Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold23
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: 3824748
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 177433 characters in sequence are not A, C, G, or T
File 5 of 14
Found at i:1116905 original size:19 final size:19
Alignment explanation
Indices: 1116883--1116946 Score: 67
Period size: 19 Copynumber: 3.2 Consensus size: 19
1116873 AAGTTACAAA
1116883 AAAATTCAAAATATTTTTT
1 AAAATTCAAAATATTTTTT
* *
1116902 AAAATTCAAAAT-TTTATA
1 AAAATTCAAAATATTTTTT
1116920 AAAATTCCAAAATTTATATTTTT
1 AAAATT-CAAAA--TAT-TTTTT
1116943 AAAA
1 AAAA
1116947 AAATTATAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
18 10 0.28
19 17 0.47
21 1 0.03
22 1 0.03
23 7 0.19
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAATTCAAAATATTTTTT
Found at i:1116925 original size:18 final size:18
Alignment explanation
Indices: 1116882--1116934 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 18
1116872 AAAGTTACAA
*
1116882 AAAAATTCAAAATATTTTT
1 AAAAATTCAAAAT-TTTAT
*
1116901 TAAAATTCAAAATTTTAT
1 AAAAATTCAAAATTTTAT
1116919 AAAAATTCCAAAATTT
1 AAAAATT-CAAAATTT
1116935 ATATTTTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
18 10 0.33
19 20 0.67
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.40
Consensus pattern (18 bp):
AAAAATTCAAAATTTTAT
Found at i:1116931 original size:26 final size:26
Alignment explanation
Indices: 1116902--1116951 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
1116892 AATATTTTTT
*
1116902 AAAATTCAAAATTTTATAAAAATTCC
1 AAAATTCAAAATTTTAAAAAAATTCC
* * *
1116928 AAAATTTATATTTTTAAAAAAATT
1 AAAATTCAAAATTTTAAAAAAATT
1116952 ATAAATTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (26 bp):
AAAATTCAAAATTTTAAAAAAATTCC
Found at i:1116935 original size:18 final size:18
Alignment explanation
Indices: 1116882--1116937 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
1116872 AAAGTTACAA
* *
1116882 AAAAATTCAAAATATTTTT
1 AAAAATTCCAAA-ATTTAT
*
1116901 TAAAATT-CAAAATTTTAT
1 AAAAATTCCAAAA-TTTAT
1116919 AAAAATTCCAAAATTTAT
1 AAAAATTCCAAAATTTAT
1116937 A
1 A
1116938 TTTTTAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
17 1 0.03
18 19 0.61
19 11 0.35
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (18 bp):
AAAAATTCCAAAATTTAT
Found at i:1116963 original size:20 final size:20
Alignment explanation
Indices: 1116938--1116976 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1116928 AAAATTTATA
1116938 TTTTTAAAAAAATTATAAAT
1 TTTTTAAAAAAATTATAAAT
1116958 TTTTTAAAAAAATTATAAA
1 TTTTTAAAAAAATTATAAA
1116977 GAATATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TTTTTAAAAAAATTATAAAT
Found at i:1122800 original size:14 final size:14
Alignment explanation
Indices: 1122781--1122810 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1122771 ATTTTGTATC
*
1122781 TTTTAACATTACAT
1 TTTTAACATCACAT
1122795 TTTTAACATCACAT
1 TTTTAACATCACAT
1122809 TT
1 TT
1122811 AAAATGAACA
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:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTTAACATCACAT
Found at i:1123999 original size:19 final size:17
Alignment explanation
Indices: 1123968--1124007 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 17
1123958 CTCATTTCTA
1123968 CTTTTTTTTATTTTTTT
1 CTTTTTTTTATTTTTTT
1123985 CTTTATTTTTAATTTTTTT
1 CTTT-TTTTT-ATTTTTTT
1124004 CTTT
1 CTTT
1124008 CTTCCTTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 4 0.19
18 5 0.24
19 12 0.57
ACGTcount: A:0.10, C:0.07, G:0.00, T:0.82
Consensus pattern (17 bp):
CTTTTTTTTATTTTTTT
Found at i:1124030 original size:21 final size:19
Alignment explanation
Indices: 1123997--1124035 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
1123987 TTATTTTTAA
*
1123997 TTTTTTTCTTTCTTCCTTG
1 TTTTTTTCTTTCTCCCTTG
1124016 TTTTTTTCATCTTCTCCCTT
1 TTTTTTTC-T-TTCTCCCTT
1124036 CTAACCTAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 1 0.06
21 8 0.47
ACGTcount: A:0.03, C:0.26, G:0.03, T:0.69
Consensus pattern (19 bp):
TTTTTTTCTTTCTCCCTTG
Found at i:1124908 original size:20 final size:21
Alignment explanation
Indices: 1124883--1124930 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
1124873 AAAAAATTTA
*
1124883 AAATAATAAT-TTTTAAAGAG
1 AAATAATAATAATTTAAAGAG
*
1124903 AAATAA-AATAATTTAAAGAT
1 AAATAATAATAATTTAAAGAG
1124923 AAATAATA
1 AAATAATA
1124931 TAAAGGTACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 3 0.12
20 20 0.83
21 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (21 bp):
AAATAATAATAATTTAAAGAG
Found at i:1125046 original size:18 final size:18
Alignment explanation
Indices: 1125020--1125054 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1125010 TTCTAGATAA
*
1125020 GTTTGGAAACTATAAAAG
1 GTTTAGAAACTATAAAAG
*
1125038 GTTTAGAAATTATAAAA
1 GTTTAGAAACTATAAAA
1125055 AATATTAATA
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:0.49, C:0.03, G:0.17, T:0.31
Consensus pattern (18 bp):
GTTTAGAAACTATAAAAG
Found at i:1128454 original size:17 final size:17
Alignment explanation
Indices: 1128432--1128471 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1128422 CTTCATTGGG
*
1128432 TAAAAATCATAAATAAA
1 TAAAAATCAAAAATAAA
*
1128449 TAAAAATTAAAAATAAA
1 TAAAAATCAAAAATAAA
1128466 -AAAAAT
1 TAAAAAT
1128472 AAAGTGGAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.23
Consensus pattern (17 bp):
TAAAAATCAAAAATAAA
Found at i:1133848 original size:10 final size:10
Alignment explanation
Indices: 1133835--1133946 Score: 70
Period size: 10 Copynumber: 10.5 Consensus size: 10
1133825 CCTTTTGCCC
1133835 TATTTTTATT
1 TATTTTTATT
1133845 TA-TTTTATT
1 TATTTTTATT
1133854 T-TATTTTATT
1 TAT-TTTTATT
*
1133864 AATTTTTATT
1 TATTTTTATT
* *
1133874 TCTTATTT-CT
1 TATT-TTTATT
1133884 TATTATTTATT
1 TATT-TTTATT
1133895 T-TTGTTTATT
1 TATT-TTTATT
1133905 TAGTTTCTTTAATTT
1 TA--TT-TTT-A-TT
1133920 TATTTTGTATT
1 TATTTT-TATT
1133931 TATTTTTAATT
1 TATTTTT-ATT
1133942 TATTT
1 TATTT
1133947 CTGGACATTA
Statistics
Matches: 82, Mismatches: 8, Indels: 23
0.73 0.07 0.20
Matches are distributed among these distances:
9 8 0.10
10 36 0.44
11 22 0.27
12 3 0.04
13 8 0.10
14 1 0.01
15 4 0.05
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (10 bp):
TATTTTTATT
Found at i:1141378 original size:24 final size:23
Alignment explanation
Indices: 1141324--1141378 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
1141314 CACATAATAA
* *
1141324 TTTTTTTTTCCTTTTTCGTATTT
1 TTTTTTTTGCCTTTTTCGTATTC
1141347 TTTGTTTTTGCACTTTTTCG-ATTAC
1 TTT-TTTTTGC-CTTTTTCGTATT-C
1141372 TTTTTTT
1 TTTTTTT
1141379 GTGAGAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 3 0.11
24 13 0.48
25 11 0.41
ACGTcount: A:0.07, C:0.13, G:0.07, T:0.73
Consensus pattern (23 bp):
TTTTTTTTGCCTTTTTCGTATTC
Found at i:1163766 original size:44 final size:45
Alignment explanation
Indices: 1163701--1163791 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
1163691 ACCTCTATTC
* * *
1163701 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
1163745 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
1163790 CA
1 CA
1163792 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:1163793 original size:16 final size:16
Alignment explanation
Indices: 1163772--1163840 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
1163762 GATTAGCTAT
1163772 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
1163788 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
1163805 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
1163821 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
1163837 TACA
1 TACA
1163841 GCGAACCAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:1163814 original size:33 final size:32
Alignment explanation
Indices: 1163772--1163840 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
1163762 GATTAGCTAT
1163772 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
1163805 TACACCTCTAATCCAATACACCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
1163837 TACA
1 TACA
1163841 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 8 0.22
33 28 0.78
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:1168469 original size:62 final size:59
Alignment explanation
Indices: 1168362--1168475 Score: 165
Period size: 62 Copynumber: 1.9 Consensus size: 59
1168352 ACTTTAATAG
* * * *
1168362 TAAATTAATAGAATATTTATCCAGATAAATATTAAGTTAAGTTTAATATTAAATCTTAT
1 TAAAATAATAGAATATTTATCCAGATAAACATTAAATTAAATTTAATATTAAATCTTAT
1168421 TAAAATAATAGAATATTTATCTACAAGATAAACATTAAATTAAATTTAATATTAA
1 TAAAATAATAGAATATTTATC--C-AGATAAACATTAAATTAAATTTAATATTAA
1168476 GATAATCACT
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
59 20 0.42
61 1 0.02
62 27 0.56
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.39
Consensus pattern (59 bp):
TAAAATAATAGAATATTTATCCAGATAAACATTAAATTAAATTTAATATTAAATCTTAT
Found at i:1168501 original size:20 final size:18
Alignment explanation
Indices: 1168454--1168502 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
1168444 CAAGATAAAC
1168454 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
1168471 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
1168491 ATTAAATTAATA
1 ATTAAATTAATA
1168503 AAATATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:1172961 original size:16 final size:16
Alignment explanation
Indices: 1172940--1172972 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1172930 TTCGCTGTAT
1172940 TGGAATTGAGGCGTAA
1 TGGAATTGAGGCGTAA
1172956 TGGAATTGAGGCGTAA
1 TGGAATTGAGGCGTAA
1172972 T
1 T
1172973 ATCAAATCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.06, G:0.36, T:0.27
Consensus pattern (16 bp):
TGGAATTGAGGCGTAA
Found at i:1173381 original size:17 final size:15
Alignment explanation
Indices: 1173350--1173388 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
1173340 TTTATACAAT
1173350 TTAAAATAATTAATA
1 TTAAAATAATTAATA
1173365 TTAAATATAATTTAATA
1 TTAAA-ATAA-TTAATA
*
1173382 ATAAAAT
1 TTAAAAT
1173389 GTTCTTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 5 0.24
16 6 0.29
17 10 0.48
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TTAAAATAATTAATA
Found at i:1173541 original size:212 final size:212
Alignment explanation
Indices: 1173174--1173779 Score: 1194
Period size: 212 Copynumber: 2.9 Consensus size: 212
1173164 ATAATAGAGC
1173174 AATGTTCTTATATGAATTTACTAAAATCAAAAAATAACTTGAGAATTATATTCTGCATAAACATA
1 AATGTTCTTATATGAATTTACTAAAATCAAAAAATAACTTGAGAATTATATTCTGCATAAACATA
1173239 ATTAACTTATATTAAGAAAAGGTTAGATGAAAATGAAATTCTACATCATAATCCATATGTTATAT
66 ATTAACTTATATTAAGAAAAGGTTAGATGAAAATGAAATTCTACATCATAATCCATATGTTATAT
1173304 AGTTTTACAACATCATAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAA
131 AGTTTTACAACATCATAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAA
1173369 ATATAATTTAATAATAA
196 ATATAATTTAATAATAA
1173386 AATGTTCTTATATGAATTTACTAAAATCAAAAAATAACTTGAGAATTATATTCTGCATAAACATA
1 AATGTTCTTATATGAATTTACTAAAATCAAAAAATAACTTGAGAATTATATTCTGCATAAACATA
1173451 ATTAACTTATATTAAGAAAAGGTTAGATGAAAATGAAATTCTACATCATAATCCATATGTTATAT
66 ATTAACTTATATTAAGAAAAGGTTAGATGAAAATGAAATTCTACATCATAATCCATATGTTATAT
1173516 AGTTTTACAACATCATAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAA
131 AGTTTTACAACATCATAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAA
1173581 ATATAATTTAATAATAA
196 ATATAATTTAATAATAA
1173598 AATGTTCTTATATGAATTTACTAAAATCAAAAAATAACTTGAGAATTATATTCTGCATAAACATA
1 AATGTTCTTATATGAATTTACTAAAATCAAAAAATAACTTGAGAATTATATTCTGCATAAACATA
1173663 ATTAACTTATATTAAGAAAAGGTTAGATGAAAATGAAATTCTACATCATAATCCATATGTTATAT
66 ATTAACTTATATTAAGAAAAGGTTAGATGAAAATGAAATTCTACATCATAATCCATATGTTATAT
* *
1173728 AGTTTTACAACATCATAATAAAATTTCTTAAATGAATTTATACAATTTAAAA
131 AGTTTTACAACATCATAATAAATTTTCTTATATGAATTTATACAATTTAAAA
1173780 AGTTTGAAGT
Statistics
Matches: 392, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
212 392 1.00
ACGTcount: A:0.47, C:0.09, G:0.07, T:0.38
Consensus pattern (212 bp):
AATGTTCTTATATGAATTTACTAAAATCAAAAAATAACTTGAGAATTATATTCTGCATAAACATA
ATTAACTTATATTAAGAAAAGGTTAGATGAAAATGAAATTCTACATCATAATCCATATGTTATAT
AGTTTTACAACATCATAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAA
ATATAATTTAATAATAA
Found at i:1173593 original size:17 final size:15
Alignment explanation
Indices: 1173562--1173600 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
1173552 TTTATACAAT
1173562 TTAAAATAATTAATA
1 TTAAAATAATTAATA
1173577 TTAAATATAATTTAATA
1 TTAAA-ATAA-TTAATA
*
1173594 ATAAAAT
1 TTAAAAT
1173601 GTTCTTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 5 0.24
16 6 0.29
17 10 0.48
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TTAAAATAATTAATA
Found at i:1177800 original size:33 final size:33
Alignment explanation
Indices: 1177756--1177839 Score: 88
Period size: 28 Copynumber: 2.7 Consensus size: 33
1177746 TCTAGGTCTG
* *
1177756 AGCCCTATACAGTATCAGTACAGTGTGGGCTTT
1 AGCCCAATACAGTATCAGTACAGTGTGGGCCTT
*
1177789 AGCCCATTACAG--T-A--ACAGTGTGGGCCTT
1 AGCCCAATACAGTATCAGTACAGTGTGGGCCTT
*
1177817 AGCCTAATACAGTAATCAGTACA
1 AGCCCAATACAGT-ATCAGTACA
1177840 AAGCAGTGAT
Statistics
Matches: 40, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
28 23 0.57
30 1 0.03
31 2 0.05
32 1 0.03
33 10 0.25
34 3 0.08
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (33 bp):
AGCCCAATACAGTATCAGTACAGTGTGGGCCTT
Found at i:1177810 original size:28 final size:28
Alignment explanation
Indices: 1177771--1177836 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
1177761 TATACAGTAT
* *
1177771 CAGT-ACAGTGTGGGCTTTAGCCCATTA
1 CAGTAACAGTGTGGGCCTTAGCCCAATA
*
1177798 CAGTAACAGTGTGGGCCTTAGCCTAATA
1 CAGTAACAGTGTGGGCCTTAGCCCAATA
1177826 CAGTAATCAGT
1 CAGTAA-CAGT
1177837 ACAAAGCAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 4 0.12
28 26 0.76
29 4 0.12
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.27
Consensus pattern (28 bp):
CAGTAACAGTGTGGGCCTTAGCCCAATA
Found at i:1178156 original size:27 final size:26
Alignment explanation
Indices: 1178126--1178290 Score: 177
Period size: 27 Copynumber: 6.2 Consensus size: 26
1178116 TATAACAATC
* *
1178126 ATTTTACCCTATCGGGGTATTTCAGTT
1 ATTTTACCCT-TCGGGGTAATTCGGTT
*
1178153 ATTTTACCCTTCGAGGATAATTCGGTT
1 ATTTTACCCTTCG-GGGTAATTCGGTT
*
1178180 ATTTTACCCTTCAGGGGTAATTCGGTC
1 ATTTTACCCTTC-GGGGTAATTCGGTT
* * *
1178207 ATTTTACCTTTCAGGGGCAATTCAGTT
1 ATTTTACCCTTC-GGGGTAATTCGGTT
* * *
1178234 ATTTTACCCTTTGAGGTTAATTCGGTC
1 ATTTTACCCTTCG-GGGTAATTCGGTT
* *
1178261 ATTTTACCCTTCGGGGTAATTTGATT
1 ATTTTACCCTTCGGGGTAATTCGGTT
1178287 ATTT
1 ATTT
1178291 GTGGCCCATA
Statistics
Matches: 115, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
26 17 0.15
27 97 0.84
28 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.19, T:0.43
Consensus pattern (26 bp):
ATTTTACCCTTCGGGGTAATTCGGTT
Found at i:1178233 original size:81 final size:80
Alignment explanation
Indices: 1178124--1178281 Score: 237
Period size: 81 Copynumber: 2.0 Consensus size: 80
1178114 GGTATAACAA
* * *
1178124 TCATTTTACCCTATCGGGGTATTTCAGTTATTTTACCCTTCGAGGATAATTCGGTTATTTTACCC
1 TCATTTTACCCTATCGGGGCAATTCAGTTATTTTACCCTTCGAGGATAATTCGGTCATTTTACCC
1178189 TTCAGGGGTAATTCGG
66 TTC-GGGGTAATTCGG
* * *
1178205 TCATTTTA-CCTTTCAGGGGCAATTCAGTTATTTTACCCTTTGAGGTTAATTCGGTCATTTTACC
1 TCATTTTACCCTATC-GGGGCAATTCAGTTATTTTACCCTTCGAGGATAATTCGGTCATTTTACC
1178269 CTTCGGGGTAATT
65 CTTCGGGGTAATT
1178282 TGATTATTTG
Statistics
Matches: 70, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
80 14 0.20
81 56 0.80
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.42
Consensus pattern (80 bp):
TCATTTTACCCTATCGGGGCAATTCAGTTATTTTACCCTTCGAGGATAATTCGGTCATTTTACCC
TTCGGGGTAATTCGG
Found at i:1179044 original size:18 final size:19
Alignment explanation
Indices: 1179021--1179062 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
1179011 ACTAGAATGA
1179021 AGAGGAG-AAGATGAAAAG
1 AGAGGAGAAAGATGAAAAG
*
1179039 AGAGGAGAAAAGATGATAAG
1 AGAGGAG-AAAGATGAAAAG
1179059 AGAG
1 AGAG
1179063 AATTCAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.33
20 14 0.67
ACGTcount: A:0.55, C:0.00, G:0.38, T:0.07
Consensus pattern (19 bp):
AGAGGAGAAAGATGAAAAG
Found at i:1187604 original size:21 final size:21
Alignment explanation
Indices: 1187570--1187609 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1187560 GGAGGGGAGT
*
1187570 AAAAATTTT-GGGGGAAAAGA
1 AAAAATTTTAGGGGTAAAAGA
1187590 AAAAATATTTAGGGGTAAAA
1 AAAAAT-TTTAGGGGTAAAA
1187610 ATGTAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 3 0.18
22 8 0.47
ACGTcount: A:0.53, C:0.00, G:0.25, T:0.23
Consensus pattern (21 bp):
AAAAATTTTAGGGGTAAAAGA
Found at i:1188140 original size:40 final size:40
Alignment explanation
Indices: 1188076--1188185 Score: 105
Period size: 40 Copynumber: 2.8 Consensus size: 40
1188066 CACACCAATT
* * * ***
1188076 TGTGGATAAGCCAGCAGTAATGCAGATAAATTTTTAGAAA
1 TGTGGACAAGCCACCAATAATGCAGATAAATTGCCAGAAA
* * *
1188116 TGTGGACAAGCCACCAATATTGCAGA-AGAGTTGCCAGCAA
1 TGTGGACAAGCCACCAATAATGCAGATA-AATTGCCAGAAA
* *
1188156 TATGGACAAGCCACCAATAATGCAAATAAA
1 TGTGGACAAGCCACCAATAATGCAGATAAA
1188186 CTGCTAGTAT
Statistics
Matches: 55, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
39 1 0.02
40 53 0.96
41 1 0.02
ACGTcount: A:0.41, C:0.17, G:0.21, T:0.21
Consensus pattern (40 bp):
TGTGGACAAGCCACCAATAATGCAGATAAATTGCCAGAAA
Found at i:1188398 original size:38 final size:37
Alignment explanation
Indices: 1188324--1188406 Score: 87
Period size: 38 Copynumber: 2.2 Consensus size: 37
1188314 GAGTAGTAAC
* * * *
1188324 AGTAAGCATGACTTAGACATGCAATTAGTAGCAGAATT
1 AGTAAGCATGACTTAAACATGCAATCAATAACAGAA-T
* * *
1188362 AGTAAGCATGATTTAAACATGCGATCAATAATAGAAT
1 AGTAAGCATGACTTAAACATGCAATCAATAACAGAAT
1188399 AGT-AGCAT
1 AGTAAGCAT
1188407 TAACATGCAT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
36 5 0.13
37 4 0.11
38 29 0.76
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (37 bp):
AGTAAGCATGACTTAAACATGCAATCAATAACAGAAT
Found at i:1196457 original size:30 final size:29
Alignment explanation
Indices: 1196388--1196464 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 29
1196378 ACGACTATAA
* *
1196388 AAAATATGAAAAGGGGTAGCTTCGGCTAC
1 AAAATATGAAAAGGGATAGCTTCAGCTAC
**
1196417 CGAATCATGAAAAGGGATAGC-TCTAGCTATC
1 AAAAT-ATGAAAAGGGATAGCTTC-AGCTA-C
1196448 AAAATATGAAAAGGGAT
1 AAAATATGAAAAGGGAT
1196465 GGTGACGACT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
29 5 0.13
30 30 0.77
31 4 0.10
ACGTcount: A:0.42, C:0.13, G:0.25, T:0.21
Consensus pattern (29 bp):
AAAATATGAAAAGGGATAGCTTCAGCTAC
Found at i:1197815 original size:21 final size:19
Alignment explanation
Indices: 1197770--1197823 Score: 54
Period size: 21 Copynumber: 2.7 Consensus size: 19
1197760 CATATGTTTT
* *
1197770 TAAAAAAAATAATTAAATA
1 TAAAAAAAATAATAAAAAA
1197789 TGAAAAAGAAATAATAAAGAAA
1 T-AAAAA-AAATAATAAA-AAA
*
1197811 TAAAAAAACTAAT
1 TAAAAAAAATAAT
1197824 TAATTAAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 1 0.03
20 11 0.38
21 14 0.48
22 3 0.10
ACGTcount: A:0.72, C:0.02, G:0.06, T:0.20
Consensus pattern (19 bp):
TAAAAAAAATAATAAAAAA
Found at i:1197834 original size:14 final size:14
Alignment explanation
Indices: 1197815--1197846 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1197805 AAGAAATAAA
*
1197815 AAAACTAATTAATT
1 AAAACTAATTAACT
1197829 AAAACTAATTAACT
1 AAAACTAATTAACT
1197843 AAAA
1 AAAA
1197847 ATAAAGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.28
Consensus pattern (14 bp):
AAAACTAATTAACT
Found at i:1198376 original size:22 final size:21
Alignment explanation
Indices: 1198341--1198417 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 21
1198331 AAAGGGTATC
* *
1198341 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
1198362 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
1198385 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
1198404 TATATATCATATCT
1 TACAAATCATATCT
1198418 AAGATTGCAT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
19 17 0.37
21 4 0.09
22 15 0.33
23 10 0.22
ACGTcount: A:0.42, C:0.16, G:0.05, T:0.38
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:1198384 original size:23 final size:22
Alignment explanation
Indices: 1198341--1198398 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
1198331 AAAGGGTATC
* *
1198341 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
1198362 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
1198385 TGCATATCATATCT
1 TACAAATCATATCT
1198399 AAGATTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:1198401 original size:19 final size:19
Alignment explanation
Indices: 1198377--1198477 Score: 136
Period size: 19 Copynumber: 5.5 Consensus size: 19
1198367 AATCATATCT
1198377 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
1198396 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
1198415 TCTAAGATTGC--AT-ATA
1 TCTAAGATTGCATATCATA
** *
1198431 TCTAAGATTATATATTATA
1 TCTAAGATTGCATATCATA
1198450 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
1198469 TCTAAGATT
1 TCTAAGATT
1198478 ATATNNNNNN
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
16 12 0.17
17 2 0.03
18 2 0.03
19 54 0.77
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.41
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:1198433 original size:16 final size:16
Alignment explanation
Indices: 1198412--1198464 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 16
1198402 ATTATATATC
1198412 ATATCTAAGATTGCAT
1 ATATCTAAGATTGCAT
**
1198428 ATATCTAAGATTATATATT
1 ATATCTAAGA-T-TGCA-T
1198447 ATATCTAAGATTGCAT
1 ATATCTAAGATTGCAT
1198463 AT
1 AT
1198465 CATATCTAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
16 13 0.43
17 3 0.10
18 3 0.10
19 11 0.37
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (16 bp):
ATATCTAAGATTGCAT
Found at i:1199100 original size:132 final size:132
Alignment explanation
Indices: 1198863--1199547 Score: 1201
Period size: 132 Copynumber: 5.2 Consensus size: 132
1198853 NNNNNATATG
* * * * *
1198863 ATTACTGGCTTCAATGTACTCCACTGTGACCACAGCGAGGTAAAATCCGCCATCTTCAATCTGCA
1 ATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCT
* * * *
1198928 ACACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCATTGTTTTCCAGGAAAGTA
66 CCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTA
1198993 GA
131 GA
1198995 ATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCT
1 ATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCT
1199060 CCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTA
66 CCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTA
1199125 GA
131 GA
*
1199127 ATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCACCATCTTCGATCTGCT
1 ATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCT
1199192 CCACTACTGCTTAGGGAGATAAGA-CATGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGT
66 CCACTACTGCTTAGGGAGATAAGATC-TGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGT
*
1199256 TGA
130 AGA
* *
1199259 ATTACTGACTTCAATGTACTCCACTATAAGCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCT
1 ATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCT
*
1199324 CCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTTCAGGGAAGTA
66 CCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTA
1199389 GA
131 GA
* * *
1199391 ATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAAGTAAAATCCGCCATCTTCGATTTGCT
1 ATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCT
1199456 CCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTA
66 CCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTA
1199521 GA
131 GA
1199523 ATTACTGGCTTCAATGTACTCCACT
1 ATTACTGGCTTCAATGTACTCCACT
1199548 NNNNNNNNNN
Statistics
Matches: 529, Mismatches: 22, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
131 1 0.00
132 527 1.00
133 1 0.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (132 bp):
ATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCT
CCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCCAGGGAAGTA
GA
Found at i:1201137 original size:14 final size:15
Alignment explanation
Indices: 1201114--1201146 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1201104 GTCGATGCTT
*
1201114 TTCCAGATAAGG-CC
1 TTCCACATAAGGTCC
1201128 TTCCACATAAGGTCC
1 TTCCACATAAGGTCC
1201143 TTCC
1 TTCC
1201147 TAGCTTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.24, C:0.33, G:0.15, T:0.27
Consensus pattern (15 bp):
TTCCACATAAGGTCC
Found at i:1201397 original size:5 final size:5
Alignment explanation
Indices: 1201387--1201420 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
1201377 CCCTGATAGA
1201387 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
1201421 TTGTCATCCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (5 bp):
TTTTG
Found at i:1202976 original size:15 final size:14
Alignment explanation
Indices: 1202956--1202988 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
1202946 TCTGGGCCTA
1202956 GTCGGAATAGTGGTT
1 GTCGGAATAG-GGTT
1202971 GTCGGAATAGGGTT
1 GTCGGAATAGGGTT
1202985 -TCGG
1 GTCGG
1202989 GACCACAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 4 0.22
15 10 0.56
ACGTcount: A:0.18, C:0.09, G:0.42, T:0.30
Consensus pattern (14 bp):
GTCGGAATAGGGTT
Found at i:1203528 original size:14 final size:15
Alignment explanation
Indices: 1203509--1203540 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1203499 GTGGTTATAG
1203509 TTAAAATA-ATAAAA
1 TTAAAATAGATAAAA
1203523 TTAAAATAGATAAAA
1 TTAAAATAGATAAAA
1203538 TTA
1 TTA
1203541 TGATGTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (15 bp):
TTAAAATAGATAAAA
Found at i:1206390 original size:24 final size:24
Alignment explanation
Indices: 1206362--1206407 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1206352 TATCATTTTT
* *
1206362 GCTGCTCATTCATTTGCTTTTGAA
1 GCTGCTCATGCATTTCCTTTTGAA
*
1206386 GCTGCTCCTGCATTTCCTTTTG
1 GCTGCTCATGCATTTCCTTTTG
1206408 GGATTGTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.11, C:0.26, G:0.17, T:0.46
Consensus pattern (24 bp):
GCTGCTCATGCATTTCCTTTTGAA
Found at i:1209474 original size:32 final size:34
Alignment explanation
Indices: 1209433--1209495 Score: 112
Period size: 32 Copynumber: 1.9 Consensus size: 34
1209423 ATATGAAAAA
1209433 TAAATAATAAAAAAATAAAAAAAA-CTAATTAAT
1 TAAATAATAAAAAAATAAAAAAAAGCTAATTAAT
1209466 TAAA-AATAAAAAAATAAAAAAAAGCTAATT
1 TAAATAATAAAAAAATAAAAAAAAGCTAATT
1209496 TGAACTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 19 0.66
33 10 0.34
ACGTcount: A:0.73, C:0.03, G:0.02, T:0.22
Consensus pattern (34 bp):
TAAATAATAAAAAAATAAAAAAAAGCTAATTAAT
Found at i:1209478 original size:24 final size:22
Alignment explanation
Indices: 1209408--1209479 Score: 85
Period size: 24 Copynumber: 3.2 Consensus size: 22
1209398 ATATTTTTTT
*
1209408 AAAAATAATAATTAAATATGAAA
1 AAAAATAATAATTAAAAAT-AAA
1209431 AATAAATAATAA--AAAAATAAA
1 AA-AAATAATAATTAAAAATAAA
1209452 AAAAACTAATTAATTAAAAATAAA
1 AAAAA-TAA-TAATTAAAAATAAA
1209476 AAAA
1 AAAA
1209480 TAAAAAAAAG
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
20 3 0.07
21 8 0.19
22 8 0.19
23 2 0.05
24 22 0.51
ACGTcount: A:0.75, C:0.01, G:0.01, T:0.22
Consensus pattern (22 bp):
AAAAATAATAATTAAAAATAAA
Found at i:1210004 original size:22 final size:21
Alignment explanation
Indices: 1209969--1210045 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 21
1209959 AAAGGGTATC
* *
1209969 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
1209990 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
1210013 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
1210032 TATATATCATATCT
1 TACAAATCATATCT
1210046 AAGATTGCAT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
19 17 0.37
21 4 0.09
22 15 0.33
23 10 0.22
ACGTcount: A:0.42, C:0.16, G:0.05, T:0.38
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:1210012 original size:23 final size:22
Alignment explanation
Indices: 1209969--1210026 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
1209959 AAAGGGTATC
* *
1209969 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
1209990 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
1210013 TGCATATCATATCT
1 TACAAATCATATCT
1210027 AAGATTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:1210029 original size:19 final size:19
Alignment explanation
Indices: 1210005--1210185 Score: 230
Period size: 19 Copynumber: 9.8 Consensus size: 19
1209995 AATCATATCT
1210005 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
1210024 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
1210043 TCTAAGATTGC--AT-ATA
1 TCTAAGATTGCATATCATA
** *
1210059 TCTAAGATTATATATTATA
1 TCTAAGATTGCATATCATA
1210078 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
1210097 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
1210116 TCTAAGATTGC--AT-ATA
1 TCTAAGATTGCATATCATA
** *
1210132 TCTAAGATTATATATTATA
1 TCTAAGATTGCATATCATA
1210151 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
1210170 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
1210186 CCTGAAGATT
Statistics
Matches: 138, Mismatches: 18, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
16 24 0.17
17 4 0.03
18 4 0.03
19 106 0.77
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:1210166 original size:54 final size:54
Alignment explanation
Indices: 1209998--1210184 Score: 222
Period size: 54 Copynumber: 3.4 Consensus size: 54
1209988 ATTACAAAAT
1209998 CATATC-T-TCTAAGATTGCATATCATATCTAAGATTATATATCATATCTAAGATTG
1 CATATCATATCTAAGATTGC--AT-ATATCTAAGATTATATATCATATCTAAGATTG
** ** *
1210053 C--AT-ATATCTAAGATTATATATTATATCTAAGATTGCATATCATATCTAAGATTA
1 CATATCATATCTAAGA-T-TGCA-TATATCTAAGATTATATATCATATCTAAGATTG
* *
1210107 TATATCATATCTAAGATTGCATATATCTAAGATTATATATTATATCTAAGATTG
1 CATATCATATCTAAGATTGCATATATCTAAGATTATATATCATATCTAAGATTG
1210161 CATATCATATCTAAGATTGCATAT
1 CATATCATATCTAAGATTGCATAT
1210185 CCCTGAAGAT
Statistics
Matches: 111, Mismatches: 13, Indels: 17
0.79 0.09 0.12
Matches are distributed among these distances:
53 3 0.03
54 89 0.80
55 5 0.05
56 4 0.04
57 10 0.09
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.41
Consensus pattern (54 bp):
CATATCATATCTAAGATTGCATATATCTAAGATTATATATCATATCTAAGATTG
Found at i:1210185 original size:73 final size:73
Alignment explanation
Indices: 1210005--1210178 Score: 348
Period size: 73 Copynumber: 2.4 Consensus size: 73
1209995 AATCATATCT
1210005 TCTAAGATTGCATATCATATCTAAGATTATATATCATATCTAAGATTGCATATATCTAAGATTAT
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATATCTAAGATTGCATATATCTAAGATTAT
1210070 ATATTATA
66 ATATTATA
1210078 TCTAAGATTGCATATCATATCTAAGATTATATATCATATCTAAGATTGCATATATCTAAGATTAT
1 TCTAAGATTGCATATCATATCTAAGATTATATATCATATCTAAGATTGCATATATCTAAGATTAT
1210143 ATATTATA
66 ATATTATA
1210151 TCTAAGATTGCATATCATATCTAAGATT
1 TCTAAGATTGCATATCATATCTAAGATT
1210179 GCATATCCCT
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 101 1.00
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (73 bp):
TCTAAGATTGCATATCATATCTAAGATTATATATCATATCTAAGATTGCATATATCTAAGATTAT
ATATTATA
Found at i:1210384 original size:30 final size:28
Alignment explanation
Indices: 1210348--1210450 Score: 109
Period size: 30 Copynumber: 3.5 Consensus size: 28
1210338 CGACCATCAA
1210348 AATTATGAAAAGAGATAGCTTTAGCTATCG
1 AATTATGAAAAG-GATAGCTTT-GCTATCG
1210378 AATTATGAAAAGGGATAG-TTTCGGCTATCG
1 AATTATGAAAA-GGATAGCTTT--GCTATCG
* *
1210408 AATCATGAAAATGGATAGTCTTTGCTATTG
1 AATTATGAAAA-GGATAG-CTTTGCTATCG
*
1210438 AATTATGGAAAGG
1 AATTATGAAAAGG
1210451 GATGTGTCAA
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
29 5 0.08
30 54 0.86
31 1 0.02
32 3 0.05
ACGTcount: A:0.37, C:0.09, G:0.23, T:0.31
Consensus pattern (28 bp):
AATTATGAAAAGGATAGCTTTGCTATCG
Found at i:1215744 original size:31 final size:31
Alignment explanation
Indices: 1215709--1215785 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
1215699 GTTACAAAAT
* *
1215709 AGTTATTGAATTA-TTCAAAAGTTTTCATTTA
1 AGTTACTGAACTATTTCAAAA-TTTTCATTTA
* *
1215740 AGTTACTGAACTATTTGAAAATTTTTATTTA
1 AGTTACTGAACTATTTCAAAATTTTCATTTA
* *
1215771 AGTCACTGAGCTATT
1 AGTTACTGAACTATT
1215786 AATTGTTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 33 0.85
32 6 0.15
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.45
Consensus pattern (31 bp):
AGTTACTGAACTATTTCAAAATTTTCATTTA
Found at i:1223597 original size:27 final size:27
Alignment explanation
Indices: 1223493--1223756 Score: 304
Period size: 27 Copynumber: 9.9 Consensus size: 27
1223483 GGGTATAACA
* *
1223493 GTCATTTTACCCTATGG-GATATTTCA
1 GTCATTTTACCCTATGGAGGTATTTCG
* *
1223519 GTCATTTTACCCTATGG-GGTATCTCA
1 GTCATTTTACCCTATGGAGGTATTTCG
* * *
1223545 TTCATTTTCCCCTA-GGGGGTATTTCG
1 GTCATTTTACCCTATGGAGGTATTTCG
* *
1223571 GTCATTCTAGCCTATGGAGGTATTTCG
1 GTCATTTTACCCTATGGAGGTATTTCG
* *
1223598 GTCA-TTTACCTTATAGAGGTATTTCG
1 GTCATTTTACCCTATGGAGGTATTTCG
* * *
1223624 ATTATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGAGGTATTTCG
*
1223651 GTCATTTTACCCTAT-GAGGGTATTTCA
1 GTCATTTTACCCTATGGA-GGTATTTCG
1223678 GTCATTTTACCCTATGGAGGTATTTCG
1 GTCATTTTACCCTATGGAGGTATTTCG
* * * * *
1223705 ATAATTCTACCCTATGGGGGTATTTCA
1 GTCATTTTACCCTATGGAGGTATTTCG
1223732 GTCATTTTACCCTATGGAGGTATTT
1 GTCATTTTACCCTATGGAGGTATTT
1223757 TGCTCATAAC
Statistics
Matches: 199, Mismatches: 34, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
25 2 0.01
26 74 0.37
27 121 0.61
28 2 0.01
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (27 bp):
GTCATTTTACCCTATGGAGGTATTTCG
Found at i:1231997 original size:11 final size:11
Alignment explanation
Indices: 1231983--1232022 Score: 80
Period size: 11 Copynumber: 3.6 Consensus size: 11
1231973 AAGCATCTTT
1231983 CAATCATCCCA
1 CAATCATCCCA
1231994 CAATCATCCCA
1 CAATCATCCCA
1232005 CAATCATCCCA
1 CAATCATCCCA
1232016 CAATCAT
1 CAATCAT
1232023 TTATCATTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.38, C:0.42, G:0.00, T:0.20
Consensus pattern (11 bp):
CAATCATCCCA
Found at i:1232001 original size:22 final size:22
Alignment explanation
Indices: 1231936--1232018 Score: 105
Period size: 22 Copynumber: 3.8 Consensus size: 22
1231926 TTTCTCACTT
1231936 TTTCAATCATCCCTA-AAGCATC
1 TTTCAATCATCCC-ACAAGCATC
*
1231958 TTTCAATCATCCCTCAAGCATC
1 TTTCAATCATCCCACAAGCATC
*
1231980 TTTCAATCATCCCACAATCATC
1 TTTCAATCATCCCACAAGCATC
***
1232002 CCACAATCATCCCACAA
1 TTTCAATCATCCCACAA
1232019 TCATTTATCA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
22 54 1.00
ACGTcount: A:0.33, C:0.37, G:0.02, T:0.28
Consensus pattern (22 bp):
TTTCAATCATCCCACAAGCATC
Found at i:1239289 original size:18 final size:20
Alignment explanation
Indices: 1239240--1239280 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1239230 TTTTGAAAAG
1239240 ATAACCATTCGATCCATATT
1 ATAACCATTCGATCCATATT
1239260 ATAACCATTCGATCCATATT
1 ATAACCATTCGATCCATATT
1239280 A
1 A
1239281 ATCATTCGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (20 bp):
ATAACCATTCGATCCATATT
Found at i:1241376 original size:18 final size:18
Alignment explanation
Indices: 1241357--1241406 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
1241347 TAATTGATAT
1241357 TTTTATTAA-TAATAATA
1 TTTTATTAATTAATAATA
* *
1241374 TTTTAATAATTAAAAATA
1 TTTTATTAATTAATAATA
1241392 TTTTATTAATTAATA
1 TTTTATTAATTAATA
1241407 TTATAATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 8 0.29
18 20 0.71
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TTTTATTAATTAATAATA
Found at i:1241406 original size:33 final size:35
Alignment explanation
Indices: 1241357--1241423 Score: 93
Period size: 33 Copynumber: 1.9 Consensus size: 35
1241347 TAATTGATAT
* *
1241357 TTTTATTAATAATAATATTTTAATA-ATTAAAAATA
1 TTTTATTAAT-ATAATATTATAATATATAAAAAATA
1241392 TTTTATTAAT-TAATATTATAATATATAAAAAA
1 TTTTATTAATATAATATTATAATATATAAAAAA
1241424 GAAAAAAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 12 0.41
34 7 0.24
35 10 0.34
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (35 bp):
TTTTATTAATATAATATTATAATATATAAAAAATA
Found at i:1241881 original size:5 final size:5
Alignment explanation
Indices: 1241866--1241908 Score: 77
Period size: 5 Copynumber: 8.4 Consensus size: 5
1241856 CTATGACTAA
1241866 TTATAT TTATT TTATT TTATT TTATT TTATT TTATT TTATT TT
1 TTAT-T TTATT TTATT TTATT TTATT TTATT TTATT TTATT TT
1241909 TTTGAGTTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 33 0.89
6 4 0.11
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTATT
Found at i:1245635 original size:13 final size:13
Alignment explanation
Indices: 1245617--1245641 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1245607 ATTTACAAGA
1245617 TTACATAATCAAT
1 TTACATAATCAAT
1245630 TTACATAATCAA
1 TTACATAATCAA
1245642 ATCCAATATA
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:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (13 bp):
TTACATAATCAAT
Found at i:1262611 original size:34 final size:34
Alignment explanation
Indices: 1262563--1262633 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
1262553 GAAGCTTTTG
1262563 GAAAAGTGAGGTGTTAAATTGTGGAGTTGAAACT
1 GAAAAGTGAGGTGTTAAATTGTGGAGTTGAAACT
*
1262597 GAAAAGTGATGTGTTAAATTGTGGAGTTGAAACT
1 GAAAAGTGAGGTGTTAAATTGTGGAGTTGAAACT
1262631 GAA
1 GAA
1262634 TAAGAACTGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.37, C:0.03, G:0.31, T:0.30
Consensus pattern (34 bp):
GAAAAGTGAGGTGTTAAATTGTGGAGTTGAAACT
Found at i:1266204 original size:44 final size:44
Alignment explanation
Indices: 1266140--1266384 Score: 305
Period size: 44 Copynumber: 5.6 Consensus size: 44
1266130 GCAACATCAG
1266140 TACATAGTACCTGCTGCATATAAATGGCACATAGCCAACACTGA
1 TACATAGTACCTGCTGCATATAAATGGCACATAGCCAACACTGA
* * * *
1266184 TACATATTACTTGCTACATATAAATGGCACATAGCCAACACTGG
1 TACATAGTACCTGCTGCATATAAATGGCACATAGCCAACACTGA
* * *
1266228 TACATAGTACCTGTTGCATATAAATGACACATAGCCAACACCGA
1 TACATAGTACCTGCTGCATATAAATGGCACATAGCCAACACTGA
* * * *
1266272 TGCGTAGTACATGTTGCATATAAATGGCACATAGCCAACACT-A
1 TACATAGTACCTGCTGCATATAAATGGCACATAGCCAACACTGA
* * * *
1266315 GTACATAGTACTTGTTGCATATAAATGACACATAGCCAACA-TCGG
1 -TACATAGTACCTGCTGCATATAAATGGCACATAGCCAACACT-GA
**
1266360 TACATAGTACCTGCTAAATATAAAT
1 TACATAGTACCTGCTGCATATAAAT
1266385 CCTAATGATA
Statistics
Matches: 173, Mismatches: 25, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
43 2 0.01
44 171 0.99
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (44 bp):
TACATAGTACCTGCTGCATATAAATGGCACATAGCCAACACTGA
Found at i:1266292 original size:88 final size:88
Alignment explanation
Indices: 1266138--1266384 Score: 359
Period size: 88 Copynumber: 2.8 Consensus size: 88
1266128 CTGCAACATC
* * * * *
1266138 AGTACATAGTACCTGCTGCATATAAATGGCACATAGCCAACACTGATACATATTACTTGCTACAT
1 AGTACATAGTACCTGTTGCATATAAATGACACATAGCCAACACCGATACATAGTACATGCTACAT
1266203 ATAAATGGCACATAGCCAACACT
66 ATAAATGGCACATAGCCAACACT
* * * * *
1266226 GGTACATAGTACCTGTTGCATATAAATGACACATAGCCAACACCGATGCGTAGTACATGTTGCAT
1 AGTACATAGTACCTGTTGCATATAAATGACACATAGCCAACACCGATACATAGTACATGCTACAT
1266291 ATAAATGGCACATAGCCAACACT
66 ATAAATGGCACATAGCCAACACT
* * * * *
1266314 AGTACATAGTACTTGTTGCATATAAATGACACATAGCCAACATCGGTACATAGTACCTGCTAAAT
1 AGTACATAGTACCTGTTGCATATAAATGACACATAGCCAACACCGATACATAGTACATGCTACAT
1266379 ATAAAT
66 ATAAAT
1266385 CCTAATGATA
Statistics
Matches: 139, Mismatches: 20, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
88 139 1.00
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (88 bp):
AGTACATAGTACCTGTTGCATATAAATGACACATAGCCAACACCGATACATAGTACATGCTACAT
ATAAATGGCACATAGCCAACACT
Found at i:1266381 original size:132 final size:132
Alignment explanation
Indices: 1266144--1266384 Score: 369
Period size: 132 Copynumber: 1.8 Consensus size: 132
1266134 CATCAGTACA
* *
1266144 TAGTACCTGCTGCATATAAATGGCACATAGCCAACACTGATACATATTACTTGCTACATATAAAT
1 TAGTACATGCTGCATATAAATGGCACATAGCCAACACTGATACATAGTACTTGCTACATATAAAT
* * **
1266209 GGCACATAGCCAACACTGGTACATAGTACCTGTTGCATATAAATGACACATAGCCAACACCGATG
66 GACACATAGCCAACACTGGTACATAGTACCTGCTAAATATAAATGACACATAGCCAACACCGATG
1266274 CG
131 CG
* * *
1266276 TAGTACATGTTGCATATAAATGGCACATAGCCAACACT-AGTACATAGTACTTGTTGCATATAAA
1 TAGTACATGCTGCATATAAATGGCACATAGCCAACACTGA-TACATAGTACTTGCTACATATAAA
1266340 TGACACATAGCCAACA-TCGGTACATAGTACCTGCTAAATATAAAT
65 TGACACATAGCCAACACT-GGTACATAGTACCTGCTAAATATAAAT
1266385 CCTAATGATA
Statistics
Matches: 98, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
131 2 0.02
132 96 0.98
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (132 bp):
TAGTACATGCTGCATATAAATGGCACATAGCCAACACTGATACATAGTACTTGCTACATATAAAT
GACACATAGCCAACACTGGTACATAGTACCTGCTAAATATAAATGACACATAGCCAACACCGATG
CG
Found at i:1266456 original size:14 final size:14
Alignment explanation
Indices: 1266437--1266470 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
1266427 ACATGGGCTT
1266437 TAACCTGTATTCTA
1 TAACCTGTATTCTA
1266451 TAACCTGTATTCTA
1 TAACCTGTATTCTA
1266465 TAACCT
1 TAACCT
1266471 TTTCATGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.29, C:0.24, G:0.06, T:0.41
Consensus pattern (14 bp):
TAACCTGTATTCTA
Found at i:1269581 original size:23 final size:23
Alignment explanation
Indices: 1269543--1269631 Score: 108
Period size: 24 Copynumber: 3.8 Consensus size: 23
1269533 TATACGCACA
*
1269543 AATGAAATATGGCACTTTGGTGC
1 AATGAAATGTGGCACTTTGGTGC
1269566 GAATGAAA-GTGGCACTTTGGTGC
1 -AATGAAATGTGGCACTTTGGTGC
* *
1269589 AATTGAAATGTGACACTTTGATGC
1 AA-TGAAATGTGGCACTTTGGTGC
*
1269613 AATCAAAATGTGGCACTTT
1 AAT-GAAATGTGGCACTTT
1269632 TTGCAATACT
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
22 2 0.04
23 20 0.35
24 35 0.61
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.30
Consensus pattern (23 bp):
AATGAAATGTGGCACTTTGGTGC
Found at i:1273410 original size:67 final size:67
Alignment explanation
Indices: 1273330--1273613 Score: 313
Period size: 67 Copynumber: 4.2 Consensus size: 67
1273320 TGTCATAACC
* * * * * *
1273330 GAGCTATAGTCTTACATATCATACCCCATGTTTAATGTCTTAGCG-GACTCTCTATGTTTCCATA
1 GAGCTATGGTCTTACACATCTTACCCCATGTTTAATGTCCTGGCGAG-CTCTCTATGTTGCCATA
*
1273394 GTT
65 GCT
* * * *
1273397 GAGCTATGATCTTATACATCTTACCCCATGTTTAATGTCCTGGCAAGCTCTTTATGTTGCCATAG
1 GAGCTATGGTCTTACACATCTTACCCCATGTTTAATGTCCTGGCGAGCTCTCTATGTTGCCATAG
1273462 CT
66 CT
* * * *
1273464 AAGCTACGGTCTTACACATTTTACCCCATGTTTAATGTCCTGGCGAGCTCTTTATGTTGCCATAG
1 GAGCTATGGTCTTACACATCTTACCCCATGTTTAATGTCCTGGCGAGCTCTCTATGTTGCCATAG
1273529 CT
66 CT
* * * * * * * *
1273531 AAGCTACGGTCTTAAACATTTTACCCCATGTTTATTGTCTTGGTG-GACTCTCTATGTTGTCATA
1 GAGCTATGGTCTTACACATCTTACCCCATGTTTAATGTCCTGGCGAG-CTCTCTATGTTGCCATA
1273595 G-T
65 GCT
1273597 CGAGCTATGGTCTTACA
1 -GAGCTATGGTCTTACA
1273614 TATTATGCCT
Statistics
Matches: 188, Mismatches: 26, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
66 2 0.01
67 185 0.98
68 1 0.01
ACGTcount: A:0.22, C:0.23, G:0.17, T:0.38
Consensus pattern (67 bp):
GAGCTATGGTCTTACACATCTTACCCCATGTTTAATGTCCTGGCGAGCTCTCTATGTTGCCATAG
CT
Found at i:1278611 original size:12 final size:12
Alignment explanation
Indices: 1278591--1278624 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1278581 TTTTTATATG
*
1278591 TTATATGTTATT
1 TTATTTGTTATT
1278603 TTATTTGTTATT
1 TTATTTGTTATT
1278615 TTATGTTGTT
1 TTAT-TTGTT
1278625 TTGTAAATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 15 0.75
13 5 0.25
ACGTcount: A:0.18, C:0.00, G:0.12, T:0.71
Consensus pattern (12 bp):
TTATTTGTTATT
Found at i:1285646 original size:6 final size:6
Alignment explanation
Indices: 1285635--1285662 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1285625 TTCTATTATC
1285635 TATCAT TATCAT TATCAT TATCAT TATC
1 TATCAT TATCAT TATCAT TATCAT TATC
1285663 CTTCTATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (6 bp):
TATCAT
Found at i:1288766 original size:15 final size:15
Alignment explanation
Indices: 1288746--1288779 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1288736 CAAACCCACC
*
1288746 AGAACAGGACAGAGT
1 AGAACAGGACAGAAT
*
1288761 AGAACATGACAGAAT
1 AGAACAGGACAGAAT
1288776 AGAA
1 AGAA
1288780 TAGAGCAAGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.53, C:0.12, G:0.26, T:0.09
Consensus pattern (15 bp):
AGAACAGGACAGAAT
Found at i:1290378 original size:26 final size:26
Alignment explanation
Indices: 1290348--1290397 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
1290338 TATCATTAAT
1290348 TGACTGAATTTAACTTATAACCCACA
1 TGACTGAATTTAACTTATAACCCACA
1290374 TGACTGAATTTAACTTATAACCCA
1 TGACTGAATTTAACTTATAACCCA
1290398 TGTCGAAACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.38, C:0.22, G:0.08, T:0.32
Consensus pattern (26 bp):
TGACTGAATTTAACTTATAACCCACA
Found at i:1291378 original size:18 final size:17
Alignment explanation
Indices: 1291342--1291384 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1291332 TATTATAACT
* *
1291342 TTAAT-ATACAATAATA
1 TTAATAATAAAATAAAA
1291358 TTAATTAATAAAATAAAA
1 TTAA-TAATAAAATAAAA
1291376 TTAATAATA
1 TTAATAATA
1291385 TAAAAACAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 4 0.17
17 6 0.26
18 13 0.57
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (17 bp):
TTAATAATAAAATAAAA
Found at i:1291379 original size:14 final size:14
Alignment explanation
Indices: 1291360--1291389 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1291350 CAATAATATT
1291360 AATTAATAAAATAA
1 AATTAATAAAATAA
*
1291374 AATTAATAATATAA
1 AATTAATAAAATAA
1291388 AA
1 AA
1291390 ACAAAAACAA
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:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AATTAATAAAATAA
Found at i:1293109 original size:23 final size:22
Alignment explanation
Indices: 1293079--1293122 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
1293069 GTAAACAGTA
1293079 TATTTTTAAT-AATGTAAAAATC
1 TATTTTTAATAAAT-TAAAAATC
1293101 TATTATTTAATAAATTAAAAAT
1 TATT-TTTAATAAATTAAAAAT
1293123 AAATATGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 4 0.20
23 13 0.65
24 3 0.15
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (22 bp):
TATTTTTAATAAATTAAAAATC
Found at i:1294322 original size:9 final size:9
Alignment explanation
Indices: 1294308--1294358 Score: 50
Period size: 9 Copynumber: 5.7 Consensus size: 9
1294298 AATATTTATT
1294308 TTTTTATAA
1 TTTTTATAA
*
1294317 TTTTTATAC
1 TTTTTATAA
*
1294326 TTTTTAATGA
1 TTTTT-ATAA
* *
1294336 CTTTAATAA
1 TTTTTATAA
1294345 TTTTT-TAA
1 TTTTTATAA
1294353 TTTTTA
1 TTTTTA
1294359 AAAATAATTT
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
8 8 0.25
9 19 0.59
10 5 0.16
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (9 bp):
TTTTTATAA
Found at i:1306262 original size:28 final size:28
Alignment explanation
Indices: 1306231--1306290 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
1306221 AATAGAATAG
*
1306231 AACAATGTAGG-CTTCAGCCCAATACAGA
1 AACAAGGTAGGCCTT-AGCCCAATACAGA
* *
1306259 AACAAGGTGGGCCTTAGCCCAATACAGT
1 AACAAGGTAGGCCTTAGCCCAATACAGA
1306287 AACA
1 AACA
1306291 TTATGCAGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 25 0.89
29 3 0.11
ACGTcount: A:0.38, C:0.25, G:0.20, T:0.17
Consensus pattern (28 bp):
AACAAGGTAGGCCTTAGCCCAATACAGA
Found at i:1317545 original size:30 final size:29
Alignment explanation
Indices: 1317511--1317574 Score: 74
Period size: 30 Copynumber: 2.2 Consensus size: 29
1317501 CTTCGACTAT
* *
1317511 TTTACTAAAAAAGGCCAATTTCCAACTTTA
1 TTTACGAAAAAAGGCCAATTT-AAACTTTA
** *
1317541 TTTACGAAAATGGGCCACTTTAAACTTTA
1 TTTACGAAAAAAGGCCAATTTAAACTTTA
1317570 TTTAC
1 TTTAC
1317575 CGGAATGGGA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 12 0.41
30 17 0.59
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (29 bp):
TTTACGAAAAAAGGCCAATTTAAACTTTA
Found at i:1319717 original size:18 final size:18
Alignment explanation
Indices: 1319694--1319731 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
1319684 TGCTAGGTGC
*
1319694 GTATCCTATCCCTTATAT
1 GTATCCTAACCCTTATAT
1319712 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
1319730 GT
1 GT
1319732 TTCTTTTTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.26, G:0.08, T:0.42
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:1320215 original size:61 final size:61
Alignment explanation
Indices: 1320086--1320276 Score: 239
Period size: 62 Copynumber: 3.1 Consensus size: 61
1320076 ATGCATTATT
* * * *
1320086 TTTTTAATATATTTGTACAAATTACTTTTAT-A-TTGT-TTCATTTAATAAAATAGAAATTG
1 TTTTGAATATATTTGTACAAATTATTTTTATAATTTGTCCT-ATTTAATAAAATAGAAGTTG
1320145 TTTTGAATATATTTGTACAAATTATTTTTATAATTTGTCCTATTTAATAAAATAGAAGTTG
1 TTTTGAATATATTTGTACAAATTATTTTTATAATTTGTCCTATTTAATAAAATAGAAGTTG
* * * *
1320206 TTTTAAATATTTTAATGGT--AAATTATTTTTATATTTTGTCCTATTTAATAAAATAGAAGTTC
1 TTTTGAATATATT--T-GTACAAATTATTTTTATAATTTGTCCTATTTAATAAAATAGAAGTTG
1320268 TTTTGAATA
1 TTTTGAATA
1320277 AGGCAATAGA
Statistics
Matches: 117, Mismatches: 9, Indels: 9
0.87 0.07 0.07
Matches are distributed among these distances:
59 29 0.25
60 1 0.01
61 34 0.29
62 50 0.43
63 1 0.01
64 2 0.02
ACGTcount: A:0.36, C:0.05, G:0.08, T:0.51
Consensus pattern (61 bp):
TTTTGAATATATTTGTACAAATTATTTTTATAATTTGTCCTATTTAATAAAATAGAAGTTG
Found at i:1323305 original size:25 final size:25
Alignment explanation
Indices: 1323271--1323342 Score: 101
Period size: 25 Copynumber: 2.8 Consensus size: 25
1323261 ACACCTTATC
*
1323271 AACTTCTTCAATTTATATTCTTCTG
1 AACTTCTTCAATTTATATTCTTCTA
*
1323296 AACTTCTTCAATTTCTATTCTTCTA
1 AACTTCTTCAATTTATATTCTTCTA
1323321 AACTTC-TCTAATTTATCATTCT
1 AACTTCTTC-AATTTAT-ATTCT
1323343 GTAACTTATG
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
24 2 0.05
25 35 0.83
26 5 0.12
ACGTcount: A:0.25, C:0.22, G:0.01, T:0.51
Consensus pattern (25 bp):
AACTTCTTCAATTTATATTCTTCTA
Found at i:1323683 original size:28 final size:28
Alignment explanation
Indices: 1323652--1323787 Score: 109
Period size: 28 Copynumber: 4.6 Consensus size: 28
1323642 GACTATTACG
1323652 AAAACCCTA-AAACCCTAATTTATTTTTT
1 AAAA-CCTATAAACCCTAATTTATTTTTT
* *
1323680 AAAAACAATAAACCCTAATTTAATTTATTTTT
1 AAAACCTATAAACCCTAATTT-A--T-TTTTT
1323712 GAAAAACC-ATAAACCCTAATTTATTTTTT
1 --AAAACCTATAAACCCTAATTTATTTTTT
* * *
1323741 AAAATCCT-TAAACCTTAAATTATTTTCTCC
1 AAAA-CCTATAAACCCTAATTTATTTT-T-T
1323771 AAAACC-ATAAACCCTAA
1 AAAACCTATAAACCCTAA
1323788 ACAAATAAAA
Statistics
Matches: 89, Mismatches: 7, Indels: 23
0.75 0.06 0.19
Matches are distributed among these distances:
27 6 0.07
28 34 0.38
29 18 0.20
30 5 0.06
31 1 0.01
32 6 0.07
33 14 0.16
34 5 0.06
ACGTcount: A:0.43, C:0.20, G:0.01, T:0.36
Consensus pattern (28 bp):
AAAACCTATAAACCCTAATTTATTTTTT
Found at i:1323709 original size:33 final size:33
Alignment explanation
Indices: 1323667--1323734 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
1323657 CCTAAAACCC
*
1323667 TAATTTATTTTTTAAAAACAATAAACCCTAATT
1 TAATTTATTTTTGAAAAACAATAAACCCTAATT
*
1323700 TAATTTATTTTTGAAAAACCATAAACCCTAATT
1 TAATTTATTTTTGAAAAACAATAAACCCTAATT
1323733 TA
1 TA
1323735 TTTTTTAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.44, C:0.13, G:0.01, T:0.41
Consensus pattern (33 bp):
TAATTTATTTTTGAAAAACAATAAACCCTAATT
Found at i:1325194 original size:6 final size:6
Alignment explanation
Indices: 1325183--1325220 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
1325173 ACCCCACCCA
*
1325183 TCCCTC TCCCTC TCCCTC TCCCTC TCCCT- TTCCTC TCC
1 TCCCTC TCCCTC TCCCTC TCCCTC TCCCTC TCCCTC TCC
1325221 TATAATGTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 4 0.14
6 25 0.86
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (6 bp):
TCCCTC
Found at i:1332275 original size:271 final size:268
Alignment explanation
Indices: 1331760--1332310 Score: 797
Period size: 271 Copynumber: 2.0 Consensus size: 268
1331750 CATGAAATGG
* *
1331760 AGAGTATTTGTATGAATTTTTTGTGGCAAAAAGGTCATATGAGTGGGATACATTGGTGTGAATGA
1 AGAGTATTTGTATGAATTTTTTGTGGCAAAAAGGTCATAAGAGTGGGATACATTGGTGCGAATGA
* *
1331825 AGGAAGTTATGTGAATTGAAGGAAAATAGGGGTTTGGGTTTTCGTAGTTTAGCTAAAATCAATTT
66 AGGAAGTTATGTGAATTAAAGGAAAATAGGGGTTTGGGTTTTCGCAGTTTAGCTAAAATCAATTT
1331890 ATCTTTACTTGCAAAACAAGGTTGGAGGAGGTTGATTAATTTTCCCAATTCGTTACTTGCAAGTA
131 ATCTTTACTTGCAAAACAAGGTT-G-GGAGGTTGATTAATTTTCCCAATTCGTTACTTGCAAGTA
* *
1331955 CTTTGAAAGCTAAATACTACCTAGATTTAGATTTTATGAATGCAAGGTTAGGAAATATACCTTCT
194 CTTTGAAAGCTAAATACTACCTAGATTTAGATTTTATGAATGCAAGGTTAGGAAATATACCTCCC
1332020 TATAC-CTGAA
259 TATACTCTG-A
* * *
1332030 AGAGTATTTGTGA-GAATTTTTTGTGGGCAAAAATGTCATGGTAAGAG-GGGAATTCATTTGTGC
1 AGAGTATTTGT-ATGAATTTTTTGT-GGCAAAAAGGTCA---TAAGAGTGGG-ATACATTGGTGC
* * * *
1332093 GAATGGAGGAAGTTATGTGAATTAAAGGAAAATGGGGGTTTGGGTTTTTGCAGTTTAGCTAAATT
60 GAATGAAGGAAGTTATGTGAATTAAAGGAAAATAGGGGTTTGGGTTTTCGCAGTTTAGCTAAAAT
* *
1332158 CAATTTATCTTTATTTGCAAAATAAGGTT-GGAGGTTGATTAATTTTCCCAATTCGTTACTTGCA
125 CAATTTATCTTTACTTGCAAAACAAGGTTGGGAGGTTGATTAATTTTCCCAATTCGTTACTTGCA
* * * *
1332222 CGTACTTTGAAAGCTAAATACTA-CTCAGATTTAGATTTTTTGAGTGGAAGGTTAGGAAATATAC
190 AGTACTTTGAAAGCTAAATACTACCT-AGATTTAGATTTTATGAATGCAAGGTTAGGAAATATAC
*
1332286 CTCCCTATACTTTGA
254 CTCCCTATACTCTGA
1332301 AGAGTATTTG
1 AGAGTATTTG
1332311 GGTTGCCAAA
Statistics
Matches: 253, Mismatches: 20, Indels: 15
0.88 0.07 0.05
Matches are distributed among these distances:
270 24 0.09
271 124 0.49
272 2 0.01
273 3 0.01
274 100 0.40
ACGTcount: A:0.31, C:0.10, G:0.23, T:0.36
Consensus pattern (268 bp):
AGAGTATTTGTATGAATTTTTTGTGGCAAAAAGGTCATAAGAGTGGGATACATTGGTGCGAATGA
AGGAAGTTATGTGAATTAAAGGAAAATAGGGGTTTGGGTTTTCGCAGTTTAGCTAAAATCAATTT
ATCTTTACTTGCAAAACAAGGTTGGGAGGTTGATTAATTTTCCCAATTCGTTACTTGCAAGTACT
TTGAAAGCTAAATACTACCTAGATTTAGATTTTATGAATGCAAGGTTAGGAAATATACCTCCCTA
TACTCTGA
Found at i:1334924 original size:26 final size:26
Alignment explanation
Indices: 1334894--1334977 Score: 132
Period size: 26 Copynumber: 3.2 Consensus size: 26
1334884 AGGAGGAAGT
* * *
1334894 ATACTGTTACTAGAAGCTTTGCTGCA
1 ATACTGTTACTGGCAGCTTTGCTGCG
1334920 ATACTGTTACTGGCAGCTTTGCTGCG
1 ATACTGTTACTGGCAGCTTTGCTGCG
*
1334946 ATACTGTTACTGGCAGCTTTACTGCG
1 ATACTGTTACTGGCAGCTTTGCTGCG
1334972 ATACTG
1 ATACTG
1334978 GTGTGTTGGT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 54 1.00
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (26 bp):
ATACTGTTACTGGCAGCTTTGCTGCG
Found at i:1340037 original size:21 final size:21
Alignment explanation
Indices: 1339991--1340055 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 21
1339981 AAAAAAAAGA
*
1339991 TTTGTCTAAGTCACTTCGTTTCTT
1 TTTGTCCAAGTCACTTC---TCTT
*
1340015 TTTGTCCAAGTTACTTCTCTT
1 TTTGTCCAAGTCACTTCTCTT
*
1340036 TTTGTCCAAGTCGCTTCTCT
1 TTTGTCCAAGTCACTTCTCT
1340056 CACTTCCTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
21 22 0.59
24 15 0.41
ACGTcount: A:0.12, C:0.25, G:0.12, T:0.51
Consensus pattern (21 bp):
TTTGTCCAAGTCACTTCTCTT
Found at i:1341996 original size:16 final size:15
Alignment explanation
Indices: 1341975--1342025 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 15
1341965 AGAGTGGAAA
1341975 GAAAATTGGAAGGATG
1 GAAAATT-GAAGGATG
*
1341991 GAAAATTGAAGGTATA
1 GAAAATTGAAGG-ATG
*
1342007 GAAAACTAGAAGGATG
1 GAAAA-TTGAAGGATG
1342023 GAA
1 GAA
1342026 CTTTCTATAG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 5 0.17
16 19 0.63
17 6 0.20
ACGTcount: A:0.49, C:0.02, G:0.31, T:0.18
Consensus pattern (15 bp):
GAAAATTGAAGGATG
Found at i:1345670 original size:199 final size:201
Alignment explanation
Indices: 1345298--1345686 Score: 620
Period size: 199 Copynumber: 1.9 Consensus size: 201
1345288 ATAACTCCGT
* * *
1345298 AAATATTTAAAAAAATATATATATGGTCCCAGTTTACAGAAATGAGGTCTCAATACCTCATTTCG
1 AAATATTTAAAAAAATATATATATGATCCCAGTTTACAGAAACGAGGTCTCAATACCTCATTTCA
* *
1345363 AAAAACCACTTGACTTACGGGACAAACCACTATACTAAACTATTTGTTCAATAAATTACAATTTA
66 AAAAACCACTTGACTTACGGAAAAAACCACTATACTAAACTATTTGTTCAATAAATTACAATTTA
* **
1345428 TCTAATCAAAATTAAATATAAAAATATAACCAACTTGTATGAATT-AATAATAATTAATATAGAC
131 TCTAATAAAAATTAAATATAAAAATATAACCAACTCATATGAATTAAATAATAATTAATATAGAC
1345492 TTAAAA
196 TTAAAA
* * * *
1345498 AAATATTTAATAAAAT-TATTTATGATCTCAGTTTACATAAACGAGGTCTCAATACCTCATTTCA
1 AAATATTTAAAAAAATATATATATGATCCCAGTTTACAGAAACGAGGTCTCAATACCTCATTTCA
*
1345562 AAAAATCACTTGACTTACGGAAAAAACCACTATACTAAACTATTTGTTCAATAAATTACAATTTA
66 AAAAACCACTTGACTTACGGAAAAAACCACTATACTAAACTATTTGTTCAATAAATTACAATTTA
* * *
1345627 TCTAATAAAAATTTAATATAATAATATAATCAACTCATATGAATTAAATAATAATTAATA
131 TCTAATAAAAATTAAATATAAAAATATAACCAACTCATATGAATTAAATAATAATTAATA
1345687 CGGGCTTACT
Statistics
Matches: 172, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
199 143 0.83
200 29 0.17
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.33
Consensus pattern (201 bp):
AAATATTTAAAAAAATATATATATGATCCCAGTTTACAGAAACGAGGTCTCAATACCTCATTTCA
AAAAACCACTTGACTTACGGAAAAAACCACTATACTAAACTATTTGTTCAATAAATTACAATTTA
TCTAATAAAAATTAAATATAAAAATATAACCAACTCATATGAATTAAATAATAATTAATATAGAC
TTAAAA
Found at i:1346959 original size:18 final size:18
Alignment explanation
Indices: 1346928--1346963 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
1346918 AATTCCAAAT
1346928 CATTCAAAACATACAACC
1 CATTCAAAACATACAACC
1346946 CATTGCAAAA-ATACAACC
1 CATT-CAAAACATACAACC
1346964 TACCATCAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.50, C:0.31, G:0.03, T:0.17
Consensus pattern (18 bp):
CATTCAAAACATACAACC
Found at i:1349743 original size:19 final size:18
Alignment explanation
Indices: 1349719--1349754 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1349709 TGAAACAAAA
*
1349719 TTGAAAGTTTTAGAAAATT
1 TTGAAAATTTT-GAAAATT
1349738 TTGAAAATTTTGAAAAT
1 TTGAAAATTTTGAAAAT
1349755 AGGGGTCACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.44, C:0.00, G:0.14, T:0.42
Consensus pattern (18 bp):
TTGAAAATTTTGAAAATT
Found at i:1349745 original size:9 final size:9
Alignment explanation
Indices: 1349719--1349754 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
1349709 TGAAACAAAA
*
1349719 TTGAAAGTT
1 TTGAAAATT
1349728 TTAGAAAATT
1 TT-GAAAATT
1349738 TTGAAAATT
1 TTGAAAATT
1349747 TTGAAAAT
1 TTGAAAAT
1349755 AGGGGTCACA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 17 0.68
10 8 0.32
ACGTcount: A:0.44, C:0.00, G:0.14, T:0.42
Consensus pattern (9 bp):
TTGAAAATT
Found at i:1353304 original size:42 final size:42
Alignment explanation
Indices: 1353245--1353336 Score: 157
Period size: 42 Copynumber: 2.2 Consensus size: 42
1353235 CTCTCAAATC
* * *
1353245 CAGCTGGATAGGCTTTCCTGCATGCTCAAAGGAAAACGCATT
1 CAGCTGGATACGCTTTCCTACATACTCAAAGGAAAACGCATT
1353287 CAGCTGGATACGCTTTCCTACATACTCAAAGGAAAACGCATT
1 CAGCTGGATACGCTTTCCTACATACTCAAAGGAAAACGCATT
1353329 CAGCTGGA
1 CAGCTGGA
1353337 CGCGCTTTTC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (42 bp):
CAGCTGGATACGCTTTCCTACATACTCAAAGGAAAACGCATT
Found at i:1353428 original size:19 final size:19
Alignment explanation
Indices: 1353389--1353440 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
1353379 GTGCTTTCAC
1353389 ACTCTCTCTTCAAAATCTCA
1 ACTCTCTC-TCAAAATCTCA
* *
1353409 ACTCTCTCTCACATTCTCA
1 ACTCTCTCTCAAAATCTCA
*
1353428 AATCTCTCTCAAA
1 ACTCTCTCTCAAA
1353441 TTTCTCTCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 20 0.71
20 8 0.29
ACGTcount: A:0.29, C:0.37, G:0.00, T:0.35
Consensus pattern (19 bp):
ACTCTCTCTCAAAATCTCA
Found at i:1354755 original size:25 final size:25
Alignment explanation
Indices: 1354727--1354776 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
1354717 AGACCTAAAT
*
1354727 CTTAAAAAACAAAACCCTAACCCTA
1 CTTAAAAAACAAAACCATAACCCTA
* *
1354752 CTTAAAAAATAAAACTATAACCCTA
1 CTTAAAAAACAAAACCATAACCCTA
1354777 AAAAAAGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.54, C:0.26, G:0.00, T:0.20
Consensus pattern (25 bp):
CTTAAAAAACAAAACCATAACCCTA
Found at i:1355473 original size:38 final size:38
Alignment explanation
Indices: 1355430--1355502 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
1355420 ACGAAAAATA
1355430 TTAATGAGTCACTGATTTGTAACTTTTCT-ATAACGATG
1 TTAATGAGTCACTGATTTGTAACTTTT-TAATAACGATG
* * * *
1355468 TTAATGGGTGATTGATTTGTCACTTTTTAATAACG
1 TTAATGAGTCACTGATTTGTAACTTTTTAATAACG
1355503 TTAGTGATTG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 1 0.03
38 29 0.97
ACGTcount: A:0.27, C:0.11, G:0.18, T:0.44
Consensus pattern (38 bp):
TTAATGAGTCACTGATTTGTAACTTTTTAATAACGATG
Found at i:1362472 original size:6 final size:6
Alignment explanation
Indices: 1362461--1362487 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1362451 TTCTCCCATT
1362461 CTTTCC CTTTCC CTTTCC CTTTCC CTT
1 CTTTCC CTTTCC CTTTCC CTTTCC CTT
1362488 CATTTCTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (6 bp):
CTTTCC
Found at i:1367988 original size:12 final size:12
Alignment explanation
Indices: 1367971--1367995 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1367961 GAATTAAAAT
1367971 AAATCATTTAAA
1 AAATCATTTAAA
1367983 AAATCATTTAAA
1 AAATCATTTAAA
1367995 A
1 A
1367996 TTACATGTAA
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:0.08, G:0.00, T:0.32
Consensus pattern (12 bp):
AAATCATTTAAA
Found at i:1368301 original size:24 final size:23
Alignment explanation
Indices: 1368277--1368503 Score: 166
Period size: 24 Copynumber: 9.8 Consensus size: 23
1368267 ACAATATATA
*
1368277 ATAAATTTGAAATAATAATACATA
1 ATAAATTT-AAATAATAATACATG
**
1368301 ATAAATTTAAA-AAT--TGGATG
1 ATAAATTTAAATAATAATACATG
* *
1368321 AT-TATTCTAATAATAATAATACCTG
1 ATAAATT-T-A-AATAATAATACATG
* *
1368346 ATAAATTCAAAATAATAATATATG
1 ATAAATT-TAAATAATAATACATG
*
1368370 ATAAATTTAAA-AATATTA-ATG
1 ATAAATTTAAATAATAATACATG
1368391 ATAAATTTAAAATAA-ATATACATG
1 ATAAATTT-AAATAATA-ATACATG
**
1368415 ATAAATTTAAATAATGTTA-ATG
1 ATAAATTTAAATAATAATACATG
* *
1368437 ATGAATTTAAAATAATAATA-TTG
1 ATAAATTT-AAATAATAATACATG
* *
1368460 ATAAATTACAAATAATAATGCATG
1 ATAAATT-TAAATAATAATACATG
*
1368484 ATAAATCTAAGATAATAATA
1 ATAAATTTAA-ATAATAATA
1368504 TACAATAAAT
Statistics
Matches: 160, Mismatches: 27, Indels: 32
0.73 0.12 0.15
Matches are distributed among these distances:
19 3 0.02
20 6 0.04
21 12 0.08
22 25 0.16
23 50 0.31
24 54 0.34
25 6 0.04
26 4 0.03
ACGTcount: A:0.54, C:0.04, G:0.07, T:0.35
Consensus pattern (23 bp):
ATAAATTTAAATAATAATACATG
Found at i:1368393 original size:45 final size:45
Alignment explanation
Indices: 1368344--1368533 Score: 172
Period size: 45 Copynumber: 4.2 Consensus size: 45
1368334 TAATAATACC
1368344 TGATAAATTCAAAATAATAATATATGATAAATTTAAA-AATATTAA
1 TGATAAATTCAAAATAATAATATATGATAAA-TTAAACAATATTAA
* * * *
1368389 TGATAAATTTAAAATAA-ATATACATGATAAATTTAAATAATGTTAA
1 TGATAAATTCAAAATAATA-ATATATGATAAA-TTAAACAATATTAA
* * * *
1368435 TGATGAATTTAAAATAATAATAT-TGATAAATTACA-AATAATAA
1 TGATAAATTCAAAATAATAATATATGATAAATTAAACAATATTAA
* * **
1368478 TGCATGATAAATCTAAGATAATAATATACAATAAATTAAACAATATTAA
1 TG-AT-A-AATTC-AAAATAATAATATATGATAAATTAAACAATATTAA
*
1368527 TAATAAA
1 TGATAAA
1368534 ACTAAAATAA
Statistics
Matches: 119, Mismatches: 17, Indels: 17
0.78 0.11 0.11
Matches are distributed among these distances:
43 8 0.07
44 7 0.06
45 40 0.34
46 31 0.26
47 14 0.12
48 11 0.09
49 8 0.07
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34
Consensus pattern (45 bp):
TGATAAATTCAAAATAATAATATATGATAAATTAAACAATATTAA
Found at i:1368397 original size:114 final size:114
Alignment explanation
Indices: 1368277--1368489 Score: 274
Period size: 114 Copynumber: 1.9 Consensus size: 114
1368267 ACAATATATA
* * *
1368277 ATAAATTTGAAAT-AATAATACATAATAAATTTAAA-AAT-TGGATGAT-TATTCTAATAATAAT
1 ATAAATTTAAAATAAAT-ATACATAATAAATTTAAATAATGTGAATGATGAATT-TAA-AATAAT
*
1368338 AATACCTGATAAATT-CAAAATAATAATATATGATAAATTTAAAAATATTAATG
63 AATA-CTGATAAATTAC-AAATAATAATACATGATAAATTTAAAAATATTAATG
* *
1368391 ATAAATTTAAAATAAATATACATGATAAATTTAAATAATGTTAATGATGAATTTAAAATAATAAT
1 ATAAATTTAAAATAAATATACATAATAAATTTAAATAATGTGAATGATGAATTTAAAATAATAAT
* *
1368456 ATTGATAAATTACAAATAATAATGCATGATAAAT
66 ACTGATAAATTACAAATAATAATACATGATAAAT
1368490 CTAAGATAAT
Statistics
Matches: 86, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
114 57 0.66
115 17 0.20
116 9 0.10
117 3 0.03
ACGTcount: A:0.54, C:0.04, G:0.07, T:0.36
Consensus pattern (114 bp):
ATAAATTTAAAATAAATATACATAATAAATTTAAATAATGTGAATGATGAATTTAAAATAATAAT
ACTGATAAATTACAAATAATAATACATGATAAATTTAAAAATATTAATG
Found at i:1368405 original size:69 final size:70
Alignment explanation
Indices: 1368277--1368545 Score: 216
Period size: 69 Copynumber: 3.9 Consensus size: 70
1368267 ACAATATATA
** * ** *
1368277 ATAAATTTGAAATAATAATACATAATAAATTTAAA-AAT-TGGATGAT-TATTCTAATAATAATA
1 ATAAATTCAAAATAATAATATATAATAAATTTAAACAATATTAATGATAAATT-TAA-AATAATA
*
1368339 ATACCTG
64 ATACATG
*
1368346 ATAAATTCAAAATAATAATATATGATAAATTTAAA-AATATTAATGATAAATTTAAAATAA-ATA
1 ATAAATTCAAAATAATAATATATAATAAATTTAAACAATATTAATGATAAATTTAAAATAATA-A
1368409 TACATG
65 TACATG
* ** * * * * *
1368415 ATAAATT-TAAATAATGTTA-ATGATGAATTTAAAATAATAATATTGATAAA-TTACAAATAATA
1 ATAAATTCAAAATAATAATATATAATAAATTT-AAACAATATTAATGATAAATTTA-AAATAATA
*
1368477 ATGCATG
64 ATACATG
* * * **
1368484 ATAAA-TCTAAGATAATAATATACAATAAA-TTAAACAATATTAATAATAAAACTAAAATAATA
1 ATAAATTC-AAAATAATAATATATAATAAATTTAAACAATATTAATGATAAATTTAAAATAATA
1368546 TTAAGTTTAA
Statistics
Matches: 162, Mismatches: 27, Indels: 22
0.77 0.13 0.10
Matches are distributed among these distances:
67 10 0.06
68 17 0.10
69 105 0.65
70 22 0.14
71 8 0.05
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34
Consensus pattern (70 bp):
ATAAATTCAAAATAATAATATATAATAAATTTAAACAATATTAATGATAAATTTAAAATAATAAT
ACATG
Found at i:1368523 original size:114 final size:114
Alignment explanation
Indices: 1368269--1368514 Score: 268
Period size: 114 Copynumber: 2.1 Consensus size: 114
1368259 TACAATAAAC
* * * *
1368269 AATATATAATAAATTTGAAATAATAATACATAATAAATTTAAAAATTGGATGATTATTCTAATAA
1 AATATATAATAAATTTAAAAAAAT-ATACATAATAAATTTAAAAATTGAATGATAATTCTAATAA
* *
1368334 TAATAATACCTGATAAATTCAAAATAATAATATATGATAAATTTAAAAAT
65 TAATAATACCTGATAAATTCAAAATAATAATACATGATAAATCTAAAAAT
* * * *
1368384 ATTA-ATGATAAATTTAAAATAAATATACATGATAAATTTAAATAATGTTAATGATGAATT-TAA
1 AATATATAATAAATTTAAAA-AAATATACATAATAAATTTAAA-AAT-TGAATGAT-AATTCTAA
* *
1368447 -AATAATAATA-TTGATAAATT-ACAAATAATAATGCATGATAAATCTAAGATAAT
62 TAATAATAATACCTGATAAATTCA-AAATAATAATACATGATAAATCTAA-A-AAT
*
1368500 AATATACAATAAATT
1 AATATATAATAAATT
1368515 AAACAATATT
Statistics
Matches: 108, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
113 1 0.01
114 61 0.56
115 20 0.19
116 15 0.14
117 11 0.10
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.35
Consensus pattern (114 bp):
AATATATAATAAATTTAAAAAAATATACATAATAAATTTAAAAATTGAATGATAATTCTAATAAT
AATAATACCTGATAAATTCAAAATAATAATACATGATAAATCTAAAAAT
Found at i:1368547 original size:23 final size:24
Alignment explanation
Indices: 1368519--1368572 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
1368509 TAAATTAAAC
*
1368519 AATATTAA-TAATAAA-ACTAAAAT
1 AATATTAAGT-ATAAACACCAAAAT
*
1368542 AATATTAAGTTTAAACACCAAAAT
1 AATATTAAGTATAAACACCAAAAT
1368566 AATATTA
1 AATATTA
1368573 GATTTGAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 12 0.44
24 15 0.56
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.31
Consensus pattern (24 bp):
AATATTAAGTATAAACACCAAAAT
Found at i:1370658 original size:18 final size:18
Alignment explanation
Indices: 1370626--1370675 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
1370616 TCAAATTTTG
*
1370626 AAAATAATTTTTAAAATTC
1 AAAAT-ATTTATAAAATTC
1370645 AAAATATTTATAAAAATTC
1 AAAATATTTAT-AAAATTC
*
1370664 TAAA-ATTTATAA
1 AAAATATTTATAA
1370676 TTTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 2 0.07
18 11 0.39
19 15 0.54
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (18 bp):
AAAATATTTATAAAATTC
Found at i:1370667 original size:27 final size:27
Alignment explanation
Indices: 1370637--1370694 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
1370627 AAATAATTTT
*
1370637 TAAAATTCAAAATATTTATAAAAATTC
1 TAAAATTCAAAATATTTATAAAAATTA
* * * *
1370664 TAAAATTTATAATTTTTTTAAAAATTA
1 TAAAATTCAAAATATTTATAAAAATTA
1370691 TAAA
1 TAAA
1370695 TTTAAAAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (27 bp):
TAAAATTCAAAATATTTATAAAAATTA
Found at i:1370704 original size:18 final size:17
Alignment explanation
Indices: 1370683--1370728 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
1370673 TAATTTTTTT
* *
1370683 AAAAATTATAAATTTAA
1 AAAAATTAAAAATATAA
1370700 AAAAATCTAAAAATATATA
1 AAAAAT-TAAAAATATA-A
1370719 AAAAATTAAA
1 AAAAATTAAA
1370729 TTTTTTATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 6 0.24
18 12 0.48
19 7 0.28
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (17 bp):
AAAAATTAAAAATATAA
Found at i:1370713 original size:44 final size:45
Alignment explanation
Indices: 1370633--1370719 Score: 108
Period size: 44 Copynumber: 2.0 Consensus size: 45
1370623 TTGAAAATAA
* *
1370633 TTTTTAAAATTCAAAATATTTATAAAAATTCTAAAATTTATAATT
1 TTTTTAAAATTCAAAATATTTATAAAAAATCTAAAATATATAATT
*
1370678 TTTTTAAAAATT-ATAA-ATTTA-AAAAAATCTAAAAATATATAA
1 TTTTT-AAAATTCAAAATATTTATAAAAAATCT-AAAATATATAA
1370720 AAAATTAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
43 8 0.22
44 15 0.41
45 8 0.22
46 6 0.16
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (45 bp):
TTTTTAAAATTCAAAATATTTATAAAAAATCTAAAATATATAATT
Found at i:1370849 original size:16 final size:16
Alignment explanation
Indices: 1370830--1370860 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1370820 TTAAAAAAGT
1370830 TTTCAAATATATATTG
1 TTTCAAATATATATTG
*
1370846 TTTCAAATTTATATT
1 TTTCAAATATATATT
1370861 TTCTAACATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.55
Consensus pattern (16 bp):
TTTCAAATATATATTG
Found at i:1371064 original size:21 final size:21
Alignment explanation
Indices: 1371040--1371079 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1371030 ACCTTTTCTA
*
1371040 AAGTTAAAAGTCAAAACTATC
1 AAGTTAAAAGGCAAAACTATC
1371061 AAGTTAAAAGGCAAAACTA
1 AAGTTAAAAGGCAAAACTA
1371080 CGTTGTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.20
Consensus pattern (21 bp):
AAGTTAAAAGGCAAAACTATC
Found at i:1374565 original size:29 final size:29
Alignment explanation
Indices: 1374517--1374601 Score: 97
Period size: 29 Copynumber: 3.0 Consensus size: 29
1374507 ATTACAACTT
1374517 TTTTTTATTTACC-AAA-ATATTACAA-AA
1 TTTTTTATTTACCAAAATATATTA-AACAA
**
1374544 TTTTTTATTTACCAAAATATA-TAAACTT
1 TTTTTTATTTACCAAAATATATTAAACAA
*
1374572 TTTTATTATTTACCAAAATATATAAAACAA
1 TTTT-TTATTTACCAAAATATATTAAACAA
1374602 AAAACAAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
27 15 0.31
28 9 0.19
29 20 0.42
30 4 0.08
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.45
Consensus pattern (29 bp):
TTTTTTATTTACCAAAATATATTAAACAA
Found at i:1374593 original size:27 final size:28
Alignment explanation
Indices: 1374495--1374592 Score: 137
Period size: 28 Copynumber: 3.5 Consensus size: 28
1374485 AAAAATAAAA
*
1374495 ATTTATCAAAATATTACAACTTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTT
**
1374523 ATTTACCAAAATATTACAA-AATTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTT
1374550 ATTTACCAAAATATATA-AACTTTTTTATT
1 ATTTACCAAAATAT-TACAACTTTTTT-TT
1374579 ATTTACCAAAATAT
1 ATTTACCAAAATAT
1374593 ATAAAACAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 22 0.35
28 24 0.39
29 16 0.26
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (28 bp):
ATTTACCAAAATATTACAACTTTTTTTT
Found at i:1374694 original size:27 final size:27
Alignment explanation
Indices: 1374673--1374766 Score: 161
Period size: 27 Copynumber: 3.5 Consensus size: 27
1374663 CGCCAATGGT
* *
1374673 ATTGGCGGCACCAAAGGTGCCAAAACC
1 ATTGGCGGCACCAATGGTGCCAATACC
1374700 ATTGGCGGCACCAATGGTGCCAATACC
1 ATTGGCGGCACCAATGGTGCCAATACC
*
1374727 ATTGGCGGCACCAATGGTGCCAATGCC
1 ATTGGCGGCACCAATGGTGCCAATACC
1374754 ATTGGCGGCACCA
1 ATTGGCGGCACCA
1374767 CTCGTATTAT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 64 1.00
ACGTcount: A:0.27, C:0.30, G:0.28, T:0.16
Consensus pattern (27 bp):
ATTGGCGGCACCAATGGTGCCAATACC
Found at i:1374946 original size:19 final size:21
Alignment explanation
Indices: 1374908--1374946 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
1374898 AATAATTGAT
*
1374908 TATATTATTGTTATTATTTTG
1 TATATTATTGTTAATATTTTG
1374929 TATATT-TTG-TAATATTTT
1 TATATTATTGTTAATATTTT
1374947 TTGTTGTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.67
Consensus pattern (21 bp):
TATATTATTGTTAATATTTTG
Found at i:1375025 original size:3 final size:3
Alignment explanation
Indices: 1375019--1375062 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
1375009 ATTATTATTA
1375019 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1375063 NNNNNNNNNN
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:1375645 original size:16 final size:16
Alignment explanation
Indices: 1375624--1375654 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1375614 GTTTATTTCG
1375624 GGTTATTTACCAAAAA
1 GGTTATTTACCAAAAA
1375640 GGTTATTTACCAAAA
1 GGTTATTTACCAAAA
1375655 TATTAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (16 bp):
GGTTATTTACCAAAAA
Found at i:1381011 original size:26 final size:26
Alignment explanation
Indices: 1380962--1381014 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
1380952 ACACACTAAA
* *
1380962 ATTATTAATTTTATACTACGAATAAT
1 ATTAATAATTTTATACTACAAATAAT
1380988 ATTAATAATTTTATACT-CAAAATAAT
1 ATTAATAATTTTATACTAC-AAATAAT
1381014 A
1 A
1381015 CACACTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 1 0.04
26 23 0.96
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (26 bp):
ATTAATAATTTTATACTACAAATAAT
Found at i:1381066 original size:62 final size:60
Alignment explanation
Indices: 1380934--1381066 Score: 151
Period size: 62 Copynumber: 2.1 Consensus size: 60
1380924 TTATACTCAA
* * ** **
1380934 AATATTACACAAAATAATACACACTAAAATTATTAATTTTATACTACGAATAATATTAAT
1 AATAATACTCAAAATAATACACACTAAAATTATTAATTTTATAAAAAAAATAATATTAAT
*
1380994 AATTTTATACTCAAAATAATACACACTAAAATTATTAATTTTACTAAAAAAAACTAACTA-TAAT
1 AA--TAATACTCAAAATAATACACACTAAAATTATTAATTTTA-TAAAAAAAA-TAA-TATTAAT
1381058 AATAATACT
1 AATAATACT
1381067 AATTTTTTAT
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
60 2 0.03
62 42 0.70
63 5 0.08
64 9 0.15
65 2 0.03
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.35
Consensus pattern (60 bp):
AATAATACTCAAAATAATACACACTAAAATTATTAATTTTATAAAAAAAATAATATTAAT
Found at i:1381161 original size:26 final size:26
Alignment explanation
Indices: 1381121--1381173 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
1381111 AACTCTTCTT
1381121 TTTTTTTTTAATTTTCTCTCTTCAGC
1 TTTTTTTTTAATTTTCTCTCTTCAGC
*
1381147 TTTTTTTTTATTTTTCTCTCTTCAGC
1 TTTTTTTTTAATTTTCTCTCTTCAGC
1381173 T
1 T
1381174 GGGTAGAGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.09, C:0.19, G:0.04, T:0.68
Consensus pattern (26 bp):
TTTTTTTTTAATTTTCTCTCTTCAGC
Found at i:1381241 original size:27 final size:27
Alignment explanation
Indices: 1381201--1381303 Score: 136
Period size: 27 Copynumber: 3.8 Consensus size: 27
1381191 ATAATACGAG
*
1381201 TGGTGCCGCGAATGGCATTGGCACCAT
1 TGGTGCCGCCAATGGCATTGGCACCAT
*
1381228 TGGTGCCGCCAATGGTATTGGCACCAT
1 TGGTGCCGCCAATGGCATTGGCACCAT
* ** *
1381255 TGGTGTCGCCAATGGTTTTGGCACCTT
1 TGGTGCCGCCAATGGCATTGGCACCAT
1381282 TGGTGCCGCCAAT-GCAATTGGC
1 TGGTGCCGCCAATGGC-ATTGGC
1381304 GTGACCAAGG
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
26 1 0.01
27 66 0.99
ACGTcount: A:0.17, C:0.25, G:0.31, T:0.27
Consensus pattern (27 bp):
TGGTGCCGCCAATGGCATTGGCACCAT
Found at i:1381421 original size:27 final size:26
Alignment explanation
Indices: 1381363--1381421 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 26
1381353 TTTTGTTTTT
*
1381363 TTATATATTTTGGTAAATAAAAAAAT
1 TTATATATTTTGGTAAATAAAAAAAG
1381389 TATATATATTTTGGTAAATAAAAAAAAG
1 T-TATATATTTTGGTAAAT-AAAAAAAG
1381417 TTATA
1 TTATA
1381422 AGTTGTACTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 1 0.03
27 21 0.70
28 8 0.27
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (26 bp):
TTATATATTTTGGTAAATAAAAAAAG
Done.