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
19542147 TGACCTCTTG
19542157 GCGGATTATCCCT
1 GCGGATTATCCCT
19542170 GCGGATTATCCCT
1 GCGGATTATCCCT
19542183 GCGGATT
1 GCGGATT
19542190 CTATCTTCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.15, C:0.27, G:0.27, T:0.30
Consensus pattern (13 bp):
GCGGATTATCCCT
Found at i:19542991 original size:26 final size:24
Alignment explanation
Indices: 19542948--19543001 Score: 63
Period size: 26 Copynumber: 2.2 Consensus size: 24
19542938 CCTAATGAGC
* *
19542948 TTATTTTATAACATTTTTATATGTTT
1 TTATTTAATAACAATTTT-TAT-TTT
*
19542974 TTATTTAATTACAATTTTTATTTT
1 TTATTTAATAACAATTTTTATTTT
19542998 TTAT
1 TTAT
19543002 GATTAAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 7 0.28
25 3 0.12
26 15 0.60
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.67
Consensus pattern (24 bp):
TTATTTAATAACAATTTTTATTTT
Found at i:19544984 original size:14 final size:14
Alignment explanation
Indices: 19544965--19544991 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19544955 TACATTGGAC
19544965 AGATTCATGCATGT
1 AGATTCATGCATGT
19544979 AGATTCATGCATG
1 AGATTCATGCATG
19544992 GGAAGATGCA
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:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (14 bp):
AGATTCATGCATGT
Found at i:19546540 original size:47 final size:48
Alignment explanation
Indices: 19546486--19546582 Score: 162
Period size: 48 Copynumber: 2.0 Consensus size: 48
19546476 GACTTTACCA
19546486 ACCAATTCACA-ACAT-TTTAGGGTGTTTTCACTTATTAAAACTTATTT
1 ACCAATTCACATA-ATATTTAGGGTGTTTTCACTTATTAAAACTTATTT
*
19546533 ACCAATTCACATAATATTTTGGGTGTTTTCACTTATTAAAACTTATTT
1 ACCAATTCACATAATATTTAGGGTGTTTTCACTTATTAAAACTTATTT
19546581 AC
1 AC
19546583 TCATGGAATG
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
47 13 0.28
48 34 0.72
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.43
Consensus pattern (48 bp):
ACCAATTCACATAATATTTAGGGTGTTTTCACTTATTAAAACTTATTT
Found at i:19550678 original size:23 final size:23
Alignment explanation
Indices: 19550648--19550920 Score: 168
Period size: 23 Copynumber: 12.3 Consensus size: 23
19550638 TAGACATGTA
19550648 TAAAAACCCTAACCTAATTAAAT
1 TAAAAACCCTAACCTAATTAAAT
* *
19550671 TAAAAACCCTAACCTAGTTTAAT
1 TAAAAACCCTAACCTAATTAAAT
* *
19550694 TAAAAATCCTAAACCCT-A--AACT
1 TAAAAACCCT-AA-CCTAATTAAAT
19550716 TAAAAACCCTAACCTAATTAAAT
1 TAAAAACCCTAACCTAATTAAAT
*
19550739 TAAAAATCCTAACCTAATTAAAT
1 TAAAAACCCTAACCTAATTAAAT
* * *
19550762 TAAAAACTCTAAACTTAA--AAAC
1 TAAAAACCCT-AACCTAATTAAAT
*** * *
19550784 CCTAACCCCTTTAACTTAA--AAA-
1 TAAAAACCC--TAACCTAATTAAAT
**** *
19550806 CCCTAA-CCTAA-TTAACTT-AA-
1 TAAAAACCCTAACCTAA-TTAAAT
19550826 -A--AACCCTAACCTAATTAAAT
1 TAAAAACCCTAACCTAATTAAAT
*
19550846 TAAAAACCCTAAACCCT-A--AACT
1 TAAAAACCCT-AA-CCTAATTAAAT
19550868 TAAAAACCCTAACCTAATTAAAT
1 TAAAAACCCTAACCTAATTAAAT
*
19550891 TAAAAATCCTAACCTAATTAAAT
1 TAAAAACCCTAACCTAATTAAAT
19550914 TAAAAAC
1 TAAAAAC
19550921 TCGCACAACT
Statistics
Matches: 200, Mismatches: 27, Indels: 46
0.73 0.10 0.17
Matches are distributed among these distances:
17 2 0.01
18 11 0.05
19 8 0.04
20 8 0.04
21 9 0.05
22 34 0.17
23 110 0.55
24 12 0.06
25 6 0.03
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.26
Consensus pattern (23 bp):
TAAAAACCCTAACCTAATTAAAT
Found at i:19550725 original size:45 final size:44
Alignment explanation
Indices: 19550666--19550919 Score: 158
Period size: 45 Copynumber: 5.8 Consensus size: 44
19550656 CTAACCTAAT
* *
19550666 TAAATTAAAAACCCTAACCTAGTTTAATTAAAAATCCTAAACCC
1 TAAATTAAAAACCCTAACCTAATTAAATTAAAAATCCTAAACCC
19550710 TAAACTTAAAAACCCTAACCTAATTAAATTAAAAATCCT-AA-CC
1 TAAA-TTAAAAACCCTAACCTAATTAAATTAAAAATCCTAAACCC
* * * *
19550753 T-AATTAAATTAA---AAACTCT-A--AACTTAAAAACCCTAACCCC
1 TAAATTAAA--AACCCTAAC-CTAATTAAATTAAAAATCCTAAACCC
* * * *
19550793 TTTAACTTAAAAACCCTAACCTAATTAACTTAAAAACCCT-AACCTAAT
1 --TAAATTAAAAACCCTAACCTAATTAAATTAAAAATCCTAAACC---C
* * *
19550841 TAAATTAAAAACCCTAAACCCT-A--AACTTAAAAACCCT-AACCTAAT
1 TAAATTAAAAACCCT-AA-CCTAATTAAATTAAAAATCCTAAACC---C
*
19550886 TAAATTAAAAATCCTAACCTAATTAAATTAAAAA
1 TAAATTAAAAACCCTAACCTAATTAAATTAAAAA
19550920 CTCGCACAAC
Statistics
Matches: 174, Mismatches: 13, Indels: 44
0.75 0.06 0.19
Matches are distributed among these distances:
38 12 0.07
39 1 0.01
40 6 0.03
41 9 0.05
42 3 0.02
43 16 0.09
44 13 0.07
45 71 0.41
46 37 0.21
47 3 0.02
48 3 0.02
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.26
Consensus pattern (44 bp):
TAAATTAAAAACCCTAACCTAATTAAATTAAAAATCCTAAACCC
Found at i:19550727 original size:68 final size:66
Alignment explanation
Indices: 19550648--19550907 Score: 302
Period size: 68 Copynumber: 4.0 Consensus size: 66
19550638 TAGACATGTA
* *
19550648 TAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAGTTTAATTAAAAATCCTAAACCCTAA
1 TAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAATCCT-AA-CCTAA
19550713 ACT
64 ACT
*
19550716 TAAAAACCCTAACCTAATTAAATTAAAAATCCTAACCTAATTAAATTAAAAA--CT---CTAAAC
1 TAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAATCCTAACCTAAAC
19550776 T
66 T
*** * * *
19550777 TAAAAACCCTAACCCCTTTAACTTAAAAACCCTAACCTAATTAACTTAAAAACCCTAACCTAATT
1 TAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAATCCTAACCT-A--
*
19550842 AAAT
63 AACT
*
19550846 TAAAAACCCTAAACCCT-A--AACTTAAAAACCCTAACCTAATTAAATTAAAAATCCTAACCTAA
1 TAAAAACCCT-AA-CCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAATCCTAACCTAA
19550908 TTAAATTAAA
Statistics
Matches: 168, Mismatches: 14, Indels: 23
0.82 0.07 0.11
Matches are distributed among these distances:
61 53 0.32
63 2 0.01
65 1 0.01
66 4 0.02
67 2 0.01
68 89 0.53
69 13 0.08
70 2 0.01
71 2 0.01
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (66 bp):
TAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAATCCTAACCTAAAC
T
Found at i:19550825 original size:28 final size:23
Alignment explanation
Indices: 19550773--19550920 Score: 194
Period size: 23 Copynumber: 6.5 Consensus size: 23
19550763 AAAAACTCTA
***
19550773 AACTTAAAAACCCTAACCCCTTT
1 AACTTAAAAACCCTAACCTAATT
19550796 AACTTAAAAACCCTAACCTAATT
1 AACTTAAAAACCCTAACCTAATT
19550819 AACTTAAAAACCCTAACCTAATT
1 AACTTAAAAACCCTAACCTAATT
*
19550842 AAATTAAAAACCCTAAACCCT-A--
1 AACTTAAAAACCCT-AA-CCTAATT
19550864 AACTTAAAAACCCTAACCTAATT
1 AACTTAAAAACCCTAACCTAATT
* *
19550887 AAATTAAAAATCCTAACCTAATT
1 AACTTAAAAACCCTAACCTAATT
*
19550910 AAATTAAAAAC
1 AACTTAAAAAC
19550921 TCGCACAACT
Statistics
Matches: 112, Mismatches: 8, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
20 3 0.03
21 3 0.03
22 13 0.12
23 87 0.78
24 3 0.03
25 3 0.03
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (23 bp):
AACTTAAAAACCCTAACCTAATT
Found at i:19550885 original size:152 final size:152
Alignment explanation
Indices: 19550648--19550922 Score: 514
Period size: 152 Copynumber: 1.8 Consensus size: 152
19550638 TAGACATGTA
* * *
19550648 TAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAGTTTAATTAAAAATCCTAAACCCTAA
1 TAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAAACCCTAA
19550713 ACTTAAAAACCCTAACCTAATTAAATTAAAAATCCTAACCTAATTAAATTAAAAACTCTAAACTT
66 ACTTAAAAACCCTAACCTAATTAAATTAAAAATCCTAACCTAATTAAATTAAAAACTCTAAACTT
19550778 AAAAACCCTAACCCCTTTAACT
131 AAAAACCCTAACCCCTTTAACT
*
19550800 TAAAAACCCTAACCTAATTAACTTAAAAACCCTAACCTAATTAAATTAAAAACCCTAAACCCTAA
1 TAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAAACCCTAA
19550865 ACTTAAAAACCCTAACCTAATTAAATTAAAAATCCTAACCTAATTAAATTAAAAACTC
66 ACTTAAAAACCCTAACCTAATTAAATTAAAAATCCTAACCTAATTAAATTAAAAACTC
19550923 GCACAACTTC
Statistics
Matches: 119, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
152 119 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (152 bp):
TAAAAACCCTAACCTAATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAAACCCTAA
ACTTAAAAACCCTAACCTAATTAAATTAAAAATCCTAACCTAATTAAATTAAAAACTCTAAACTT
AAAAACCCTAACCCCTTTAACT
Found at i:19554088 original size:125 final size:125
Alignment explanation
Indices: 19553836--19554081 Score: 368
Period size: 125 Copynumber: 2.0 Consensus size: 125
19553826 CCCAAACATG
* * * *
19553836 CTACTGTAGCAAAAGCGCGTTAATGAGGGCGCGATTTTACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCAACGAGGGCGCGATTTGACAAATTCTTCTAAAATAGCATCCTGC
* * *
19553901 TAGAAGCAATTTTATACTATTTGTTCAGAAACGTAAAAAAAAATTTATTTCTTCCATAAC
66 TAGAAACAATTTTATACTATTTGATCAGAAACGTAAAAAAAAATTTACTTCTTCCATAAC
*
19553961 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTGACAAATTCTTCTAAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCAACGAGGGCGCGATTTGACAAATTCTTCTAAAATAGCATCCTGC
* ***
19554026 TAGAAACGATTTTATACTATTTGATCAGAAACGTGAACTCAAAA-TTACTTCTTCCA
66 TAGAAACAATTTTATACTATTTGATCAGAAACGT-AAAAAAAAATTTACTTCTTCCA
19554082 AGACCTAAAA
Statistics
Matches: 108, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
125 102 0.94
126 6 0.06
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.30
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCAACGAGGGCGCGATTTGACAAATTCTTCTAAAATAGCATCCTGC
TAGAAACAATTTTATACTATTTGATCAGAAACGTAAAAAAAAATTTACTTCTTCCATAAC
Done.