Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 145 of 163
Found at i:39457424 original size:24 final size:24
Alignment explanation
Indices: 39457397--39457442 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
39457387 TACCATACAA
39457397 TTCAT-ATATCATTTCACATTCAAT
1 TTCATAATATCATTTCA-ATTCAAT
*
39457421 TTCATAATCTCATTTCAATTCA
1 TTCATAATATCATTTCAATTCA
39457443 TCATCAATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.33, C:0.22, G:0.00, T:0.46
Consensus pattern (24 bp):
TTCATAATATCATTTCAATTCAAT
Found at i:39460927 original size:2 final size:2
Alignment explanation
Indices: 39460920--39460952 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
39460910 ACATGGTGGG
39460920 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
39460953 ATATATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:39460957 original size:2 final size:2
Alignment explanation
Indices: 39460952--39460986 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
39460942 TCTCTCTCTC
39460952 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
39460987 GCCTTGGGAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:39464657 original size:14 final size:16
Alignment explanation
Indices: 39464638--39464671 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
39464628 TTAAATAAAA
39464638 ATAATATA-AA-TTTT
1 ATAATATATAACTTTT
39464652 ATAATATATAACTTTT
1 ATAATATATAACTTTT
39464668 ATAA
1 ATAA
39464672 AAAAAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 2 0.11
16 8 0.44
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
ATAATATATAACTTTT
Found at i:39464662 original size:16 final size:16
Alignment explanation
Indices: 39464641--39464671 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39464631 AATAAAAATA
39464641 ATATAAATTTTATAAT
1 ATATAAATTTTATAAT
*
39464657 ATATAACTTTTATAA
1 ATATAAATTTTATAA
39464672 AAAAAATTAT
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:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATAAATTTTATAAT
Found at i:39466229 original size:30 final size:32
Alignment explanation
Indices: 39466195--39466266 Score: 96
Period size: 31 Copynumber: 2.3 Consensus size: 32
39466185 AAGTTTCAAT
*
39466195 TCAGTCACTCAA-CTT-TCAAAAAGTAACAAA
1 TCAGTCACTCAATCTTATCAAAAAATAACAAA
* *
39466225 TCAGTCAC-CAATGTTATCAAAAAATGACAAA
1 TCAGTCACTCAATCTTATCAAAAAATAACAAA
39466256 TCAGTCACTCA
1 TCAGTCACTCA
39466267 TTAACATTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 3 0.08
30 10 0.28
31 21 0.58
32 2 0.06
ACGTcount: A:0.44, C:0.24, G:0.08, T:0.24
Consensus pattern (32 bp):
TCAGTCACTCAATCTTATCAAAAAATAACAAA
Found at i:39471245 original size:23 final size:22
Alignment explanation
Indices: 39471203--39471251 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
39471193 TGATCTATTA
*
39471203 CATTATGCATTTTAGATAAGTG
1 CATTATGCATGTTAGATAAGTG
39471225 CATTCATGCATGTTA-ATTAAGTG
1 CATT-ATGCATGTTAGA-TAAGTG
39471248 -ATTA
1 CATTA
39471252 CTAAATTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
21 1 0.04
22 8 0.33
23 15 0.62
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (22 bp):
CATTATGCATGTTAGATAAGTG
Found at i:39472204 original size:10 final size:11
Alignment explanation
Indices: 39472186--39472214 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
39472176 AAACACACCT
39472186 AAAAGAGAAAG
1 AAAAGAGAAAG
39472197 AAAA-AGAAAG
1 AAAAGAGAAAG
39472207 AAAAGAGA
1 AAAAGAGA
39472215 CAGCCTGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (11 bp):
AAAAGAGAAAG
Found at i:39478727 original size:366 final size:369
Alignment explanation
Indices: 39478040--39478774 Score: 1413
Period size: 366 Copynumber: 2.0 Consensus size: 369
39478030 GCACCACTGG
39478040 TGATGCCTACCCAATAGACACCATTGGTAATCCTTATGACCACCCGTATACCCATATTTTTTCTT
1 TGATGCCTACCCAATAGACACCATTGGTAATCCTTATGACCACCCGTATACCCATATTTTTTCTT
*
39478105 GTACTTTTATGAGTGTCGCCTATTTAGGAGACACCATTTAATATTATATATATATTTTTTTTTTT
66 GTACTTTTATGAGTGTCGCCTATTTAGGAGACACCATTTAATATTATATATATATTTTTTATTTT
39478170 AGTATAAAATAATAATAATAACAAAATAAAAAAAATTGTGTCAGATTTTTAAAATGGTGTCGCCT
131 AGTATAAAATAATAATAATAACAAAATAAAAAAAATTGTGTCAGATTTTTAAAATGGTGTCGCCT
39478235 ATCAAGGAGGCACTACCCCCTCCCATGTATACCATTTTGGTAAATAATGGGGAATGTATTATTTT
196 ATCAAGGAGGCACTA-CCCCTCCCATGTATACCATTTTGGTAAATAATGGGGAATGTATTATTTT
39478300 GGTTTTTAATTATTATTATTTTTGTATTAATTTCGTAAAAAAATCTGTTTTCCTCTATTCTCCAT
260 GGTTTTTAATTATTATTATTTTTGTATTAATTTCGTAAAAAAATCTGTTTTCCTCTATTCTCCAT
39478365 TCCTTTTAACGCATTTTTTCTATGTTTTTCATTTGTTAAAATTAA
325 TCCTTTTAACGCATTTTTTCTATGTTTTTCATTTGTTAAAATTAA
39478410 TGATGCCTACCCAATAGACACCATTGGTAATCCTTATGACCACCCGTATACCCATATTTTTTCTT
1 TGATGCCTACCCAATAGACACCATTGGTAATCCTTATGACCACCCGTATACCCATATTTTTTCTT
39478475 GTACTTTTATGAGTGTCGCCTATTTAGGAGACACCATTTAATATT-TATATATATTTTTTATTTT
66 GTACTTTTATGAGTGTCGCCTATTTAGGAGACACCATTTAATATTATATATATATTTTTTATTTT
*
39478539 AGTATAAAATAATAATAATAACAAAATAAAAAAAATTGTGTCAGATTTTTAAAGTGGTGTCGCCT
131 AGTATAAAATAATAATAATAACAAAATAAAAAAAATTGTGTCAGATTTTTAAAATGGTGTCGCCT
*
39478604 ATTAAGGAGGCACTA-CCC-CCCATGTATACCATTTTGGTAAATAATGGGGAATGTATTATTTTG
196 ATCAAGGAGGCACTACCCCTCCCATGTATACCATTTTGGTAAATAATGGGGAATGTATTATTTTG
39478667 GTTTTTAATTATTATTATTTTTGTATTAATTTCGTAAAAAAATCTGTTTTCCTCTATTCTCCATT
261 GTTTTTAATTATTATTATTTTTGTATTAATTTCGTAAAAAAATCTGTTTTCCTCTATTCTCCATT
39478732 CCTTTTAACGCATTTTTTCTATGTTTTTCATTTGTTAAAATTA
326 CCTTTTAACGCATTTTTTCTATGTTTTTCATTTGTTAAAATTA
39478775 GTCTCTTTAC
Statistics
Matches: 362, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
366 153 0.42
367 3 0.01
369 96 0.27
370 110 0.30
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.42
Consensus pattern (369 bp):
TGATGCCTACCCAATAGACACCATTGGTAATCCTTATGACCACCCGTATACCCATATTTTTTCTT
GTACTTTTATGAGTGTCGCCTATTTAGGAGACACCATTTAATATTATATATATATTTTTTATTTT
AGTATAAAATAATAATAATAACAAAATAAAAAAAATTGTGTCAGATTTTTAAAATGGTGTCGCCT
ATCAAGGAGGCACTACCCCTCCCATGTATACCATTTTGGTAAATAATGGGGAATGTATTATTTTG
GTTTTTAATTATTATTATTTTTGTATTAATTTCGTAAAAAAATCTGTTTTCCTCTATTCTCCATT
CCTTTTAACGCATTTTTTCTATGTTTTTCATTTGTTAAAATTAA
Found at i:39480268 original size:19 final size:19
Alignment explanation
Indices: 39480246--39480290 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
39480236 TTATATTAGG
39480246 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
39480265 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
39480284 ATTTAAT
1 ATTTAAT
39480291 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:39481953 original size:29 final size:30
Alignment explanation
Indices: 39481904--39482133 Score: 166
Period size: 29 Copynumber: 7.8 Consensus size: 30
39481894 TTTTGGATAT
*
39481904 TCGGGGGT-AAAATGGTAATTTTGGTGAAA
1 TCGGGGTTAAAAATGGTAATTTTGGTGAAA
*
39481933 TCAGGGTTAAAAATGG-AATTTT-G-GAAA
1 TCGGGGTTAAAAATGGTAATTTTGGTGAAA
*
39481960 GTTCGGGGGT-AAAATGGTAATTTTTGGTGAAA
1 --TCGGGGTTAAAAATGGTAA-TTTTGGTGAAA
* *
39481992 TCAGGGTTAAAAATGG-AA-TTT--TAAAA
1 TCGGGGTTAAAAATGGTAATTTTGGTGAAA
*
39482018 GGTTCGGGGGT-AAAATGGTAATTTTTGGTGAAA
1 ---TCGGGGTTAAAAATGGTAA-TTTTGGTGAAA
* * **
39482051 TTGGGGTTAAAAATAG-AATTTTGGAT-AGT
1 TCGGGGTTAAAAATGGTAATTTTGG-TGAAA
*
39482080 TCAGGGG-T-AAAATGGTAATTTTTGATGAAA
1 TC-GGGGTTAAAAATGGTAA-TTTTGGTGAAA
39482110 TCGGGGTTAAAAATGG-AATTTTGG
1 TCGGGGTTAAAAATGGTAATTTTGG
39482134 AAAGTTCGGG
Statistics
Matches: 156, Mismatches: 21, Indels: 48
0.69 0.09 0.21
Matches are distributed among these distances:
26 4 0.03
27 4 0.03
28 24 0.15
29 49 0.31
30 43 0.28
31 24 0.15
32 4 0.03
33 4 0.03
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.33
Consensus pattern (30 bp):
TCGGGGTTAAAAATGGTAATTTTGGTGAAA
Found at i:39482003 original size:59 final size:59
Alignment explanation
Indices: 39481894--39482144 Score: 391
Period size: 59 Copynumber: 4.3 Consensus size: 59
39481884 AAAACGAGAC
*
39481894 TTTTGGATA-TTCGGGGGTAAAATGGTAA-TTTTGGTGAAATCAGGGTTAAAAATGGAA
1 TTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAA
39481951 TTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAA
1 TTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAA
* ** *
39482010 TTTT-AAAAGGTTCGGGGGTAAAATGGTAATTTTTGGTGAAATTGGGGTTAAAAATAGAA
1 TTTTGGAAA-GTTCGGGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAA
* * * *
39482069 TTTTGGATAGTTCAGGGGTAAAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGAA
1 TTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAA
39482128 TTTTGGAAAGTTCGGGG
1 TTTTGGAAAGTTCGGGG
39482145 ACCTATAAGC
Statistics
Matches: 177, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
57 8 0.05
58 22 0.12
59 145 0.82
60 2 0.01
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.33
Consensus pattern (59 bp):
TTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAA
Found at i:39484089 original size:6 final size:6
Alignment explanation
Indices: 39484080--39484163 Score: 58
Period size: 6 Copynumber: 14.8 Consensus size: 6
39484070 GACTTTTCTT
*
39484080 TTTAAA TTTATAA --TAATA TT-AAA TTTAAA -TTAAA TTCAAA TTTAAA
1 TTTAAA TTTA-AA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
39484126 TTT-AA TTTAAA -ATAAA TTTAAGA -TTAAA -ATAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAA
39484164 TTTTCAAATG
Statistics
Matches: 62, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
4 1 0.02
5 25 0.40
6 33 0.53
7 3 0.05
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:39484103 original size:17 final size:16
Alignment explanation
Indices: 39484097--39484163 Score: 64
Period size: 17 Copynumber: 4.0 Consensus size: 16
39484087 TTATAATAAT
39484097 ATTAAATTTAAA-TTAA
1 ATTAAA-TTAAATTTAA
39484113 ATTCAAATTTAAATTTAA
1 ATT-AAA-TTAAATTTAA
* *
39484131 TTTAAAATAAATTTAA
1 ATTAAATTAAATTTAA
*
39484147 GATTAAAATAAATTTAA
1 -ATTAAATTAAATTTAA
39484164 TTTTCAAATG
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
16 12 0.27
17 27 0.60
18 6 0.13
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (16 bp):
ATTAAATTAAATTTAA
Found at i:39484113 original size:11 final size:11
Alignment explanation
Indices: 39484098--39484166 Score: 61
Period size: 11 Copynumber: 6.2 Consensus size: 11
39484088 TATAATAATA
39484098 TTAAATTTAAA-
1 TTAAA-TTAAAT
39484109 TTAAATTCAAAT
1 TTAAATT-AAAT
*
39484121 TTAAATTTAAT
1 TTAAATTAAAT
*
39484132 TTAAAATAAAT
1 TTAAATTAAAT
39484143 TTAAGATTAAA-
1 TTAA-ATTAAAT
* *
39484154 ATAAATTTAAT
1 TTAAATTAAAT
39484165 TT
1 TT
39484167 TCAAATGGTT
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
10 7 0.15
11 28 0.60
12 12 0.26
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (11 bp):
TTAAATTAAAT
Found at i:39484152 original size:28 final size:28
Alignment explanation
Indices: 39484099--39484163 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
39484089 ATAATAATAT
* *
39484099 TAAATTTAAATTAAATTCAAATTTAAAT
1 TAAATTTAAAATAAATTCAAATTTAAAA
* *
39484127 TTAATTTAAAATAAATTTAAGA-TTAAAA
1 TAAATTTAAAATAAATTCAA-ATTTAAAA
39484155 TAAATTTAA
1 TAAATTTAA
39484164 TTTTCAAATG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 30 0.97
29 1 0.03
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (28 bp):
TAAATTTAAAATAAATTCAAATTTAAAA
Found at i:39484172 original size:17 final size:16
Alignment explanation
Indices: 39484122--39484166 Score: 72
Period size: 17 Copynumber: 2.8 Consensus size: 16
39484112 AATTCAAATT
39484122 TAAATTTAATTTAAAA
1 TAAATTTAATTTAAAA
*
39484138 TAAATTTAAGATTAAAA
1 TAAATTTAA-TTTAAAA
39484155 TAAATTTAATTT
1 TAAATTTAATTT
39484167 TCAAATGGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 11 0.42
17 15 0.58
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (16 bp):
TAAATTTAATTTAAAA
Found at i:39490192 original size:8 final size:8
Alignment explanation
Indices: 39490174--39490227 Score: 54
Period size: 8 Copynumber: 6.4 Consensus size: 8
39490164 AACCCAATTA
39490174 TTTTTATTT
1 TTTTTA-TT
39490183 TTTTTATT
1 TTTTTATT
*
39490191 TTTCTATCT
1 TTTTTAT-T
39490200 TATTTTATT
1 T-TTTTATT
*
39490209 TGTTTATT
1 TTTTTATT
*
39490217 TATTTATT
1 TTTTTATT
39490225 TTT
1 TTT
39490228 GTCCAAGAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
8 23 0.61
9 10 0.26
10 5 0.13
ACGTcount: A:0.15, C:0.04, G:0.02, T:0.80
Consensus pattern (8 bp):
TTTTTATT
Found at i:39490205 original size:22 final size:21
Alignment explanation
Indices: 39490176--39490227 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
39490166 CCCAATTATT
39490176 TTTATTTTTTTTATTT-TTCTA
1 TTTATTTTTTTTATTTATT-TA
* *
39490197 TCTTATTTTATTTGTTTATTTA
1 T-TTATTTTTTTTATTTATTTA
39490219 TTTATTTTT
1 TTTATTTTT
39490228 GTCCAAGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 8 0.31
22 16 0.62
23 2 0.08
ACGTcount: A:0.15, C:0.04, G:0.02, T:0.79
Consensus pattern (21 bp):
TTTATTTTTTTTATTTATTTA
Found at i:39491529 original size:15 final size:16
Alignment explanation
Indices: 39491500--39491529 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39491490 AGTAGGAGGG
39491500 AATATGATAATACTTA
1 AATATGATAATACTTA
39491516 AATATGAT-ATACTT
1 AATATGATAATACTT
39491530 TTGGATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (16 bp):
AATATGATAATACTTA
Found at i:39491786 original size:19 final size:19
Alignment explanation
Indices: 39491764--39491808 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
39491754 TTATATTAGG
39491764 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
39491783 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
39491802 ATTTAAT
1 ATTTAAT
39491809 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:39491831 original size:14 final size:14
Alignment explanation
Indices: 39491808--39491837 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
39491798 TTGTATTTAA
*
39491808 TTTATGTTTATCTT
1 TTTATATTTATCTT
39491822 TTTATATTTATCTT
1 TTTATATTTATCTT
39491836 TT
1 TT
39491838 AGAGTTTAAA
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:0.17, C:0.07, G:0.03, T:0.73
Consensus pattern (14 bp):
TTTATATTTATCTT
Found at i:39492628 original size:16 final size:17
Alignment explanation
Indices: 39492607--39492646 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
39492597 CTTTAACTTC
*
39492607 TTTATTTTCTA-TTTCT
1 TTTATTTTATACTTTCT
39492623 TTTA-TTTATACTTTCT
1 TTTATTTTATACTTTCT
39492639 TTTATTTT
1 TTTATTTT
39492647 TAATTCTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 5 0.24
16 13 0.62
17 3 0.14
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTATTTTATACTTTCT
Found at i:39494125 original size:13 final size:13
Alignment explanation
Indices: 39494109--39494134 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39494099 ATAAAAAACT
39494109 AAAAGAAAAGAAA
1 AAAAGAAAAGAAA
39494122 AAAAGAAAAGAAA
1 AAAAGAAAAGAAA
39494135 CAGCAATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAGAAA
Found at i:39506206 original size:35 final size:34
Alignment explanation
Indices: 39506137--39506206 Score: 79
Period size: 35 Copynumber: 2.0 Consensus size: 34
39506127 GATATTACTG
* **
39506137 TTAAAAATTACTTTTAAAAAATAAAATATTTATT
1 TTAAAAATTACTTATAAAAAATAAAATAAATATT
*
39506171 TTAAACATTATCTTATAAAATAAT-AAATAAATATT
1 TTAAAAATTA-CTTATAAAA-AATAAAATAAATATT
39506206 T
1 T
39506207 AAATAATATA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
34 9 0.30
35 18 0.60
36 3 0.10
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (34 bp):
TTAAAAATTACTTATAAAAAATAAAATAAATATT
Found at i:39506230 original size:19 final size:19
Alignment explanation
Indices: 39506188--39506228 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
39506178 TTATCTTATA
* *
39506188 AAATAATAAATAAATATTT
1 AAATAATATATAAATAATT
39506207 AAATAATATATAAATTAATT
1 AAATAATATATAAA-TAATT
39506227 AA
1 AA
39506229 TATTATAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AAATAATATATAAATAATT
Found at i:39520900 original size:2 final size:2
Alignment explanation
Indices: 39520893--39520917 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39520883 TTGAACAGTG
39520893 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
39520918 TAAATATTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39537148 original size:22 final size:24
Alignment explanation
Indices: 39537123--39537168 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
39537113 AATGCATAAA
39537123 ATAATAA-ACTTAT-AT-TAAATAT
1 ATAATAATA-TTATAATGTAAATAT
39537145 ATAATAATATTATAATGTAAATAT
1 ATAATAATATTATAATGTAAATAT
39537169 TAAGAAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 11 0.52
23 3 0.14
24 7 0.33
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (24 bp):
ATAATAATATTATAATGTAAATAT
Found at i:39537265 original size:14 final size:14
Alignment explanation
Indices: 39537246--39537277 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
39537236 GGTACGAGTT
39537246 AATATTATAATGTA
1 AATATTATAATGTA
39537260 AATATTATAATGTA
1 AATATTATAATGTA
39537274 AATA
1 AATA
39537278 ATGTTAAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (14 bp):
AATATTATAATGTA
Found at i:39543409 original size:27 final size:25
Alignment explanation
Indices: 39543372--39543430 Score: 64
Period size: 27 Copynumber: 2.3 Consensus size: 25
39543362 AATGATAAAT
39543372 AAATAAACAAACAAAAAAATAATAA
1 AAATAAACAAACAAAAAAATAATAA
** *
39543397 AAATAAATGCAAATTAAATAATAATAA
1 AAATAAA--CAAACAAAAAAATAATAA
*
39543424 TAATAAA
1 AAATAAA
39543431 AGAGATAACA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 7 0.25
27 21 0.75
ACGTcount: A:0.73, C:0.05, G:0.02, T:0.20
Consensus pattern (25 bp):
AAATAAACAAACAAAAAAATAATAA
Found at i:39543479 original size:19 final size:18
Alignment explanation
Indices: 39543455--39543511 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 18
39543445 AATGGCATGA
*
39543455 AAATAAATAACAAATAGAT
1 AAATAAATAA-AAATAAAT
*
39543474 AAATAAACAAAAAATTAAAT
1 AAATAAA-TAAAAA-TAAAT
39543494 AAA-AAATAAAAATTAAAT
1 AAATAAATAAAAA-TAAAT
39543512 GCTAAAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
18 11 0.33
19 13 0.39
20 9 0.27
ACGTcount: A:0.74, C:0.04, G:0.02, T:0.21
Consensus pattern (18 bp):
AAATAAATAAAAATAAAT
Found at i:39543484 original size:16 final size:16
Alignment explanation
Indices: 39543455--39543503 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
39543445 AATGGCATGA
39543455 AAATAAAT-AACAAAT
1 AAATAAATAAACAAAT
*
39543470 AGATAAATAAACAAA-
1 AAATAAATAAACAAAT
39543485 AAATTAAATAAA-AAAT
1 AAA-TAAATAAACAAAT
39543501 AAA
1 AAA
39543504 AATTAAATGC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
15 12 0.41
16 17 0.59
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.18
Consensus pattern (16 bp):
AAATAAATAAACAAAT
Found at i:39543535 original size:14 final size:14
Alignment explanation
Indices: 39543518--39543546 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
39543508 AAATGCTAAA
39543518 ATAAACAATAAAAT
1 ATAAACAATAAAAT
39543532 ATAAACAATAAAAT
1 ATAAACAATAAAAT
39543546 A
1 A
39543547 ATTGAGATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (14 bp):
ATAAACAATAAAAT
Found at i:39543536 original size:19 final size:18
Alignment explanation
Indices: 39543483--39543536 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
39543473 TAAATAAACA
* *
39543483 AAAAATTAAATAAAAAAT
1 AAAAATAAAATATAAAAT
* *
39543501 AAAAATTAAATGCTAAAAT
1 AAAAATAAAAT-ATAAAAT
39543520 AAACAATAAAATATAAA
1 AAA-AATAAAATATAAA
39543537 CAATAAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 11 0.37
19 12 0.40
20 7 0.23
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.22
Consensus pattern (18 bp):
AAAAATAAAATATAAAAT
Found at i:39545640 original size:22 final size:21
Alignment explanation
Indices: 39545598--39545645 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 21
39545588 GTCATTAATG
* *
39545598 AGAAGTTGATGAATTAGGCTT
1 AGAAATTGATGAATTAAGCTT
39545619 -GAAATTGATAGATATTAAGCTT
1 AGAAATTGAT-GA-ATTAAGCTT
39545641 AGAAA
1 AGAAA
39545646 ATGGAAAGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 8 0.36
21 2 0.09
22 8 0.36
23 4 0.18
ACGTcount: A:0.42, C:0.04, G:0.23, T:0.31
Consensus pattern (21 bp):
AGAAATTGATGAATTAAGCTT
Found at i:39547172 original size:33 final size:32
Alignment explanation
Indices: 39547108--39547191 Score: 84
Period size: 33 Copynumber: 2.6 Consensus size: 32
39547098 ATCGCTGGCA
*
39547108 CCCCTGCCTCATTCGATGTTGTAGCCCGCATG
1 CCCCTACCTCATTCGATGTTGTAGCCCGCATG
**
39547140 CCCCTACCTCATCTGCGA-GTTGTAGCTTGCATG
1 CCCCTACCTCAT-T-CGATGTTGTAGCCCGCATG
*
39547173 -CCCTAGCCTCGTTCG-TGTT
1 CCCCTA-CCTCATTCGATGTT
39547192 CCCTAGCCTG
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
31 5 0.11
32 17 0.39
33 19 0.43
34 3 0.07
ACGTcount: A:0.12, C:0.36, G:0.21, T:0.31
Consensus pattern (32 bp):
CCCCTACCTCATTCGATGTTGTAGCCCGCATG
Found at i:39550541 original size:3 final size:3
Alignment explanation
Indices: 39550533--39550557 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
39550523 AATCCAAGCT
39550533 TGG TGG TGG TGG TGG TGG TGG TGG T
1 TGG TGG TGG TGG TGG TGG TGG TGG T
39550558 AAAAATTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.64, T:0.36
Consensus pattern (3 bp):
TGG
Found at i:39551017 original size:23 final size:24
Alignment explanation
Indices: 39550978--39551024 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
39550968 ATTTAGTAAG
39550978 CAATAACAATCTCATAAAAAAAAT
1 CAATAACAATCTCATAAAAAAAAT
* *
39551002 CAATAA-AATTTCATAAAAGAAAT
1 CAATAACAATCTCATAAAAAAAAT
39551025 AGAAAGAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.62, C:0.13, G:0.02, T:0.23
Consensus pattern (24 bp):
CAATAACAATCTCATAAAAAAAAT
Found at i:39556875 original size:3 final size:3
Alignment explanation
Indices: 39556867--39556891 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
39556857 GAGTTTTTCC
39556867 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
39556892 TGATAAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:39562270 original size:2 final size:2
Alignment explanation
Indices: 39562263--39562289 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
39562253 CTCCACTTTC
39562263 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
39562290 ATTTTTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39562721 original size:20 final size:20
Alignment explanation
Indices: 39562698--39562739 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
39562688 AATTCATGGA
39562698 ATATATAA-TTAATTAAAACT
1 ATATATAACTT-ATTAAAACT
* *
39562718 ATATTTAACTTTTTAAAACT
1 ATATATAACTTATTAAAACT
39562738 AT
1 AT
39562740 TTTAGTTACT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (20 bp):
ATATATAACTTATTAAAACT
Found at i:39584998 original size:23 final size:24
Alignment explanation
Indices: 39584948--39585005 Score: 66
Period size: 23 Copynumber: 2.4 Consensus size: 24
39584938 GATGTGAGAA
*
39584948 AAAAATTAAAATATGATTTTATATT
1 AAAAA-TAAAATATGATTTAATATT
39584973 AAAAATAAAAT-TGATTTGAATA-T
1 AAAAATAAAATATGATTT-AATATT
*
39584996 AAATATAAAA
1 AAAAATAAAA
39585006 ATTATAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 16 0.53
24 9 0.30
25 5 0.17
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (24 bp):
AAAAATAAAATATGATTTAATATT
Found at i:39585958 original size:2 final size:2
Alignment explanation
Indices: 39585953--39585987 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
39585943 GTGTGTGTGT
*
39585953 GA GA GA GA GA GA GA GA GA GA GA GA GA GG GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
39585988 TTTAAAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (2 bp):
GA
Found at i:39602281 original size:52 final size:52
Alignment explanation
Indices: 39602203--39602393 Score: 244
Period size: 52 Copynumber: 3.7 Consensus size: 52
39602193 AATGAAAAAG
* *
39602203 GGTCCAATGAGTAAGTGTCATCGTGAGTACATGAATCTTTCAAGGATTATAA
1 GGTCCAATGACTAAGTGTCATCATGAGTACATGAATCTTTCAAGGATTATAA
* *
39602255 GGTCCAATGACTAAGTGTCATCGTGAGTACATGAAT-TCTTCACGGATTATAA
1 GGTCCAATGACTAAGTGTCATCATGAGTACATGAATCT-TTCAAGGATTATAA
* * *
39602307 GGTCCGATGACTAAGTGTCATCATTAGTACATGAATCCTTCACAGG-TTATAA
1 GGTCCAATGACTAAGTGTCATCATGAGTACATGAATCTTTCA-AGGATTATAA
* * * *
39602359 -GTTCGATGACTAAGTGTCATCATGAGCATATGAAT
1 GGTCCAATGACTAAGTGTCATCATGAGTACATGAAT
39602394 TTCTTTACAG
Statistics
Matches: 125, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
51 32 0.26
52 91 0.73
53 2 0.02
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.31
Consensus pattern (52 bp):
GGTCCAATGACTAAGTGTCATCATGAGTACATGAATCTTTCAAGGATTATAA
Found at i:39602398 original size:104 final size:104
Alignment explanation
Indices: 39602203--39602432 Score: 279
Period size: 104 Copynumber: 2.2 Consensus size: 104
39602193 AATGAAAAAG
* * * *
39602203 GGTCCAATGAGTAAGTGTCATCGTGAGTACATGAATCTTTCAAGGATTATAAGGTCCAATGACTA
1 GGTCCGATGACTAAGTGTCATCATGAGTACATGAATCCTTCAAGGATTATAAGGTCCAATGACTA
* * * *
39602268 AGTGTCATCGTGAGTACATGAATTCTTCACGGATTATA-A
66 AGTGTCATCATGAGCACATGAATTCTTCACAGAATA-AGA
* * *
39602307 GGTCCGATGACTAAGTGTCATCATTAGTACATGAATCCTTCACAGG-TTATAA-GTTCGATGACT
1 GGTCCGATGACTAAGTGTCATCATGAGTACATGAATCCTTCA-AGGATTATAAGGTCCAATGACT
* *
39602370 AAGTGTCATCATGAGCATATGAATTTCTTTACAGAATAAGA
65 AAGTGTCATCATGAGCACATGAA-TTCTTCACAGAATAAGA
39602411 GGTCCGATGACTATA-TGTCATC
1 GGTCCGATGACTA-AGTGTCATC
39602433 GTAAGTATTA
Statistics
Matches: 109, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
103 30 0.28
104 75 0.69
105 4 0.04
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (104 bp):
GGTCCGATGACTAAGTGTCATCATGAGTACATGAATCCTTCAAGGATTATAAGGTCCAATGACTA
AGTGTCATCATGAGCACATGAATTCTTCACAGAATAAGA
Found at i:39602477 original size:60 final size:61
Alignment explanation
Indices: 39602388--39602506 Score: 141
Period size: 60 Copynumber: 2.0 Consensus size: 61
39602378 TCATGAGCAT
* * * *
39602388 ATGAATTTCTTTACAGAATAAGAGGTCCGATGACTATATGTCATCGTAAGTATTAAATGAA
1 ATGAATTCCATTACAGAATAAGAGGTCCGACGACTATATGTCATCGTAAGTATCAAATGAA
* * * * * *
39602449 ATGAATTCCATTACGGATTAAG-GGTCCGACGAGTTTGTGTCATCGTGAGTATCAAATG
1 ATGAATTCCATTACAGAATAAGAGGTCCGACGACTATATGTCATCGTAAGTATCAAATG
39602507 CGAGTTGAGG
Statistics
Matches: 48, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
60 30 0.62
61 18 0.38
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.32
Consensus pattern (61 bp):
ATGAATTCCATTACAGAATAAGAGGTCCGACGACTATATGTCATCGTAAGTATCAAATGAA
Found at i:39608018 original size:21 final size:21
Alignment explanation
Indices: 39607992--39608031 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
39607982 AGTAGTTATA
*
39607992 TGCATAGATGTATCGGTAGTT
1 TGCATACATGTATCGGTAGTT
*
39608013 TGCATACTTGTATCGGTAG
1 TGCATACATGTATCGGTAG
39608032 AAGTTATAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.12, G:0.28, T:0.38
Consensus pattern (21 bp):
TGCATACATGTATCGGTAGTT
Found at i:39610961 original size:23 final size:22
Alignment explanation
Indices: 39610918--39610961 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
39610908 GTTTCTTTAC
*
39610918 TTGTAAAAATATCTCACCAAAG
1 TTGTAAAAATATCTCAACAAAG
39610940 TTGTACAAAATATAC-CAACAAA
1 TTGTA-AAAATAT-CTCAACAAA
39610962 AAATAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 5 0.26
23 13 0.68
24 1 0.05
ACGTcount: A:0.50, C:0.18, G:0.07, T:0.25
Consensus pattern (22 bp):
TTGTAAAAATATCTCAACAAAG
Found at i:39623064 original size:24 final size:24
Alignment explanation
Indices: 39623037--39623092 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
39623027 CGGCGGCGGC
*
39623037 GGTGGTGAGCTTTTTGATGGTGGT
1 GGTGGTGACCTTTTTGATGGTGGT
39623061 GGTGGTGACCTTTTTGATGGTGGT
1 GGTGGTGACCTTTTTGATGGTGGT
39623085 GGTGGTGA
1 GGTGGTGA
39623093 TGGTGATGGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.09, C:0.05, G:0.46, T:0.39
Consensus pattern (24 bp):
GGTGGTGACCTTTTTGATGGTGGT
Found at i:39623093 original size:15 final size:15
Alignment explanation
Indices: 39623075--39623124 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
39623065 GTGACCTTTT
39623075 TGATGGTGGTGGTGG
1 TGATGGTGGTGGTGG
*
39623090 TGA---TGGTGATGG
1 TGATGGTGGTGGTGG
*
39623102 TGATGGTGGTGGCGG
1 TGATGGTGGTGGTGG
39623117 TGATGGTG
1 TGATGGTG
39623125 ATGATGATGA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
12 11 0.38
15 18 0.62
ACGTcount: A:0.10, C:0.02, G:0.56, T:0.32
Consensus pattern (15 bp):
TGATGGTGGTGGTGG
Found at i:39623099 original size:21 final size:21
Alignment explanation
Indices: 39623051--39623124 Score: 76
Period size: 21 Copynumber: 3.4 Consensus size: 21
39623041 GTGAGCTTTT
**
39623051 TGATGGTGGTGGTGGTGACCTTTT
1 TGATGGTGGTGGTGGTGA---TGG
39623075 TGATGGTGGTGGTGGTGATGG
1 TGATGGTGGTGGTGGTGATGG
* **
39623096 TGATGGTGATGGTGGTGGCGG
1 TGATGGTGGTGGTGGTGATGG
39623117 TGATGGTG
1 TGATGGTG
39623125 ATGATGATGA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
21 27 0.60
24 18 0.40
ACGTcount: A:0.09, C:0.04, G:0.51, T:0.35
Consensus pattern (21 bp):
TGATGGTGGTGGTGGTGATGG
Found at i:39623105 original size:27 final size:27
Alignment explanation
Indices: 39623075--39623133 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
39623065 GTGACCTTTT
* *
39623075 TGATGGTGGTGGTGGTGATGGTGATGG
1 TGATGGTGGTGGCGGTGATGGTGATGA
39623102 TGATGGTGGTGGCGGTGATGGTGATGA
1 TGATGGTGGTGGCGGTGATGGTGATGA
39623129 TGATG
1 TGATG
39623134 ATGATGACGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.14, C:0.02, G:0.53, T:0.32
Consensus pattern (27 bp):
TGATGGTGGTGGCGGTGATGGTGATGA
Found at i:39623125 original size:6 final size:6
Alignment explanation
Indices: 39623081--39623139 Score: 55
Period size: 6 Copynumber: 9.3 Consensus size: 6
39623071 TTTTTGATGG
* * *
39623081 TGGTGG TGGTGA TGGTGA TGGTGA TGGTGG TGGCGGTGA TGGTGA TGATGA
1 TGGTGA TGGTGA TGGTGA TGGTGA TGGTGA T---GGTGA TGGTGA TGGTGA
*
39623132 TGATGA TG
1 TGGTGA TG
39623140 ACGATGAAGC
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
6 41 0.89
9 5 0.11
ACGTcount: A:0.15, C:0.02, G:0.51, T:0.32
Consensus pattern (6 bp):
TGGTGA
Found at i:39623125 original size:21 final size:21
Alignment explanation
Indices: 39623075--39623127 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
39623065 GTGACCTTTT
* *
39623075 TGATGGTGGTGGTGGTGATGG
1 TGATGGTGATGGTGGTGACGG
*
39623096 TGATGGTGATGGTGGTGGCGG
1 TGATGGTGATGGTGGTGACGG
39623117 TGATGGTGATG
1 TGATGGTGATG
39623128 ATGATGATGA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.11, C:0.02, G:0.55, T:0.32
Consensus pattern (21 bp):
TGATGGTGATGGTGGTGACGG
Found at i:39623735 original size:1 final size:1
Alignment explanation
Indices: 39623698--39623726 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
39623688 TCCTTTTAGC
39623698 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
39623727 ACAATTTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:39626608 original size:21 final size:21
Alignment explanation
Indices: 39626582--39626632 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
39626572 GCATATTGGG
39626582 AATGGAAATTATGGTTATAGA
1 AATGGAAATTATGGTTATAGA
39626603 AATGGAAATTATGGTTATAGA
1 AATGGAAATTATGGTTATAGA
39626624 AATGGAAAT
1 AATGGAAAT
39626633 GATATGGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.45, C:0.00, G:0.24, T:0.31
Consensus pattern (21 bp):
AATGGAAATTATGGTTATAGA
Found at i:39628221 original size:13 final size:13
Alignment explanation
Indices: 39628190--39628233 Score: 54
Period size: 12 Copynumber: 3.4 Consensus size: 13
39628180 AATAATGCAT
*
39628190 ATAAAATATAAAA
1 ATAATATATAAAA
*
39628203 AT-ATATTTAAAA
1 ATAATATATAAAA
39628215 ATAATATATAATAA
1 ATAATATATAA-AA
39628229 ATAAT
1 ATAAT
39628234 GAAATATATG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 10 0.38
13 9 0.35
14 7 0.27
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
ATAATATATAAAA
Found at i:39628239 original size:34 final size:33
Alignment explanation
Indices: 39628177--39628242 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 33
39628167 ATATGCGTCA
39628177 AAAAATAATGCATATAAAATATAAAAATATATTT
1 AAAAATAAT-CATATAAAATATAAAAATATATTT
39628211 AAAAATAAT-ATATAATAA-ATAATGAAATATAT
1 AAAAATAATCATATAA-AATATAA--AAATATAT
39628243 GGTTTAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
32 10 0.34
33 2 0.07
34 17 0.59
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.32
Consensus pattern (33 bp):
AAAAATAATCATATAAAATATAAAAATATATTT
Found at i:39629105 original size:13 final size:13
Alignment explanation
Indices: 39629070--39629104 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 13
39629060 ATAAACGAAT
39629070 AAGAAAAATTAAA
1 AAGAAAAATTAAA
39629083 AAGCAAAAATTAAA
1 AAG-AAAAATTAAA
39629097 ACAGAAAA
1 A-AGAAAA
39629105 TAGAAGTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 3 0.15
14 15 0.75
15 2 0.10
ACGTcount: A:0.74, C:0.06, G:0.09, T:0.11
Consensus pattern (13 bp):
AAGAAAAATTAAA
Found at i:39630023 original size:26 final size:26
Alignment explanation
Indices: 39629981--39630056 Score: 73
Period size: 26 Copynumber: 2.9 Consensus size: 26
39629971 TCTCATCCCT
* *
39629981 ATTTTATCCCC-AATAAAATTTTGATG
1 ATTTTA-CCCCTAGTAAAATTTTGACG
** * *
39630007 ATTTTACCTTTGGTAAAATTTTAACG
1 ATTTTACCCCTAGTAAAATTTTGACG
*
39630033 ATTTTGCCCCTAGTAAAATTTTGA
1 ATTTTACCCCTAGTAAAATTTTGA
39630057 GAAATATGTT
Statistics
Matches: 38, Mismatches: 11, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
25 2 0.05
26 36 0.95
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (26 bp):
ATTTTACCCCTAGTAAAATTTTGACG
Found at i:39632643 original size:20 final size:19
Alignment explanation
Indices: 39632620--39632672 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 19
39632610 ATAACGTGTG
*
39632620 AATTTTTTAAAAATAGACTA
1 AATTTTTTAAAAATA-AATA
39632640 AATTTTATTAAAAAATAAATA
1 AATTTT-TT-AAAAATAAATA
*
39632661 AATATTTTAAAA
1 AATTTTTTAAAA
39632673 GGACTGTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 4 0.14
20 8 0.28
21 10 0.34
22 7 0.24
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (19 bp):
AATTTTTTAAAAATAAATA
Found at i:39632662 original size:21 final size:21
Alignment explanation
Indices: 39632620--39632672 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
39632610 ATAACGTGTG
*
39632620 AATTTTTT-AAAAATAGACTA
1 AATTTTTTAAAAAATAGAATA
39632640 AATTTTATTAAAAAATA-AATA
1 AATTTT-TTAAAAAATAGAATA
*
39632661 AATATTTTAAAA
1 AATTTTTTAAAA
39632673 GGACTGTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 12 0.41
21 10 0.34
22 7 0.24
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (21 bp):
AATTTTTTAAAAAATAGAATA
Found at i:39638552 original size:18 final size:19
Alignment explanation
Indices: 39638529--39638572 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
39638519 GAAAAATAAA
39638529 AAAATTATTAAT-ATTTCT
1 AAAATTATTAATAATTTCT
* **
39638547 AAAATTTTTGGTAATTTCT
1 AAAATTATTAATAATTTCT
39638566 AAAATTA
1 AAAATTA
39638573 ATATTATTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (19 bp):
AAAATTATTAATAATTTCT
Found at i:39638701 original size:56 final size:57
Alignment explanation
Indices: 39638618--39638732 Score: 137
Period size: 56 Copynumber: 2.0 Consensus size: 57
39638608 TATTAATTAT
* * * *
39638618 TTGACTCAAATCTCCTTATATAGTAATAATGTATATTAAT-CAATATTTAATAGTTAA
1 TTGACTCAAATCTCCTTATATACTAAT-ATATATATTAATACAATATTTAAGAGGTAA
* *
39638675 TTGACTC-AGTCTCCTCT-TATACTAATATATATATTAATATAATATTTAAGAGGTAA
1 TTGACTCAAATCTCCT-TATATACTAATATATATATTAATACAATATTTAAGAGGTAA
39638731 TT
1 TT
39638733 CACTAAAACT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
55 11 0.22
56 31 0.62
57 8 0.16
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (57 bp):
TTGACTCAAATCTCCTTATATACTAATATATATATTAATACAATATTTAAGAGGTAA
Found at i:39644988 original size:18 final size:19
Alignment explanation
Indices: 39644958--39644993 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
39644948 ACTCGAAAAA
*
39644958 TTCAAAATAATTTTTAAAT
1 TTCAAAATAATTTATAAAT
39644977 TTCAAAAT-ATTTATAAA
1 TTCAAAATAATTTATAAA
39644994 AATTCCAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (19 bp):
TTCAAAATAATTTATAAAT
Found at i:39645003 original size:19 final size:19
Alignment explanation
Indices: 39644953--39645003 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
39644943 ATCATACTCG
39644953 AAAAATTCAAAATAATTTT
1 AAAAATTCAAAATAATTTT
* *
39644972 TAAATTTCAAAAT-ATTTAT
1 AAAAATTCAAAATAATTT-T
*
39644991 AAAAATTCCAAAT
1 AAAAATTCAAAAT
39645004 TTTCAAAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:39650389 original size:21 final size:20
Alignment explanation
Indices: 39650365--39650403 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
39650355 CAAATAAACG
39650365 GGAAAGAAAGAAAGAAGGAGA
1 GGAAAGAAAG-AAGAAGGAGA
39650386 GGAAAGAAAGAAGAAGGA
1 GGAAAGAAAGAAGAAGGA
39650404 AAGAAAGGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (20 bp):
GGAAAGAAAGAAGAAGGAGA
Found at i:39650392 original size:17 final size:15
Alignment explanation
Indices: 39650370--39650410 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 15
39650360 AAACGGGAAA
39650370 GAAAGAAAGAAGGAGAG
1 GAAAGAAAGAA-GA-AG
39650387 GAAAGAAAGAAGAAG
1 GAAAGAAAGAAGAAG
39650402 GAAAGAAAG
1 GAAAGAAAG
39650411 GTAATGTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 11 0.46
16 2 0.08
17 11 0.46
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (15 bp):
GAAAGAAAGAAGAAG
Found at i:39650495 original size:19 final size:19
Alignment explanation
Indices: 39650450--39650495 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
39650440 GTATGATATC
*
39650450 TTTTTAAAATCGTATTTTA
1 TTTTTAAAATCGTATTTAA
**
39650469 TTTATTAAAATTTTATTTAA
1 TTT-TTAAAATCGTATTTAA
39650489 TTTTTAA
1 TTTTTAA
39650496 CAGATTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (19 bp):
TTTTTAAAATCGTATTTAA
Found at i:39653844 original size:15 final size:15
Alignment explanation
Indices: 39653821--39653859 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
39653811 TCATCCAATG
39653821 CCTCTTCTTCTTCCT
1 CCTCTTCTTCTTCCT
*
39653836 CCTCCTCTTCTTCCT
1 CCTCTTCTTCTTCCT
39653851 CCTCTTCTT
1 CCTCTTCTT
39653860 GTTGCTCTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (15 bp):
CCTCTTCTTCTTCCT
Found at i:39655693 original size:30 final size:30
Alignment explanation
Indices: 39655593--39655694 Score: 73
Period size: 30 Copynumber: 3.4 Consensus size: 30
39655583 TAAATATAAA
*
39655593 AAATATGTTATTTATTAAAATGGTACAAAAT
1 AAATAT-TTATTTACTAAAATGGTACAAAAT
* * * * * * *
39655624 ATATTTTTATATACCAAAATAGTATCCACA-
1 AAATATTTATTTACTAAAATGGTA-CAAAAT
* **
39655654 CACCA-TTATTTACTAAAATGGTACAAAAT
1 AAATATTTATTTACTAAAATGGTACAAAAT
39655683 AAATATTTATTT
1 AAATATTTATTT
39655695 TGTATCATTT
Statistics
Matches: 47, Mismatches: 21, Indels: 7
0.63 0.28 0.09
Matches are distributed among these distances:
28 3 0.06
29 17 0.36
30 20 0.43
31 7 0.15
ACGTcount: A:0.45, C:0.11, G:0.06, T:0.38
Consensus pattern (30 bp):
AAATATTTATTTACTAAAATGGTACAAAAT
Found at i:39655748 original size:16 final size:16
Alignment explanation
Indices: 39655727--39655776 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
39655717 TGATGGGGGT
39655727 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
39655743 ATTATTTT-TTATATT-
1 ATTATTTTGATA-ATTA
*
39655758 A-TATTTTGGTAATTA
1 ATTATTTTGATAATTA
39655773 ATTA
1 ATTA
39655777 GCTAGGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:39656151 original size:94 final size:95
Alignment explanation
Indices: 39655973--39656240 Score: 388
Period size: 94 Copynumber: 2.9 Consensus size: 95
39655963 ATTACTTTTG
*
39655973 TAAATCAATAAATATGAACAATATTTTTTACTTACTACTACTTACCAACAACAAAATAAAATTAC
1 TAAATCAATAAATATGAACAATATTTTTTACTTACTACTAC-TACTAACAACAAAATAAAATTAC
* ***
39656038 TAATTA--ATTTTTTTAAATATTATTAAATTT
65 TAACTAGCA-AAATTTAAATATTATTAAATTT
* * * *
39656068 TAAATCAATAAATATGTATAAT-GTTTTTACTTACTACTACTACTAACAATAAAATAAAATTACT
1 TAAATCAATAAATATGAACAATATTTTTTACTTACTACTACTACTAACAACAAAATAAAATTACT
39656132 AACTAGCAAAATTTAAATATTATTAAATTT
66 AACTAGCAAAATTTAAATATTATTAAATTT
39656162 TAAATCAATAAATATGAACAATATTTTTTACTTACTA-T--TACTAACAACAAAATAAAATTACT
1 TAAATCAATAAATATGAACAATATTTTTTACTTACTACTACTACTAACAACAAAATAAAATTACT
39656224 AACTAGCAAAA-TTAAAT
66 AACTAGCAAAATTTAAAT
39656241 TAAAATAAAT
Statistics
Matches: 157, Mismatches: 13, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
91 6 0.04
92 34 0.22
93 26 0.17
94 57 0.36
95 34 0.22
ACGTcount: A:0.49, C:0.12, G:0.02, T:0.38
Consensus pattern (95 bp):
TAAATCAATAAATATGAACAATATTTTTTACTTACTACTACTACTAACAACAAAATAAAATTACT
AACTAGCAAAATTTAAATATTATTAAATTT
Found at i:39656223 original size:20 final size:21
Alignment explanation
Indices: 39656198--39656242 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
39656188 TTTACTTACT
39656198 ATTACTAAC-AACAAAATAAA
1 ATTACTAACTAACAAAATAAA
* *
39656218 ATTACTAACTAGCAAAATTAA
1 ATTACTAACTAACAAAATAAA
39656239 ATTA
1 ATTA
39656243 AAATAAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.58, C:0.13, G:0.02, T:0.27
Consensus pattern (21 bp):
ATTACTAACTAACAAAATAAA
Found at i:39656588 original size:6 final size:6
Alignment explanation
Indices: 39656577--39656648 Score: 56
Period size: 6 Copynumber: 11.7 Consensus size: 6
39656567 ACACATTACA
* * * *
39656577 TTTTCT TTTTCT TTTTCT TTCTCCT TCTTCT CTTTCT TCCTTCT TCTTTCT
1 TTTTCT TTTTCT TTTTCT TT-TTCT TTTTCT TTTTCT T-TTTCT T-TTTCT
* *
39656628 TTCTCT TTTT-T CTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTT
39656649 TCTCTCAATT
Statistics
Matches: 51, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
5 4 0.08
6 32 0.63
7 15 0.29
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (6 bp):
TTTTCT
Found at i:39656612 original size:19 final size:19
Alignment explanation
Indices: 39656585--39656631 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
39656575 CATTTTCTTT
* *
39656585 TTCTTTTTCTTTCTCCTTC
1 TTCTCTTTCTTCCTCCTTC
*
39656604 TTCTCTTTCTTCCTTCTTC
1 TTCTCTTTCTTCCTCCTTC
39656623 TT-TCTTTCT
1 TTCTCTTTCT
39656632 CTTTTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (19 bp):
TTCTCTTTCTTCCTCCTTC
Found at i:39656634 original size:13 final size:13
Alignment explanation
Indices: 39656578--39656653 Score: 54
Period size: 13 Copynumber: 5.8 Consensus size: 13
39656568 CACATTACAT
*
39656578 TTTCTTTTTCTT-
1 TTTCTTTCTCTTC
39656590 TTTCTTTCTCCTTC
1 TTTCTTTCT-CTTC
39656604 TTCTCTTTCTTCCTTC
1 TT-TCTTTC-T-CTTC
39656620 -TTCTTTCT-TTC
1 TTTCTTTCTCTTC
*
39656631 TCTTTTTTCT-TTC
1 T-TTCTTTCTCTTC
39656644 TTT-TTTCTCT
1 TTTCTTTCTCT
39656654 CAATTTTCGT
Statistics
Matches: 55, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
11 8 0.15
12 11 0.20
13 15 0.27
14 8 0.15
15 7 0.13
16 6 0.11
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTCTTTCTCTTC
Found at i:39657320 original size:14 final size:14
Alignment explanation
Indices: 39657301--39657331 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
39657291 TTGTGAATTT
*
39657301 GAAAAAAAGAAAAA
1 GAAAAAAAAAAAAA
39657315 GAAAAAAAAAAAAA
1 GAAAAAAAAAAAAA
39657329 GAA
1 GAA
39657332 GCTACGCTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (14 bp):
GAAAAAAAAAAAAA
Found at i:39658208 original size:9 final size:9
Alignment explanation
Indices: 39658194--39658222 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
39658184 GGTGCCCAAT
39658194 CATCACAGA
1 CATCACAGA
39658203 CATCACAGA
1 CATCACAGA
39658212 CATCACAGA
1 CATCACAGA
39658221 CA
1 CA
39658223 ACCCCTGTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.45, C:0.34, G:0.10, T:0.10
Consensus pattern (9 bp):
CATCACAGA
Found at i:39667150 original size:22 final size:22
Alignment explanation
Indices: 39667125--39667166 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
39667115 CATAAATAGG
*
39667125 AAAAAGTAGTTTCAAGAATAAA
1 AAAAAATAGTTTCAAGAATAAA
39667147 AAAAAATAGTTTCAAGAATA
1 AAAAAATAGTTTCAAGAATA
39667167 TGAAAGGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.60, C:0.05, G:0.12, T:0.24
Consensus pattern (22 bp):
AAAAAATAGTTTCAAGAATAAA
Found at i:39667186 original size:17 final size:17
Alignment explanation
Indices: 39667160--39667196 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
39667150 AAATAGTTTC
*
39667160 AAGAATATGAAAGGTTA
1 AAGAAGATGAAAGGTTA
39667177 AAGAAGATGAAAGGTTA
1 AAGAAGATGAAAGGTTA
39667194 AAG
1 AAG
39667197 GTTAAGAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.27, T:0.19
Consensus pattern (17 bp):
AAGAAGATGAAAGGTTA
Found at i:39667201 original size:24 final size:24
Alignment explanation
Indices: 39667169--39667215 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
39667159 CAAGAATATG
39667169 AAAGGTTAA-AGAAGATGAAAGGTT
1 AAAGGTTAAGAG-AGATGAAAGGTT
39667193 AAAGGTTAAGAGAGATGAAAGGT
1 AAAGGTTAAGAGAGATGAAAGGT
39667216 GGAACATCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 20 0.91
25 2 0.09
ACGTcount: A:0.49, C:0.00, G:0.32, T:0.19
Consensus pattern (24 bp):
AAAGGTTAAGAGAGATGAAAGGTT
Found at i:39667953 original size:16 final size:15
Alignment explanation
Indices: 39667929--39667973 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
39667919 TGACCCTAGA
39667929 CAAAATCTTGTCTTTT
1 CAAAATCTT-TCTTTT
* *
39667945 CAAAGTCTTTCATTT
1 CAAAATCTTTCTTTT
*
39667960 CAAATTCTTTCTTT
1 CAAAATCTTTCTTT
39667974 AAGCACTCCA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
15 17 0.68
16 8 0.32
ACGTcount: A:0.24, C:0.20, G:0.04, T:0.51
Consensus pattern (15 bp):
CAAAATCTTTCTTTT
Found at i:39672244 original size:8 final size:8
Alignment explanation
Indices: 39672231--39672256 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
39672221 TAAAGGATGG
39672231 ATATGAGA
1 ATATGAGA
39672239 ATATGAGA
1 ATATGAGA
39672247 ATATGAGA
1 ATATGAGA
39672255 AT
1 AT
39672257 TTGTACTGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.23, T:0.27
Consensus pattern (8 bp):
ATATGAGA
Found at i:39673222 original size:63 final size:63
Alignment explanation
Indices: 39673149--39673284 Score: 236
Period size: 63 Copynumber: 2.2 Consensus size: 63
39673139 ATTAAAAACT
* * * *
39673149 AAATAATTTTTACTTTTATTAAACAATGTGATTATATTTTGTACTTATATTTATTAGTTTACC
1 AAATAATTTTTACTTTTATTAAACAATGTAATTATATTTAGTACTTATATTTACTAATTTACC
39673212 AAATAATTTTTACTTTTATTAAACAATGTAATTATATTTAGTACTTATATTTACTAATTTACC
1 AAATAATTTTTACTTTTATTAAACAATGTAATTATATTTAGTACTTATATTTACTAATTTACC
39673275 AAATAATTTT
1 AAATAATTTT
39673285 CTAACATAAA
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 69 1.00
ACGTcount: A:0.37, C:0.08, G:0.04, T:0.51
Consensus pattern (63 bp):
AAATAATTTTTACTTTTATTAAACAATGTAATTATATTTAGTACTTATATTTACTAATTTACC
Found at i:39692182 original size:21 final size:21
Alignment explanation
Indices: 39692158--39692203 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
39692148 ATATTTTCGA
*
39692158 TTTAATTTTAATATT-TTTATT
1 TTTAAATTTAAT-TTATTTATT
*
39692179 TTTAAATTTAGTTTATTTATT
1 TTTAAATTTAATTTATTTATT
39692200 TTTA
1 TTTA
39692204 TTTAAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (21 bp):
TTTAAATTTAATTTATTTATT
Found at i:39692187 original size:27 final size:28
Alignment explanation
Indices: 39692157--39692215 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 28
39692147 TATATTTTCG
* **
39692157 ATTTAATTTTA-ATATTTTTATTTTTAA
1 ATTTAAGTTTATATATTTTTATTTAAAA
*
39692184 ATTT-AGTTTATTTATTTTTATTTAAAA
1 ATTTAAGTTTATATATTTTTATTTAAAA
39692211 ATTTA
1 ATTTA
39692216 GGTTAACATC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 5 0.19
27 21 0.81
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (28 bp):
ATTTAAGTTTATATATTTTTATTTAAAA
Found at i:39692480 original size:29 final size:28
Alignment explanation
Indices: 39692448--39692519 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 28
39692438 ATACTATATA
* *
39692448 TATTATGGATTATCGTGTTAATTACAATT
1 TATTA-GGATTATCATGTTAACTACAATT
*
39692477 TATTAGGAGTTATCATGTTAACTATAATT
1 TATTAGGA-TTATCATGTTAACTACAATT
39692506 TATTAGGGATTATC
1 TATTA-GGATTATC
39692520 TATGCATTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 3 0.08
29 32 0.84
30 3 0.08
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.46
Consensus pattern (28 bp):
TATTAGGATTATCATGTTAACTACAATT
Found at i:39692489 original size:50 final size:50
Alignment explanation
Indices: 39692393--39692489 Score: 115
Period size: 50 Copynumber: 1.9 Consensus size: 50
39692383 ATATAGTAGA
* ***
39692393 ATATATATTAGGGACTATCGTGTTAGCTACAATTTACTTTTTGTTATACT
1 ATATATATTAGGGACTATCGTGTTAACTACAATTTACTTGGAGTTATACT
* * *
39692443 ATATATATTATGGATTATCGTGTTAATTACAATTTA-TTAGGAGTTAT
1 ATATATATTAGGGACTATCGTGTTAACTACAATTTACTT-GGAGTTAT
39692490 CATGTTAACT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
49 2 0.05
50 37 0.95
ACGTcount: A:0.31, C:0.08, G:0.14, T:0.46
Consensus pattern (50 bp):
ATATATATTAGGGACTATCGTGTTAACTACAATTTACTTGGAGTTATACT
Found at i:39692622 original size:29 final size:29
Alignment explanation
Indices: 39692590--39692646 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
39692580 GAGGATTATC
* *
39692590 GTGTTAGTTACAATTTATTAGGGGCTATT
1 GTGTTAGCTACAATTTATTAGGGACTATT
*
39692619 GTGTTAGCTATAATTTATTAGGGACTAT
1 GTGTTAGCTACAATTTATTAGGGACTAT
39692647 CTATGCATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.26, C:0.07, G:0.23, T:0.44
Consensus pattern (29 bp):
GTGTTAGCTACAATTTATTAGGGACTATT
Found at i:39692654 original size:128 final size:128
Alignment explanation
Indices: 39692423--39693376 Score: 1469
Period size: 128 Copynumber: 7.5 Consensus size: 128
39692413 TGTTAGCTAC
* * *
39692423 AATTTACTTTTTGTTATACTATATATATTATGGATTATCGTGTTAATTACAATTTATTAGGAGTT
1 AATTTACTTTTTGTTATACTATATATATTATGGATTATCGTGTTAGTTACAATTTATTAGGGGCT
* * * * *
39692488 ATCATGTTAACTATAATTTATTAGGGATTATCTATGCATTAAAACAAATGTAATAGTATTGAA
66 ATCGTGTTAGCTATAATTTATTAGGGACTATCTATGCATTAAAATAGATGTAATAGTATTGAA
* *
39692551 AAATTACTTTTTGTTATACTGTATATATTGA-GGATTATCGTGTTAGTTACAATTTATTAGGGGC
1 AATTTACTTTTTGTTATACTATATATATT-ATGGATTATCGTGTTAGTTACAATTTATTAGGGGC
* *
39692615 TATTGTGTTAGCTATAATTTATTAGGGACTATCTATGCATTAAAATAGGTGTAATAGTATTGAA
65 TATCGTGTTAGCTATAATTTATTAGGGACTATCTATGCATTAAAATAGATGTAATAGTATTGAA
* *
39692679 AATTTACTTTTTGTTATACTATATATATTATGGATTATCGTGTTAGTTACAATTTATTAGGAGTT
1 AATTTACTTTTTGTTATACTATATATATTATGGATTATCGTGTTAGTTACAATTTATTAGGGGCT
* * * * *
39692744 ATCATGTTAACTATAATTTATTAGGGATTATCTATGCATTAAAACAAATGTAATAGTATTGAA
66 ATCGTGTTAGCTATAATTTATTAGGGACTATCTATGCATTAAAATAGATGTAATAGTATTGAA
* * **
39692807 AAATTACTTTTTGTTATACTGTATATATTGGGGATTATCGTGTTAGTTACAATTTATTAGGGGCT
1 AATTTACTTTTTGTTATACTATATATATTATGGATTATCGTGTTAGTTACAATTTATTAGGGGCT
* *
39692872 ATTGTGTTAGCTATAATTTATTAGGGACTATCTATGCATTAAAATAGGTGTAATAGTATTGAA
66 ATCGTGTTAGCTATAATTTATTAGGGACTATCTATGCATTAAAATAGATGTAATAGTATTGAA
* *
39692935 AATTTACTTTTTGTTATACTATATATATTATGGATTATCGTGTTAGTTACAATTTATTAGGAGTT
1 AATTTACTTTTTGTTATACTATATATATTATGGATTATCGTGTTAGTTACAATTTATTAGGGGCT
* * * * *
39693000 ATCATGTTAACTATAATTTATTAGGGATTATCTATGCATTAAAACAAATGTAATAGTATTGAA
66 ATCGTGTTAGCTATAATTTATTAGGGACTATCTATGCATTAAAATAGATGTAATAGTATTGAA
* * **
39693063 AAATTACTTTTTGTTATACTGTATATATTGGGGATTATCGTGTTAGTTACAATTTATTAGGGGCT
1 AATTTACTTTTTGTTATACTATATATATTATGGATTATCGTGTTAGTTACAATTTATTAGGGGCT
* * *
39693128 ATTGTGTTAGCTATAATTTATTAAGGACTATCTATGCATTAAAATAGGTGTAATAGTATTGAA
66 ATCGTGTTAGCTATAATTTATTAGGGACTATCTATGCATTAAAATAGATGTAATAGTATTGAA
* * * *
39693191 AATTTACTTTTTGTTATACTATATATATTAAGGACTATCGTGTTAGTTATAATTTATTAGGGACT
1 AATTTACTTTTTGTTATACTATATATATTATGGATTATCGTGTTAGTTACAATTTATTAGGGGCT
*
39693256 ATCGTGTTTGCTATAATTTATTAGGGACTATCTATGCATTAAAATAGATGTAATAGTATTGAA
66 ATCGTGTTAGCTATAATTTATTAGGGACTATCTATGCATTAAAATAGATGTAATAGTATTGAA
* * *
39693319 AATTTACTTTTTGTTATACTATATATATTAGGGACTATCGTGTTAGCTACAATTTATT
1 AATTTACTTTTTGTTATACTATATATATTATGGATTATCGTGTTAGTTACAATTTATT
39693377 TTCAGATATA
Statistics
Matches: 747, Mismatches: 77, Indels: 4
0.90 0.09 0.00
Matches are distributed among these distances:
127 1 0.00
128 745 1.00
129 1 0.00
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (128 bp):
AATTTACTTTTTGTTATACTATATATATTATGGATTATCGTGTTAGTTACAATTTATTAGGGGCT
ATCGTGTTAGCTATAATTTATTAGGGACTATCTATGCATTAAAATAGATGTAATAGTATTGAA
Found at i:39692736 original size:29 final size:28
Alignment explanation
Indices: 39692704--39692775 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 28
39692694 ATACTATATA
* **
39692704 TATTATGGATTATCGTGTTAGTTACAATT
1 TATTA-GGATTATCATGTTAACTACAATT
*
39692733 TATTAGGAGTTATCATGTTAACTATAATT
1 TATTAGGA-TTATCATGTTAACTACAATT
39692762 TATTAGGGATTATC
1 TATTA-GGATTATC
39692776 TATGCATTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 3 0.08
29 31 0.84
30 3 0.08
ACGTcount: A:0.31, C:0.07, G:0.17, T:0.46
Consensus pattern (28 bp):
TATTAGGATTATCATGTTAACTACAATT
Found at i:39692864 original size:29 final size:29
Alignment explanation
Indices: 39692832--39692903 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
39692822 ATACTGTATA
* *
39692832 TATTGGGGATTATCGTGTTAGTTACAATT
1 TATTGGGGACTATCGTGTTAGCTACAATT
* *
39692861 TATTAGGGG-CTATTGTGTTAGCTATAATT
1 TATT-GGGGACTATCGTGTTAGCTACAATT
*
39692890 TATTAGGGACTATC
1 TATTGGGGACTATC
39692904 TATGCATTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
28 3 0.09
29 28 0.80
30 4 0.11
ACGTcount: A:0.25, C:0.08, G:0.24, T:0.43
Consensus pattern (29 bp):
TATTGGGGACTATCGTGTTAGCTACAATT
Found at i:39692878 original size:256 final size:256
Alignment explanation
Indices: 39692423--39693376 Score: 1730
Period size: 256 Copynumber: 3.7 Consensus size: 256
39692413 TGTTAGCTAC
*
39692423 AATTTACTTTTTGTTATACTATATATATTATGGATTATCGTGTTAATTACAATTTATTAGGAGTT
1 AATTTACTTTTTGTTATACTATATATATTATGGATTATCGTGTTAGTTACAATTTATTAGGAGTT
39692488 ATCATGTTAACTATAATTTATTAGGGATTATCTATGCATTAAAACAAATGTAATAGTATTGAAAA
66 ATCATGTTAACTATAATTTATTAGGGATTATCTATGCATTAAAACAAATGTAATAGTATTGAAAA
*
39692553 ATTACTTTTTGTTATACTGTATATATTGAGGATTATCGTGTTAGTTACAATTTATTAGGGGCTAT
131 ATTACTTTTTGTTATACTGTATATATTGGGGATTATCGTGTTAGTTACAATTTATTAGGGGCTAT
39692618 TGTGTTAGCTATAATTTATTAGGGACTATCTATGCATTAAAATAGGTGTAATAGTATTGAA
196 TGTGTTAGCTATAATTTATTAGGGACTATCTATGCATTAAAATAGGTGTAATAGTATTGAA
39692679 AATTTACTTTTTGTTATACTATATATATTATGGATTATCGTGTTAGTTACAATTTATTAGGAGTT
1 AATTTACTTTTTGTTATACTATATATATTATGGATTATCGTGTTAGTTACAATTTATTAGGAGTT
39692744 ATCATGTTAACTATAATTTATTAGGGATTATCTATGCATTAAAACAAATGTAATAGTATTGAAAA
66 ATCATGTTAACTATAATTTATTAGGGATTATCTATGCATTAAAACAAATGTAATAGTATTGAAAA
39692809 ATTACTTTTTGTTATACTGTATATATTGGGGATTATCGTGTTAGTTACAATTTATTAGGGGCTAT
131 ATTACTTTTTGTTATACTGTATATATTGGGGATTATCGTGTTAGTTACAATTTATTAGGGGCTAT
39692874 TGTGTTAGCTATAATTTATTAGGGACTATCTATGCATTAAAATAGGTGTAATAGTATTGAA
196 TGTGTTAGCTATAATTTATTAGGGACTATCTATGCATTAAAATAGGTGTAATAGTATTGAA
39692935 AATTTACTTTTTGTTATACTATATATATTATGGATTATCGTGTTAGTTACAATTTATTAGGAGTT
1 AATTTACTTTTTGTTATACTATATATATTATGGATTATCGTGTTAGTTACAATTTATTAGGAGTT
39693000 ATCATGTTAACTATAATTTATTAGGGATTATCTATGCATTAAAACAAATGTAATAGTATTGAAAA
66 ATCATGTTAACTATAATTTATTAGGGATTATCTATGCATTAAAACAAATGTAATAGTATTGAAAA
39693065 ATTACTTTTTGTTATACTGTATATATTGGGGATTATCGTGTTAGTTACAATTTATTAGGGGCTAT
131 ATTACTTTTTGTTATACTGTATATATTGGGGATTATCGTGTTAGTTACAATTTATTAGGGGCTAT
*
39693130 TGTGTTAGCTATAATTTATTAAGGACTATCTATGCATTAAAATAGGTGTAATAGTATTGAA
196 TGTGTTAGCTATAATTTATTAGGGACTATCTATGCATTAAAATAGGTGTAATAGTATTGAA
* * * *
39693191 AATTTACTTTTTGTTATACTATATATATTAAGGACTATCGTGTTAGTTATAATTTATTAGG-GAC
1 AATTTACTTTTTGTTATACTATATATATTATGGATTATCGTGTTAGTTACAATTTATTAGGAG-T
* ** * * *
39693255 TATCGTGTTTGCTATAATTTATTAGGGACTATCTATGCATTAAAATAGATGTAATAGTATTGAAA
65 TATCATGTTAACTATAATTTATTAGGGATTATCTATGCATTAAAACAAATGTAATAGTATTGAAA
* * * * *
39693320 ATTTACTTTTTGTTATACTATATATATTAGGGACTATCGTGTTAGCTACAATTTATT
130 AATTACTTTTTGTTATACTGTATATATTGGGGATTATCGTGTTAGTTACAATTTATT
39693377 TTCAGATATA
Statistics
Matches: 679, Mismatches: 18, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
255 1 0.00
256 678 1.00
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (256 bp):
AATTTACTTTTTGTTATACTATATATATTATGGATTATCGTGTTAGTTACAATTTATTAGGAGTT
ATCATGTTAACTATAATTTATTAGGGATTATCTATGCATTAAAACAAATGTAATAGTATTGAAAA
ATTACTTTTTGTTATACTGTATATATTGGGGATTATCGTGTTAGTTACAATTTATTAGGGGCTAT
TGTGTTAGCTATAATTTATTAGGGACTATCTATGCATTAAAATAGGTGTAATAGTATTGAA
Found at i:39692992 original size:29 final size:28
Alignment explanation
Indices: 39692960--39693031 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 28
39692950 ATACTATATA
* **
39692960 TATTATGGATTATCGTGTTAGTTACAATT
1 TATTA-GGATTATCATGTTAACTACAATT
*
39692989 TATTAGGAGTTATCATGTTAACTATAATT
1 TATTAGGA-TTATCATGTTAACTACAATT
39693018 TATTAGGGATTATC
1 TATTA-GGATTATC
39693032 TATGCATTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 3 0.08
29 31 0.84
30 3 0.08
ACGTcount: A:0.31, C:0.07, G:0.17, T:0.46
Consensus pattern (28 bp):
TATTAGGATTATCATGTTAACTACAATT
Found at i:39693120 original size:29 final size:29
Alignment explanation
Indices: 39693098--39693159 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
39693088 TATTGGGGAT
*
39693098 TATCGTGTTAGTTACAATTTATTAGGGGC
1 TATCGTGTTAGCTACAATTTATTAGGGGC
* * * *
39693127 TATTGTGTTAGCTATAATTTATTAAGGAC
1 TATCGTGTTAGCTACAATTTATTAGGGGC
39693156 TATC
1 TATC
39693160 TATGCATTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.27, C:0.10, G:0.19, T:0.44
Consensus pattern (29 bp):
TATCGTGTTAGCTACAATTTATTAGGGGC
Found at i:39693248 original size:29 final size:29
Alignment explanation
Indices: 39693216--39693287 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
39693206 ATACTATATA
* *
39693216 TATTAAGGACTATCGTGTTAGTTATAATT
1 TATTAGGGACTATCGTGTTAGCTATAATT
*
39693245 TATTAGGGACTATCGTGTTTGCTATAATT
1 TATTAGGGACTATCGTGTTAGCTATAATT
39693274 TATTAGGGACTATC
1 TATTAGGGACTATC
39693288 TATGCATTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.28, C:0.10, G:0.19, T:0.43
Consensus pattern (29 bp):
TATTAGGGACTATCGTGTTAGCTATAATT
Found at i:39694665 original size:19 final size:19
Alignment explanation
Indices: 39694641--39694683 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
39694631 AAATATAAAT
39694641 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATATTAAATAA
* *
39694660 TAAATAATATATTAAATAT
1 TAAATAAAATATTAAATAA
39694679 TAAAT
1 TAAAT
39694684 CCTAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATATTAAATAA
Found at i:39694681 original size:26 final size:25
Alignment explanation
Indices: 39694648--39694700 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 25
39694638 AATTAAATAC
39694648 AAATTTAAA-TAATAAATAATATATT
1 AAATTTAAACTAATAAA-AATATATT
39694673 AAATATTAAATCCTAATAAAAATATATT
1 AAAT-TTAAA--CTAATAAAAATATATT
39694701 TTAAAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
25 4 0.17
26 5 0.21
28 8 0.33
29 7 0.29
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (25 bp):
AAATTTAAACTAATAAAAATATATT
Found at i:39696201 original size:13 final size:13
Alignment explanation
Indices: 39696183--39696219 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
39696173 CTGGACATAT
39696183 AATAAAATA-AATA
1 AATAAAATATAA-A
39696196 AATAAAATATAAA
1 AATAAAATATAAA
39696209 AATAAAA-ATAA
1 AATAAAATATAA
39696220 TTGGGTTGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.17
13 17 0.74
14 2 0.09
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (13 bp):
AATAAAATATAAA
Found at i:39697448 original size:21 final size:21
Alignment explanation
Indices: 39697410--39697456 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
39697400 TATTTTCTTT
** *
39697410 TGAAAATCTACAGTTTGCTTC
1 TGAAAATCTACAAATTGCTGC
*
39697431 TGAAAATCTATAAATTGCTGC
1 TGAAAATCTACAAATTGCTGC
39697452 TGAAA
1 TGAAA
39697457 TTTAAGAACA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (21 bp):
TGAAAATCTACAAATTGCTGC
Found at i:39699735 original size:19 final size:19
Alignment explanation
Indices: 39699711--39699753 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
39699701 AAATGTAAAT
39699711 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
39699730 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
39699749 TAAAT
1 TAAAT
39699754 CCTAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:39705281 original size:16 final size:16
Alignment explanation
Indices: 39705257--39705287 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39705247 TCAACTTCTG
*
39705257 CACCTTTCTGTATCCT
1 CACCCTTCTGTATCCT
39705273 CACCCTTCTGTATCC
1 CACCCTTCTGTATCC
39705288 CCAAACCATA
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:0.13, C:0.42, G:0.06, T:0.39
Consensus pattern (16 bp):
CACCCTTCTGTATCCT
Found at i:39705623 original size:16 final size:17
Alignment explanation
Indices: 39705582--39705625 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
39705572 CGTTTAATGT
39705582 TTATATATTTT-GTTAAA
1 TTATAT-TTTTAGTTAAA
*
39705599 TTATTTTTTTAGTTAAA
1 TTATATTTTTAGTTAAA
39705616 TTA-ATTTTTA
1 TTATATTTTTA
39705626 TTTTTTTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 10 0.42
17 14 0.58
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.64
Consensus pattern (17 bp):
TTATATTTTTAGTTAAA
Found at i:39711910 original size:26 final size:27
Alignment explanation
Indices: 39711881--39711966 Score: 70
Period size: 26 Copynumber: 3.1 Consensus size: 27
39711871 TTTAATGATT
39711881 ATTATTAAATATAATTTAATAAAAA-A
1 ATTATTAAATATAATTTAATAAAAATA
* * *
39711907 ATTAATT-AATTTAATTATATTTTAACATAATT
1 ATT-ATTAAATATAATT-TA--ATAA-A-AATA
39711939 ATTATTAAATATAATTTAAT-AAAATA
1 ATTATTAAATATAATTTAATAAAAATA
39711965 AT
1 AT
39711967 ATATAATTTA
Statistics
Matches: 46, Mismatches: 6, Indels: 16
0.68 0.09 0.24
Matches are distributed among these distances:
26 16 0.35
27 6 0.13
28 1 0.02
29 4 0.09
30 1 0.02
31 7 0.15
32 11 0.24
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (27 bp):
ATTATTAAATATAATTTAATAAAAATA
Found at i:39711947 original size:58 final size:58
Alignment explanation
Indices: 39711878--39712022 Score: 197
Period size: 58 Copynumber: 2.5 Consensus size: 58
39711868 AATTTTAATG
*
39711878 ATTATTATTAAATATAATTTAATAAAAAAAT-TAATTAATTTAATTATA-TTTTAACATA
1 ATTATTATTAAATATAATTTAATAAAAAAATAT-A-TAATTTAATAATATTTTTAACATA
* *
39711936 ATTATTATTAAATATAATTTAATAAAATAATATATAATTTAATAATATTTTTAATATA
1 ATTATTATTAAATATAATTTAATAAAAAAATATATAATTTAATAATATTTTTAACATA
*
39711994 ATTATTATTAAAATATGAA-TTAGTAAAAA
1 ATTATTATT-AAATAT-AATTTAATAAAAA
39712023 TTATAATATA
Statistics
Matches: 78, Mismatches: 5, Indels: 7
0.87 0.06 0.08
Matches are distributed among these distances:
57 12 0.15
58 49 0.63
59 15 0.19
60 2 0.03
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (58 bp):
ATTATTATTAAATATAATTTAATAAAAAAATATATAATTTAATAATATTTTTAACATA
Found at i:39711954 original size:32 final size:30
Alignment explanation
Indices: 39711878--39712015 Score: 94
Period size: 29 Copynumber: 4.7 Consensus size: 30
39711868 AATTTTAATG
*
39711878 ATTATTATTAAATATAATT-TAATAAAAAA
1 ATTATTATTAAATATAATTATAATAAAATA
* * *
39711907 ATTA--ATT-AATTTAATTATATTTTAACATA
1 ATTATTATTAAATATAATTATA--ATAAAATA
39711936 ATTATTATTAAATATAATT-TAATAAAATA
1 ATTATTATTAAATATAATTATAATAAAATA
* * * *
39711965 ATATATAATTTAATA-ATATT-T-TTAATATA
1 AT-TATTATTAAATATA-ATTATAATAAAATA
39711994 ATTATTATTAAAATATGAATTA
1 ATTATTATT-AAATAT-AATTA
39712016 GTAAAAATTA
Statistics
Matches: 84, Mismatches: 13, Indels: 22
0.71 0.11 0.18
Matches are distributed among these distances:
26 8 0.10
27 5 0.06
28 6 0.07
29 34 0.40
30 17 0.20
31 6 0.07
32 8 0.10
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (30 bp):
ATTATTATTAAATATAATTATAATAAAATA
Found at i:39712026 original size:25 final size:24
Alignment explanation
Indices: 39711997--39712047 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
39711987 TAATATAATT
*
39711997 ATTATTAAAATATGA-ATTAGTAAAA
1 ATTA-TAAAATATAATATTAG-AAAA
*
39712022 ATTATAATATATAATATTAGAAAA
1 ATTATAAAATATAATATTAGAAAA
39712046 AT
1 AT
39712048 AATATATAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (24 bp):
ATTATAAAATATAATATTAGAAAA
Found at i:39717017 original size:12 final size:12
Alignment explanation
Indices: 39717000--39717029 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
39716990 CCTCTTTCAG
39717000 GTGCTGTAATCA
1 GTGCTGTAATCA
*
39717012 GTGCTGTAATCG
1 GTGCTGTAATCA
39717024 GTGCTG
1 GTGCTG
39717030 AAGGAAGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.17, G:0.33, T:0.33
Consensus pattern (12 bp):
GTGCTGTAATCA
Found at i:39724520 original size:18 final size:18
Alignment explanation
Indices: 39724497--39724532 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
39724487 TAAAATATTA
39724497 TAAATTAAAAAATTAAAT
1 TAAATTAAAAAATTAAAT
* *
39724515 TAAATTTAAATATTAAAT
1 TAAATTAAAAAATTAAAT
39724533 GTTTAAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAATTAAAAAATTAAAT
Found at i:39724574 original size:12 final size:13
Alignment explanation
Indices: 39724557--39724591 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
39724547 TCGAATCATA
*
39724557 TTTTAAATTT-TT
1 TTTTAAATTTACT
39724569 TTTTAAATTTACT
1 TTTTAAATTTACT
39724582 TTTTAAATTT
1 TTTTAAATTT
39724592 CGAACGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTAAATTTACT
Found at i:39724586 original size:13 final size:12
Alignment explanation
Indices: 39724557--39724592 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
39724547 TCGAATCATA
*
39724557 TTTTAAATTTTT
1 TTTTAAATTTCT
39724569 TTTTAAATTTACT
1 TTTTAAATTT-CT
39724582 TTTTAAATTTC
1 TTTTAAATTTC
39724593 GAACGAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTTAAATTTCT
Found at i:39724913 original size:15 final size:13
Alignment explanation
Indices: 39724871--39724913 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
39724861 AATTTTAAAA
*
39724871 TTTTAATAAATAAT
1 TTTTAA-AAATTAT
39724885 TTTTAAAAATTAT
1 TTTTAAAAATTAT
39724898 TTATTAAAATATTAT
1 TT-TTAAAA-ATTAT
39724913 T
1 T
39724914 ATATATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 8 0.31
14 12 0.46
15 6 0.23
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TTTTAAAAATTAT
Found at i:39729809 original size:18 final size:18
Alignment explanation
Indices: 39729769--39729803 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
39729759 TAAATAATAA
*
39729769 AATATTATTATTTATTAT
1 AATATTATTATTAATTAT
39729787 AATATTATTATTAATTA
1 AATATTATTATTAATTA
39729804 ATATATCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
AATATTATTATTAATTAT
Found at i:39731773 original size:39 final size:39
Alignment explanation
Indices: 39731719--39731812 Score: 179
Period size: 39 Copynumber: 2.4 Consensus size: 39
39731709 TGCAAGGCCC
39731719 ATGCCAACATGGATTTGAGGCCTGCAATTTCAAATGCCT
1 ATGCCAACATGGATTTGAGGCCTGCAATTTCAAATGCCT
*
39731758 ATGCCAACAGGGATTTGAGGCCTGCAATTTCAAATGCCT
1 ATGCCAACATGGATTTGAGGCCTGCAATTTCAAATGCCT
39731797 ATGCCAACATGGATTT
1 ATGCCAACATGGATTT
39731813 CAGGGCTATG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 53 1.00
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (39 bp):
ATGCCAACATGGATTTGAGGCCTGCAATTTCAAATGCCT
Found at i:39733834 original size:16 final size:16
Alignment explanation
Indices: 39733800--39733832 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
39733790 ATGTTTGAAA
*
39733800 TTATATTATTTTATCT
1 TTATATTATTTTAACT
39733816 TTATA-TATTTTAACT
1 TTATATTATTTTAACT
39733831 TT
1 TT
39733833 TAAAATGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATATTATTTTAACT
Found at i:39739564 original size:18 final size:18
Alignment explanation
Indices: 39739541--39739593 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
39739531 AACATGGGCG
39739541 GTGGATACATCGAAGGTA
1 GTGGATACATCGAAGGTA
* ** *
39739559 GTGGATACATTGAAAATG
1 GTGGATACATCGAAGGTA
*
39739577 GTGGATATATCGAAGGT
1 GTGGATACATCGAAGGT
39739594 GAACACATGT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.34, C:0.08, G:0.32, T:0.26
Consensus pattern (18 bp):
GTGGATACATCGAAGGTA
Found at i:39746710 original size:14 final size:14
Alignment explanation
Indices: 39746691--39746728 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
39746681 TGTTTCACTG
39746691 AAAATGACTTCCGA
1 AAAATGACTTCCGA
* *
39746705 AAAATGATTTCTGA
1 AAAATGACTTCCGA
39746719 AAAATGACTT
1 AAAATGACTT
39746729 ACTTTTCTGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (14 bp):
AAAATGACTTCCGA
Found at i:39746942 original size:16 final size:17
Alignment explanation
Indices: 39746910--39746943 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
39746900 GCTTATTTAA
*
39746910 TTAATCATATTTTAATT
1 TTAATCATATCTTAATT
39746927 TTAATCA-ATCTTAATT
1 TTAATCATATCTTAATT
39746943 T
1 T
39746944 ACTTAATTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (17 bp):
TTAATCATATCTTAATT
Found at i:39746944 original size:21 final size:21
Alignment explanation
Indices: 39746905--39746944 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
39746895 ATAAAGCTTA
* *
39746905 TTTAATTAATCATATTTTAAT
1 TTTAATCAATCATAATTTAAT
*
39746926 TTTAATCAATCTTAATTTA
1 TTTAATCAATCATAATTTA
39746945 CTTAATTGTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTAATCAATCATAATTTAAT
Done.