Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008913.1 Hibiscus syriacus cultivar Beakdansim tig00112216_pilon, whole genome shotgun sequence
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: 629305
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 4
Found at i:15537 original size:19 final size:19
Alignment explanation
Indices: 15509--15551 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
15499 GTTGTCGGAA
*
15509 GTATCGTCGGGTCACTTAG
1 GTATCATCGGGTCACTTAG
15528 GTATCATCGGGTCACTTAG
1 GTATCATCGGGTCACTTAG
15547 GTATC
1 GTATC
15552 GTGATTTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.19, C:0.21, G:0.28, T:0.33
Consensus pattern (19 bp):
GTATCATCGGGTCACTTAG
Found at i:16026 original size:16 final size:16
Alignment explanation
Indices: 15992--16026 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
15982 TTTATTAATC
*
15992 TTTTTAAAAAAAAAGT
1 TTTTTAAAAAAAAACT
*
16008 TTTTTAAAAAAACACT
1 TTTTTAAAAAAAAACT
16024 TTT
1 TTT
16027 ATGCGGATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.43
Consensus pattern (16 bp):
TTTTTAAAAAAAAACT
Found at i:16175 original size:19 final size:19
Alignment explanation
Indices: 16147--16189 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
16137 GTTGTCGGAA
*
16147 GTATCGTCGGGTCACTTAG
1 GTATCATCGGGTCACTTAG
16166 GTATCATCGGGTCACTTAG
1 GTATCATCGGGTCACTTAG
16185 GTATC
1 GTATC
16190 GTGATTTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.19, C:0.21, G:0.28, T:0.33
Consensus pattern (19 bp):
GTATCATCGGGTCACTTAG
Found at i:16467 original size:638 final size:639
Alignment explanation
Indices: 14889--16716 Score: 3394
Period size: 638 Copynumber: 2.9 Consensus size: 639
14879 GCTGTCGGAA
* *
14889 GTATCATCGGGTCACTTAGGTATCGTGATTTCTTCATTTAGGGTTTGACTTTGGCATTCTCTTCA
1 GTATCATCGGGTCACTTAGGTATCGTGATTTCTTCATTTGGGGTTTGACTTTGACATTCTCTTCA
* *
14954 TTGACTGTTCGATGTGGTTTATGGGTTATGGGTCGTCGTTTTTGGTTGTTCACTGGGTGGAGGTT
66 TTGACTGTTCGATGTGGTTTATGGGTTCTGGGTCGTCGTTTTTGGTTGTTCACCGGGTGGAGGTT
15019 CAGTCGGTGGCAACAATGGTGATGGGTGTAGACATAAGGATTGGAATAAGGATTTTCAAAGTTTT
131 CAGTCGGTGGCAACAATGGTGATGGGTGTAGACATAAGGATTGGAATAAGGATTTTCAAAGTTTT
15084 GAGGTATTTTTAAGATTTGAGAAATATTTGGACATTTTTAAAATATATATAATTTAATTTTTTTA
196 GAGGTATTTTTAAGATTTGAGAAATATTTGGACATTTTTAAAATATATATAATTTAATTTTTTTA
15149 ATTTTCAAAATTACCTAAGTACGATATGTGTTATTTAATAACAGAATTAAGTCGATGTTGTAATT
261 ATTTTCAAAATTACCTAAGTACGATATGTGTTATTTAATAACAGAATTAAGTCGATGTTGTAATT
15214 GAAGCACCTAAAAATATAAGGATGAGAACGTTAAGTATTTGGATCGATAAAAAA-AATTTTAAAT
326 GAAGCACCTAAAAATATAAGGATGAGAACGTTAAGTATTTGGATCGATAAAAAATAA-TTTAAAT
15278 ACTTAAATAAAAAATATAATTTAGATATTTATTTTATATTATGCATATTAAGAACGAAATTCTTT
390 ACTTAAATAAAAAATATAATTTAGATATTTATTTTATATTATGCATATTAAGAACGAAATTCTTT
15343 TTTATTAATC-TTTT-AAAAAAAAGTTTTTTAAAAAAACACTTTTATGCGGATGTAAAATGATTT
455 TTTATTAATCTTTTTAAAAAAAAAGTTTTTTAAAAAAACACTTTTATGCGGATGTAAAATGATTT
*
15406 TCTGATATATATAATAACCTTTTGTATCAAGCATGGCTATAGTAACCTTCGTCATCACCCTTGAC
520 TCTGATATATATAATAACATTTTGTATCAAGCATGGCTATAGTAACCTTCG--ATCACCCTTGAC
15471 ATCTTTTTTGTCGGTTGTTGTTGCTCTCGTTGTCGGAAGTATCGTCGGGTCACTTAG
583 ATCTTTTTTGTCGGTTGTTGTTGCTCTCGTTGTCGGAAGTATCGTCGGGTCACTTAG
* *
15528 GTATCATCGGGTCACTTAGGTATCGTGATTTCTTTATTTGGGGTTTGACTTTGACATTCTCGTCA
1 GTATCATCGGGTCACTTAGGTATCGTGATTTCTTCATTTGGGGTTTGACTTTGACATTCTCTTCA
* *
15593 TTGACTGTTCGATGTGGTTTATGGGTTCTAGGTCGTCGTTTTTGGTTGTTCATCGGGTGGAGGTT
66 TTGACTGTTCGATGTGGTTTATGGGTTCTGGGTCGTCGTTTTTGGTTGTTCACCGGGTGGAGGTT
15658 CAGTCGGTGGCAACAATGGTGATGGGTGTAGACATAAGGATTGGAATAAGGATTTTCAAAGTTTT
131 CAGTCGGTGGCAACAATGGTGATGGGTGTAGACATAAGGATTGGAATAAGGATTTTCAAAGTTTT
15723 GAGGTATTTTTAAGATTTGAGAAATATTTGGACATTTTTAAAATATATATAATTTAATTTTTTTA
196 GAGGTATTTTTAAGATTTGAGAAATATTTGGACATTTTTAAAATATATATAATTTAATTTTTTTA
15788 ATTTTCAAAATTACCTAAGTACGATATGTGTTATTTAATAACAGAATTAAGTCGATGTTGTAATT
261 ATTTTCAAAATTACCTAAGTACGATATGTGTTATTTAATAACAGAATTAAGTCGATGTTGTAATT
*
15853 GAAGCACCTAAAAATATAAGGATGAGAACGTTAAGTAGTTGGATCGATAAAAAATAATTTAAATA
326 GAAGCACCTAAAAATATAAGGATGAGAACGTTAAGTATTTGGATCGATAAAAAATAATTTAAATA
*
15918 CTTAAATAAAAATTATAATTTAGATATTTATTTTATATTATGCATATTAAGAACGAAATTCTTTT
391 CTTAAATAAAAAATATAATTTAGATATTTATTTTATATTATGCATATTAAGAACGAAATTCTTTT
15983 TTATTAATCTTTTTAAAAAAAAAGTTTTTTAAAAAAACACTTTTATGCGGATGTAAAATGATTTT
456 TTATTAATCTTTTTAAAAAAAAAGTTTTTTAAAAAAACACTTTTATGCGGATGTAAAATGATTTT
16048 CTGATATATATAATAACATTTTGTATCAAGCATGGCTATAGTAACCTTCG-TCACCCTTGACATC
521 CTGATATATATAATAACATTTTGTATCAAGCATGGCTATAGTAACCTTCGATCACCCTTGACATC
16112 TTTTTTGTCGGTTGTTGTTGCTCTCGTTGTCGGAAGTATCGTCGGGTCACTTAG
586 TTTTTTGTCGGTTGTTGTTGCTCTCGTTGTCGGAAGTATCGTCGGGTCACTTAG
*
16166 GTATCATCGGGTCACTTAGGTATCGTGATTTCTTCATTTGGGGTTTAACTTTGACATTCTCTTCA
1 GTATCATCGGGTCACTTAGGTATCGTGATTTCTTCATTTGGGGTTTGACTTTGACATTCTCTTCA
* *
16231 TTGATTGTTAGATGTGGTTTATGGGTTCTGGGTCGTCGTTTTTGGTTGTTCACCGGGTGGAGGTT
66 TTGACTGTTCGATGTGGTTTATGGGTTCTGGGTCGTCGTTTTTGGTTGTTCACCGGGTGGAGGTT
16296 CAGTCGGTGGCAACAATGGTGATGGGTGTAGACATAAGGATTGGAATAAGGATTTTCAAAGTTTT
131 CAGTCGGTGGCAACAATGGTGATGGGTGTAGACATAAGGATTGGAATAAGGATTTTCAAAGTTTT
*
16361 GAGGTATTTTTAAGATTTGAGAAATATTTGGACATTTTTAATATATATATAATTTAATTTTTTTA
196 GAGGTATTTTTAAGATTTGAGAAATATTTGGACATTTTTAAAATATATATAATTTAATTTTTTTA
16426 ATTTTCAAAATTACCTAAGTACGATATGTGTTATTTAATAACAGAATTAAGTCGATGTTGTAATT
261 ATTTTCAAAATTACCTAAGTACGATATGTGTTATTTAATAACAGAATTAAGTCGATGTTGTAATT
*
16491 GAAGCACCTAAAAATATAAGGATGAGAACATTAAGTATTTGGATCGATAAAAAATAATTTAAATA
326 GAAGCACCTAAAAATATAAGGATGAGAACGTTAAGTATTTGGATCGATAAAAAATAATTTAAATA
16556 CTTAAATAAAAAATATAATTTAGATATTTATTTTATATTATGCATATTAAGAACGAAATTCTTTT
391 CTTAAATAAAAAATATAATTTAGATATTTATTTTATATTATGCATATTAAGAACGAAATTCTTTT
* * * *
16621 TTATTAATTTTTTTTAAAAAAAAAGTTTTTTTAATAAAACACTTTTATGCGCACGTAAAATGATT
456 TTATTAA-TCTTTTTAAAAAAAAAG-TTTTTTAAAAAAACACTTTTATGCGGATGTAAAATGATT
*
16686 TTCTAATATATATAATAACATTTTGTATCAA
519 TTCTGATATATATAATAACATTTTGTATCAA
16717 AATGTATCCT
Statistics
Matches: 1157, Mismatches: 27, Indels: 9
0.97 0.02 0.01
Matches are distributed among these distances:
638 519 0.45
639 467 0.40
640 72 0.06
641 99 0.09
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.40
Consensus pattern (639 bp):
GTATCATCGGGTCACTTAGGTATCGTGATTTCTTCATTTGGGGTTTGACTTTGACATTCTCTTCA
TTGACTGTTCGATGTGGTTTATGGGTTCTGGGTCGTCGTTTTTGGTTGTTCACCGGGTGGAGGTT
CAGTCGGTGGCAACAATGGTGATGGGTGTAGACATAAGGATTGGAATAAGGATTTTCAAAGTTTT
GAGGTATTTTTAAGATTTGAGAAATATTTGGACATTTTTAAAATATATATAATTTAATTTTTTTA
ATTTTCAAAATTACCTAAGTACGATATGTGTTATTTAATAACAGAATTAAGTCGATGTTGTAATT
GAAGCACCTAAAAATATAAGGATGAGAACGTTAAGTATTTGGATCGATAAAAAATAATTTAAATA
CTTAAATAAAAAATATAATTTAGATATTTATTTTATATTATGCATATTAAGAACGAAATTCTTTT
TTATTAATCTTTTTAAAAAAAAAGTTTTTTAAAAAAACACTTTTATGCGGATGTAAAATGATTTT
CTGATATATATAATAACATTTTGTATCAAGCATGGCTATAGTAACCTTCGATCACCCTTGACATC
TTTTTTGTCGGTTGTTGTTGCTCTCGTTGTCGGAAGTATCGTCGGGTCACTTAG
Found at i:17126 original size:28 final size:29
Alignment explanation
Indices: 17093--17148 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
17083 GTGAATCGTG
* * *
17093 TTTTTATTTAAATGGAAACAA-TATAAAT
1 TTTTTATCTAAACGAAAACAATTATAAAT
17121 TTTTTATCTAAACGAAAACAATTATAAA
1 TTTTTATCTAAACGAAAACAATTATAAA
17149 CGTTGTTGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 18 0.75
29 6 0.25
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.39
Consensus pattern (29 bp):
TTTTTATCTAAACGAAAACAATTATAAAT
Found at i:17714 original size:44 final size:43
Alignment explanation
Indices: 17562--17808 Score: 215
Period size: 42 Copynumber: 5.8 Consensus size: 43
17552 ATTAAGACTT
* * * * *
17562 CTAATTTTTT-AATATTA-TTTTTACTTTTACAATTGAAACTCA
1 CTAATTTTTTCAATCTCACTTTTTACCTTTATAATTGAAGC-CA
* * * *
17604 -TAATTTTTGT-AATATTACCTTTTATCTTTATAATTG-AGCCA
1 CTAATTTTT-TCAATCTCACTTTTTACCTTTATAATTGAAGCCA
** *
17645 CTAATTTTTGAAATCTCACTTTTTACATTTATAATTGAAGTCCA
1 CTAATTTTTTCAATCTCACTTTTTACCTTTATAATTGAAG-CCA
* * *
17689 C-AATTTTTTTCAATCGCACATTTTACCTTTATAAATGAGAGCC-
1 CTAA-TTTTTTCAATCTCACTTTTTACCTTTATAATTGA-AGCCA
* *
17732 CTAA-TTTTTCAATCTCACTTTTTGCCTTTATAATTGAAGCCC
1 CTAATTTTTTCAATCTCACTTTTTACCTTTATAATTGAAGCCA
17774 CTAATTTTTTCTAATCTCA-TTTTCTACCTTTATAA
1 CTAATTTTTTC-AATCTCACTTTT-TACCTTTATAA
17809 CTGACGTTGT
Statistics
Matches: 170, Mismatches: 22, Indels: 24
0.79 0.10 0.11
Matches are distributed among these distances:
41 14 0.08
42 72 0.42
43 29 0.17
44 53 0.31
45 2 0.01
ACGTcount: A:0.29, C:0.17, G:0.06, T:0.48
Consensus pattern (43 bp):
CTAATTTTTTCAATCTCACTTTTTACCTTTATAATTGAAGCCA
Found at i:17746 original size:86 final size:86
Alignment explanation
Indices: 17623--17808 Score: 220
Period size: 86 Copynumber: 2.2 Consensus size: 86
17613 TAATATTACC
* *
17623 TTTTATCTTTAT-AATTGAGCCACTAATTTTTGAAATCTCACTTTTTACATTTATAATTGAAGTC
1 TTTTACCTTTATAAATAGAGCCACTAATTTTTGAAATCTCACTTTTTACATTTATAATTGAAG-C
17687 CAC-AATTTTTT-TCAATCGCACA
65 CACTAATTTTTTCT-AATCGCA-A
* * *
17709 TTTTACCTTTATAAATGAGAGCC-CTAATTTTT-CAATCTCACTTTTTGCCTTTATAATTGAAGC
1 TTTTACCTTTATAAAT-AGAGCCACTAATTTTTGAAATCTCACTTTTTACATTTATAATTGAAGC
* * *
17772 CCCTAATTTTTTCTAATCTCAT
65 CACTAATTTTTTCTAATCGCAA
17794 TTTCTACCTTTATAA
1 TTT-TACCTTTATAA
17809 CTGACGTTGT
Statistics
Matches: 87, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
85 6 0.07
86 63 0.72
87 13 0.15
88 5 0.06
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.46
Consensus pattern (86 bp):
TTTTACCTTTATAAATAGAGCCACTAATTTTTGAAATCTCACTTTTTACATTTATAATTGAAGCC
ACTAATTTTTTCTAATCGCAA
Found at i:21786 original size:19 final size:19
Alignment explanation
Indices: 21732--21824 Score: 99
Period size: 19 Copynumber: 5.2 Consensus size: 19
21722 AATAATAATT
*
21732 ATAAAACTTAAAACTAAAA
1 ATAAAACTTAAAACTAACA
21751 ATAAAACTTAAAACTAACA
1 ATAAAACTTAAAACTAACA
**
21770 ATAAAACTTAACCCTAAC-
1 ATAAAACTTAAAACTAACA
21788 ----AA-TTAAAACTAACA
1 ATAAAACTTAAAACTAACA
**
21802 ATAAAACTTAACCCTAACA
1 ATAAAACTTAAAACTAACA
21821 ATAA
1 ATAA
21825 TCCTAGATTT
Statistics
Matches: 61, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
13 9 0.15
14 2 0.03
18 2 0.03
19 48 0.79
ACGTcount: A:0.60, C:0.18, G:0.00, T:0.22
Consensus pattern (19 bp):
ATAAAACTTAAAACTAACA
Found at i:21796 original size:32 final size:32
Alignment explanation
Indices: 21758--21822 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
21748 AAAATAAAAC
21758 TTAAAACTAACAATAAAACTTAACCCTAACAA
1 TTAAAACTAACAATAAAACTTAACCCTAACAA
21790 TTAAAACTAACAATAAAACTTAACCCTAACAA
1 TTAAAACTAACAATAAAACTTAACCCTAACAA
21822 T
1 T
21823 AATCCTAGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.55, C:0.22, G:0.00, T:0.23
Consensus pattern (32 bp):
TTAAAACTAACAATAAAACTTAACCCTAACAA
Found at i:22129 original size:28 final size:29
Alignment explanation
Indices: 22093--22249 Score: 112
Period size: 29 Copynumber: 5.3 Consensus size: 29
22083 AATATATAAT
* *
22093 TATATTAAATTATGATCAAATTAATAGAA
1 TATACTAAATTAAGATCAAATTAATAGAA
* *
22122 TATA-TAAATAATAAGAACTAAA-TATATA-AT
1 TATACTAAAT--TAAGATC-AAATTA-ATAGAA
22152 TATACTAAATTAAGATCAAATTAATAGAA
1 TATACTAAATTAAGATCAAATTAATAGAA
* * * *
22181 TGTA-TAAAATAATAAAAACTAAA-TATATA-AT
1 TATACT-AAAT--TAAGATC-AAATTA-ATAGAA
22212 TATACTAAATTAAGATCAAATTAATAGAA
1 TATACTAAATTAAGATCAAATTAATAGAA
22241 TATA-TAAAT
1 TATACTAAAT
22250 AATAAAAACT
Statistics
Matches: 100, Mismatches: 13, Indels: 31
0.69 0.09 0.22
Matches are distributed among these distances:
28 23 0.23
29 32 0.32
30 12 0.12
31 26 0.26
32 7 0.07
ACGTcount: A:0.57, C:0.04, G:0.05, T:0.34
Consensus pattern (29 bp):
TATACTAAATTAAGATCAAATTAATAGAA
Found at i:22217 original size:60 final size:59
Alignment explanation
Indices: 22067--22281 Score: 376
Period size: 59 Copynumber: 3.6 Consensus size: 59
22057 AAAAGCTTAC
* * *
22067 TAAATAATAAGAACTAAATATATAATTATATTAAATTATGATCAAATTAATAGAATATA
1 TAAATAATAAAAACTAAATATATAATTATACTAAATTAAGATCAAATTAATAGAATATA
* *
22126 TAAATAATAAGAACTAAATATATAATTATACTAAATTAAGATCAAATTAATAGAATGTA
1 TAAATAATAAAAACTAAATATATAATTATACTAAATTAAGATCAAATTAATAGAATATA
22185 TAAAATAATAAAAACTAAATATATAATTATACTAAATTAAGATCAAATTAATAGAATATA
1 T-AAATAATAAAAACTAAATATATAATTATACTAAATTAAGATCAAATTAATAGAATATA
22245 TAAATAATAAAAACTAAATATATAATTATACTAAATT
1 TAAATAATAAAAACTAAATATATAATTATACTAAATT
22282 TTTAACTACC
Statistics
Matches: 150, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
59 93 0.62
60 57 0.38
ACGTcount: A:0.58, C:0.05, G:0.04, T:0.33
Consensus pattern (59 bp):
TAAATAATAAAAACTAAATATATAATTATACTAAATTAAGATCAAATTAATAGAATATA
Found at i:23133 original size:2 final size:2
Alignment explanation
Indices: 23126--23158 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
23116 TTATCTATCT
23126 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 T
23159 TGTTAGGATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:26458 original size:29 final size:29
Alignment explanation
Indices: 26423--26480 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
26413 AGTGACGTGA
26423 GGATTATTCATGAATGTAAATTACGTATT
1 GGATTATTCATGAATGTAAATTACGTATT
*
26452 GGATTATTCATGAATGTAAATTATGTATT
1 GGATTATTCATGAATGTAAATTACGTATT
26481 TTTATTCAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.43
Consensus pattern (29 bp):
GGATTATTCATGAATGTAAATTACGTATT
Found at i:28809 original size:50 final size:51
Alignment explanation
Indices: 28729--28828 Score: 157
Period size: 50 Copynumber: 2.0 Consensus size: 51
28719 TGCTAAACTC
* * *
28729 TGTCTTATGCTTATTTTATATATCGAA-TTTTGATTTCTAAACGATGTCGG
1 TGTCGTATGCTTATTTTATATATAGAATTTTTGACTTCTAAACGATGTCGG
*
28779 TGTCGTATGCTTATTTTGTATATAGAATTTTTGACTTCTAAACGATGTCG
1 TGTCGTATGCTTATTTTATATATAGAATTTTTGACTTCTAAACGATGTCG
28829 TCTGGATATT
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
50 24 0.53
51 21 0.47
ACGTcount: A:0.24, C:0.12, G:0.17, T:0.47
Consensus pattern (51 bp):
TGTCGTATGCTTATTTTATATATAGAATTTTTGACTTCTAAACGATGTCGG
Found at i:35303 original size:23 final size:23
Alignment explanation
Indices: 35277--35330 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
35267 AAACGTGCCG
35277 CAAAGACAGAAATAAATATGACA
1 CAAAGACAGAAATAAATATGACA
* * *
35300 CAAAGACAGAGATAAATGTGTCA
1 CAAAGACAGAAATAAATATGACA
35323 CAAAGACA
1 CAAAGACA
35331 AACATGTTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.13
Consensus pattern (23 bp):
CAAAGACAGAAATAAATATGACA
Found at i:41746 original size:15 final size:15
Alignment explanation
Indices: 41728--41758 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
41718 AAATTCTAAA
41728 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
41743 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
41758 T
1 T
41759 CATCGATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:51483 original size:28 final size:28
Alignment explanation
Indices: 51434--51490 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
51424 CTCTTTGTAT
*
51434 ACATTATGTCATCGAATCAATGCTTGAA
1 ACATTATGTCACCGAATCAATGCTTGAA
* * *
51462 ACATTATGTCGCCGAGTTAATGCTTGAA
1 ACATTATGTCACCGAATCAATGCTTGAA
51490 A
1 A
51491 GGAACGGTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Consensus pattern (28 bp):
ACATTATGTCACCGAATCAATGCTTGAA
Found at i:54110 original size:16 final size:16
Alignment explanation
Indices: 54082--54115 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
54072 AATATTGATT
54082 TTATTTGATAACAAAA
1 TTATTTGATAACAAAA
54098 TTATTCTGA-AACAAAA
1 TTATT-TGATAACAAAA
54114 TT
1 TT
54116 GAGAATAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.82
17 3 0.18
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (16 bp):
TTATTTGATAACAAAA
Found at i:54655 original size:45 final size:45
Alignment explanation
Indices: 54507--54670 Score: 201
Period size: 45 Copynumber: 3.7 Consensus size: 45
54497 ATTCAAGGTT
*
54507 TTTA-ATTATTGGGTTGCCAAAAA-TAAAATCAAAGGATTAGTTCA
1 TTTAGATTATTGGATTG-CAAAAATTAAAATCAAAGGATTAGTTCA
* *
54551 TTTTGATTACTTGG-TTGCAGAAATTAAAAATCAAAGGATTAGTTCA
1 TTTAGATTA-TTGGATTGCAAAAATT-AAAATCAAAGGATTAGTTCA
* * *
54597 TTTAGATTATTGGATTGCAAAAATTATAATTAAAGGATTTGTTCA
1 TTTAGATTATTGGATTGCAAAAATTAAAATCAAAGGATTAGTTCA
* *
54642 TTTCGATTGTTGGATTGCAAAAA-TAAAAT
1 TTTAGATTATTGGATTGCAAAAATTAAAAT
54671 ATGTTTTGGG
Statistics
Matches: 105, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
44 13 0.12
45 50 0.48
46 42 0.40
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.38
Consensus pattern (45 bp):
TTTAGATTATTGGATTGCAAAAATTAAAATCAAAGGATTAGTTCA
Found at i:54936 original size:58 final size:57
Alignment explanation
Indices: 54781--54950 Score: 196
Period size: 58 Copynumber: 2.9 Consensus size: 57
54771 ATCTTGCGTA
* * * * *
54781 GATTCTAACTTCATAAGAAAAATAAATCGTTTAATTTATTTTCTTGAGAATATTAAAT
1 GATTCTAACTTTATAAGTAAAATAAATAG-TTGATTTATTTTCTTGAGAATCTTAAAT
* * *
54839 GATTCTAACTTTATAAGTAAACTAAGTAGTTGAGCTTATTTTCTTGAGAATCTTAAAT
1 GATTCTAACTTTATAAGTAAAATAAATAGTTGA-TTTATTTTCTTGAGAATCTTAAAT
* * * * *
54897 GATTCTAACTTTGTACGTAAAATAAATATTTGGATTTATTTACTTAAGAATCTT
1 GATTCTAACTTTATAAGTAAAATAAATAGTT-GATTTATTTTCTTGAGAATCTT
54951 GAATAAAGAG
Statistics
Matches: 94, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
57 3 0.03
58 89 0.95
59 2 0.02
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.42
Consensus pattern (57 bp):
GATTCTAACTTTATAAGTAAAATAAATAGTTGATTTATTTTCTTGAGAATCTTAAAT
Found at i:55047 original size:38 final size:38
Alignment explanation
Indices: 55005--55118 Score: 122
Period size: 39 Copynumber: 2.9 Consensus size: 38
54995 AATGATTCAA
55005 GTTTTTAAAAGGAAATAAATCAGTGAATTTATTTTCCT
1 GTTTTTAAAAGGAAATAAATCAGTGAATTTATTTTCCT
* * * *
55043 GTTTTATAAAATGAAATAAAT-TGTTGGATGTATTTTCCT
1 GTTTT-TAAAAGGAAATAAATCAG-TGAATTTATTTTCCT
* * * *
55082 ATTTAGTAAAAGAAAATAAATCATTGAATTTATTTTC
1 GTTT-TTAAAAGGAAATAAATCAGTGAATTTATTTTC
55119 ATAAGAATCT
Statistics
Matches: 60, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
38 6 0.10
39 54 0.90
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.43
Consensus pattern (38 bp):
GTTTTTAAAAGGAAATAAATCAGTGAATTTATTTTCCT
Found at i:55198 original size:42 final size:42
Alignment explanation
Indices: 55136--55257 Score: 155
Period size: 39 Copynumber: 3.0 Consensus size: 42
55126 TCTTATATGA
*
55136 TTCTGTTTTGTAAAAGGAAATAAATTGTTAGATTTTATTTTT
1 TTCTGTTTTGTAAAAGGAAATAAATTGTTAGAATTTATTTTT
*
55178 TTTTGTTTTGTAAAAGGAAAT-AATTCGTT-GAATTTA--TTT
1 TTCTGTTTTGTAAAAGGAAATAAATT-GTTAGAATTTATTTTT
* * *
55217 TTCTATTTTGTAAAAGAAAATAAATTATTA-AATTTATTTTT
1 TTCTGTTTTGTAAAAGGAAATAAATTGTTAGAATTTATTTTT
55258 CTAAGAATCT
Statistics
Matches: 69, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
39 29 0.42
40 4 0.06
41 13 0.19
42 23 0.33
ACGTcount: A:0.34, C:0.02, G:0.11, T:0.52
Consensus pattern (42 bp):
TTCTGTTTTGTAAAAGGAAATAAATTGTTAGAATTTATTTTT
Found at i:55239 original size:139 final size:135
Alignment explanation
Indices: 54961--55495 Score: 499
Period size: 139 Copynumber: 3.9 Consensus size: 135
54951 GAATAAAGAG
* * * *
54961 ATAAATTATTGAATTTATTTTCTTAGAAATCTTAAATGATTCAAGTTTT-TAAAAGGAAATAAAT
1 ATAAATCATTGAATTTATTTTCTAAG-AATCTTATATGATTC-TGTTTTGTAAAAGGAAATAAAT
* * * * * * * *
55025 CAGTGA-ATTTATTTTCCTGTTTTATAAAATG-AAATAAATTGTTGGATGTATTTTCCTATTTAG
64 C-GTTAGATTTATTTTTCTGTTTTGTAAAA-GAAAATAAATCGTTGAATTTATTTTTCTATTTTG
55088 TAAAAGAAA
127 TAAAAGAAA
*
55097 ATAAATCATTGAATTTATTTTCATAAGAATCTTATATGATTCTGTTTTGTAAAAGGAAATAAATT
1 ATAAATCATTGAATTTATTTTC-TAAGAATCTTATATGATTCTGTTTTGTAAAAGGAAATAAATC
* * *
55162 GTTAGATTTTATTTTTTTTTGTTTTGTAAAAGGAAATAATTCGTTGAATTTATTTTTCTATTTTG
65 GTTAGA-TTTA--TTTTTCTGTTTTGTAAAAGAAAATAAATCGTTGAATTTATTTTTCTATTTTG
55227 TAAAAGAAA
127 TAAAAGAAA
* * * * * *
55236 ATAAATTATTAAATTTATTTTTCTAAGAATCTTACATAATTCTAG-TTTGTACAAGAAAAATAAA
1 ATAAATCATTGAATTTA-TTTTCTAAGAATCTTATATGATTCT-GTTTTGTAAAAG-GAAATAAA
* * * * * * *
55300 TCATTGGATTTATTTTTCTATTTCGTAAAAGAAAAATAAACCATTGGATTT-TGTTTTCCTATTT
63 TCGTTAGATTTATTTTTCTGTTTTGTAAAAG-AAAATAAATCGTTGAATTTAT-TTTT-CTATTT
* *
55364 TATAAAATAAA
125 TGTAAAAGAAA
* * * * * * *
55375 ATAACTCGTTCAATTTATTTCCTTGATAATCTTATATGATTCT-TAGTTGTAAAAGGAAATAAAT
1 ATAAATCATTGAATTTATTTTC-TAAGAATCTTATATGATTCTGT-TTTGTAAAAGGAAATAAAT
** *
55439 CGTTAGATTTATTTCCCTATGTTT-TAAAAGAAAATAAATCGTTGAATTTATTTTTCT
64 CGTTAGATTTATTTTTCTGT-TTTGTAAAAGAAAATAAATCGTTGAATTTATTTTTCT
55496 TGGAAATTAA
Statistics
Matches: 327, Mismatches: 54, Indels: 36
0.78 0.13 0.09
Matches are distributed among these distances:
135 8 0.02
136 53 0.16
137 44 0.13
138 54 0.17
139 150 0.46
140 18 0.06
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.45
Consensus pattern (135 bp):
ATAAATCATTGAATTTATTTTCTAAGAATCTTATATGATTCTGTTTTGTAAAAGGAAATAAATCG
TTAGATTTATTTTTCTGTTTTGTAAAAGAAAATAAATCGTTGAATTTATTTTTCTATTTTGTAAA
AGAAA
Found at i:55332 original size:40 final size:39
Alignment explanation
Indices: 55275--55363 Score: 117
Period size: 40 Copynumber: 2.2 Consensus size: 39
55265 TCTTACATAA
* *
55275 TTCTAGTTTGTACAAGAAAAATAAATCATTGGATTTAT-TT
1 TTCTA-TTTGTAAAAGAAAAATAAACCATTGGATTT-TGTT
55315 TTCTATTTCGTAAAAGAAAAATAAACCATTGGATTTTGTT
1 TTCTATTT-GTAAAAGAAAAATAAACCATTGGATTTTGTT
55355 TTCCTATTT
1 TT-CTATTT
55364 TATAAAATAA
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
39 4 0.09
40 34 0.77
41 6 0.14
ACGTcount: A:0.35, C:0.10, G:0.11, T:0.44
Consensus pattern (39 bp):
TTCTATTTGTAAAAGAAAAATAAACCATTGGATTTTGTT
Found at i:55378 original size:40 final size:40
Alignment explanation
Indices: 55288--55375 Score: 115
Period size: 40 Copynumber: 2.2 Consensus size: 40
55278 TAGTTTGTAC
* *
55288 AAGAAAAATAAATCATTGGATTTATTTTTCTATTTCGTAA
1 AAGAAAAATAAACCATTGGATTTATTTTTCTATTTCATAA
*
55328 AAGAAAAATAAACCATTGGATTT-TGTTTTCCTATTTTATAA
1 AAGAAAAATAAACCATTGGATTTAT-TTTT-CTATTTCATAA
*
55369 AATAAAA
1 AAGAAAA
55376 TAACTCGTTC
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
39 1 0.02
40 26 0.62
41 15 0.36
ACGTcount: A:0.43, C:0.08, G:0.09, T:0.40
Consensus pattern (40 bp):
AAGAAAAATAAACCATTGGATTTATTTTTCTATTTCATAA
Found at i:61286 original size:23 final size:23
Alignment explanation
Indices: 61217--61309 Score: 75
Period size: 23 Copynumber: 4.1 Consensus size: 23
61207 GGTTCTACGC
* *
61217 GGTCCTTCGGGA-TAATCTATAT
1 GGTCCTTCGGGACAAATCTATGT
* ** *
61239 GGTCATTCGGGACATTTCTACGT
1 GGTCCTTCGGGACAAATCTATGT
*
61262 GGTCCTTCGGGACAAACCTATGT
1 GGTCCTTCGGGACAAATCTATGT
*
61285 GG-CACTTCGGTG-CAATTCTATGT
1 GGTC-CTTCGG-GACAAATCTATGT
61308 GG
1 GG
61310 CACTTAGGTG
Statistics
Matches: 55, Mismatches: 13, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
22 12 0.22
23 42 0.76
24 1 0.02
ACGTcount: A:0.19, C:0.22, G:0.27, T:0.32
Consensus pattern (23 bp):
GGTCCTTCGGGACAAATCTATGT
Found at i:61310 original size:23 final size:23
Alignment explanation
Indices: 61274--61330 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
61264 TCCTTCGGGA
* *
61274 CAAACCTATGTGGCACTTCGGTG
1 CAAATCTATGTGGCACTTAGGTG
*
61297 CAATTCTATGTGGCACTTAGGTG
1 CAAATCTATGTGGCACTTAGGTG
61320 CAAAT-TATGTG
1 CAAATCTATGTG
61331 AGATGTGGTG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 6 0.20
23 24 0.80
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.32
Consensus pattern (23 bp):
CAAATCTATGTGGCACTTAGGTG
Found at i:61502 original size:17 final size:17
Alignment explanation
Indices: 61480--61513 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
61470 AAAATGATTA
*
61480 TAAAAGTGTACATTGTT
1 TAAAAGTCTACATTGTT
*
61497 TAAAAGTCTATATTGTT
1 TAAAAGTCTACATTGTT
61514 ATTGACATGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (17 bp):
TAAAAGTCTACATTGTT
Found at i:67096 original size:28 final size:29
Alignment explanation
Indices: 67064--67118 Score: 103
Period size: 28 Copynumber: 1.9 Consensus size: 29
67054 TCTCATTTGG
67064 AAAGAAATTTATTCTATGT-GCAAAGATT
1 AAAGAAATTTATTCTATGTAGCAAAGATT
67092 AAAGAAATTTATTCTATGTAGCAAAGA
1 AAAGAAATTTATTCTATGTAGCAAAGA
67119 AATTTATTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 19 0.73
29 7 0.27
ACGTcount: A:0.45, C:0.07, G:0.15, T:0.33
Consensus pattern (29 bp):
AAAGAAATTTATTCTATGTAGCAAAGATT
Found at i:67973 original size:17 final size:18
Alignment explanation
Indices: 67951--67987 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
67941 ATTTTTATTG
67951 TTCGAA-CTCTCCCTTTT
1 TTCGAATCTCTCCCTTTT
67968 TTCGAATTCTCTCCCTTTT
1 TTCGAA-TCTCTCCCTTTT
67987 T
1 T
67988 ATGGTTACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
19 12 0.67
ACGTcount: A:0.11, C:0.32, G:0.05, T:0.51
Consensus pattern (18 bp):
TTCGAATCTCTCCCTTTT
Found at i:69880 original size:21 final size:21
Alignment explanation
Indices: 69827--69881 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
69817 TAACTATTCA
*
69827 TTTGTTTCAAACTAGTTCTTT
1 TTTGTTTCAAATTAGTTCTTT
69848 TTTGTTTCAAATTAGTTCTTT
1 TTTGTTTCAAATTAGTTCTTT
69869 TTTGTTTCAAATT
1 TTTGTTTCAAATT
69882 TAACGACCGC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.20, C:0.11, G:0.09, T:0.60
Consensus pattern (21 bp):
TTTGTTTCAAATTAGTTCTTT
Found at i:74702 original size:4 final size:4
Alignment explanation
Indices: 74693--74720 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
74683 ACCATCAATT
74693 TTCA TTCA TTCA TTCA TTCA TTCA TTCA
1 TTCA TTCA TTCA TTCA TTCA TTCA TTCA
74721 ATGGCTGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (4 bp):
TTCA
Found at i:84017 original size:55 final size:55
Alignment explanation
Indices: 83952--84058 Score: 178
Period size: 55 Copynumber: 1.9 Consensus size: 55
83942 GAGTTTACTT
* * *
83952 GATGATGTGGTAATTACAAAAAAAATAATTATATAATTTTAATTTGAAGTAACCA
1 GATGACGTGGTAATAACAAAAAAAATAAATATATAATTTTAATTTGAAGTAACCA
*
84007 GATGACGTGGTAATAACGAAAAAAATAAATATATAATTTTAATTTGAAGTAA
1 GATGACGTGGTAATAACAAAAAAAATAAATATATAATTTTAATTTGAAGTAA
84059 ACTATGATAT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.49, C:0.05, G:0.14, T:0.33
Consensus pattern (55 bp):
GATGACGTGGTAATAACAAAAAAAATAAATATATAATTTTAATTTGAAGTAACCA
Found at i:85410 original size:51 final size:51
Alignment explanation
Indices: 85304--85413 Score: 141
Period size: 51 Copynumber: 2.2 Consensus size: 51
85294 GAATTGAAGG
* * * **
85304 TGTAAACACTGTGTACACTGATTTTGAAGAGGAAATTGCTTGAACTGAAGG
1 TGTAAACACTGTGGACACTAATTTTGAAGAGGAAATTGCTTGAACTAAAAC
* *
85355 TGTAAACACTGTGGATACTAATTTTGAAGAGGAAATTG-TTGGAATTAAAAC
1 TGTAAACACTGTGGACACTAATTTTGAAGAGGAAATTGCTT-GAACTAAAAC
85406 TGTAAACA
1 TGTAAACA
85414 ATGTAGTCTG
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
50 2 0.04
51 49 0.96
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (51 bp):
TGTAAACACTGTGGACACTAATTTTGAAGAGGAAATTGCTTGAACTAAAAC
Found at i:87131 original size:40 final size:40
Alignment explanation
Indices: 87040--87133 Score: 136
Period size: 40 Copynumber: 2.4 Consensus size: 40
87030 TAAAAATAAT
87040 TATATATATATATATATAATATTAATAAATTTAATTTAAA
1 TATATATATATATATATAATATTAATAAATTTAATTTAAA
* * * *
87080 T-TAAAAAATATATATATAATATTTATATATTTAATTTAAA
1 TAT-ATATATATATATATAATATTAATAAATTTAATTTAAA
87120 TATATATATATATA
1 TATATATATATATA
87134 CCTGGCCTGA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
39 1 0.02
40 44 0.96
41 1 0.02
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (40 bp):
TATATATATATATATATAATATTAATAAATTTAATTTAAA
Found at i:96673 original size:37 final size:37
Alignment explanation
Indices: 96626--96716 Score: 103
Period size: 37 Copynumber: 2.3 Consensus size: 37
96616 AAAATGTTAG
*
96626 ATAAGAAAAAAATAATGTCAAATAAATGA-AAGGAAAAAAA
1 ATAA-AAAAAAATAA--T-AAATAAATCAGAAGGAAAAAAA
*
96666 ATAAAAAAAAATAATAAATAAATCAGAAGGAAAAATA
1 ATAAAAAAAAATAATAAATAAATCAGAAGGAAAAAAA
96703 ATAATAAAGAAAAT
1 ATAA-AAA-AAAAT
96717 GAAAAGAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
36 9 0.20
37 15 0.33
38 3 0.07
39 15 0.33
40 4 0.09
ACGTcount: A:0.71, C:0.02, G:0.10, T:0.16
Consensus pattern (37 bp):
ATAAAAAAAAATAATAAATAAATCAGAAGGAAAAAAA
Found at i:96725 original size:27 final size:27
Alignment explanation
Indices: 96669--96731 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
96659 AAAAAAAATA
* *
96669 AAAAAAAATAATAAATAAATCAGAAGG
1 AAAAAAAATAATAAAAAAATCAGAAAG
* *
96696 AAAAATAATAATAAAGAAAATGA-AAAG
1 AAAAAAAATAATAAA-AAAATCAGAAAG
*
96723 AAAACAAAT
1 AAAAAAAAT
96732 TAAAATTACG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
27 24 0.83
28 5 0.17
ACGTcount: A:0.73, C:0.03, G:0.10, T:0.14
Consensus pattern (27 bp):
AAAAAAAATAATAAAAAAATCAGAAAG
Found at i:97730 original size:3 final size:3
Alignment explanation
Indices: 97722--97765 Score: 56
Period size: 3 Copynumber: 14.7 Consensus size: 3
97712 AAAATCCTGC
97722 AAT AAT AAT AAT AAT AAT -AT AAT -AT AAT AATT AAT AAT ATAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT A-AT AA
97766 AGAAAATAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
2 4 0.11
3 27 0.73
4 6 0.16
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:97745 original size:17 final size:18
Alignment explanation
Indices: 97722--97765 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
97712 AAAATCCTGC
97722 AATAATAATAATAA-TAAT
1 AATAAT-ATAATAATTAAT
97740 -ATAATATAATAATTAAT
1 AATAATATAATAATTAAT
97757 AAT-ATATAA
1 AATAATATAA
97766 AGAAAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 7 0.29
17 15 0.62
18 2 0.08
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AATAATATAATAATTAAT
Found at i:97748 original size:22 final size:22
Alignment explanation
Indices: 97723--97765 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
97713 AAATCCTGCA
97723 ATAATAA-TAATAATAATATAAT
1 ATAATAATTAATAAT-ATATAAT
97745 ATAATAATTAATAATATATAA
1 ATAATAATTAATAATATATAA
97766 AGAAAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
ATAATAATTAATAATATATAAT
Found at i:97773 original size:23 final size:23
Alignment explanation
Indices: 97725--97775 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
97715 ATCCTGCAAT
* *
97725 AATAA-TAATAATAATATAATAT
1 AATAATTAATAATAATATAAGAA
97747 AATAATTAATAAT-ATATAAAGAA
1 AATAATTAATAATAATAT-AAGAA
97770 AATAAT
1 AATAAT
97776 CTTAGTGACT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 9 0.36
23 16 0.64
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (23 bp):
AATAATTAATAATAATATAAGAA
Found at i:97981 original size:21 final size:21
Alignment explanation
Indices: 97930--97982 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
97920 ATTATGACTA
97930 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
97951 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
97972 TCGCAATGCGA
1 TCGCAATGCGA
97983 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:98037 original size:21 final size:21
Alignment explanation
Indices: 97972--98044 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
97962 TTTTCCCAAT
** *
97972 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTTGGAAAA
* *
97992 TCGAAATGTGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
98013 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
*
98034 TCGCAACGCGA
1 TCGCAATGCGA
98045 TACTGACTAT
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
20 10 0.23
21 34 0.77
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAATTTGGAAAA
Found at i:98057 original size:41 final size:39
Alignment explanation
Indices: 98012--98139 Score: 130
Period size: 41 Copynumber: 3.2 Consensus size: 39
98002 AATTTGGAAA
*
98012 ATCGCAATGCGAATTTGGAAAATCGCAACGCGATACTGACT
1 ATCGCAACGCGAATTT--AAAATCGCAACGCGATACTGACT
**
98053 ATCGCAACGCGATAATACAAAATCGCAACGCGATACTGACT
1 ATCGCAACGCG--AATTTAAAATCGCAACGCGATACTGACT
* * ***
98094 TTCGCAACGCGATACTTACTTTCGCAACGCGATACTGACT
1 ATCGCAACGCGA-ATTTAAAATCGCAACGCGATACTGACT
*
98134 TTCGCA
1 ATCGCA
98140 GCGAGATAAT
Statistics
Matches: 74, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
39 1 0.01
40 27 0.36
41 43 0.58
43 3 0.04
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.23
Consensus pattern (39 bp):
ATCGCAACGCGAATTTAAAATCGCAACGCGATACTGACT
Found at i:98147 original size:20 final size:20
Alignment explanation
Indices: 98034--98139 Score: 142
Period size: 20 Copynumber: 5.2 Consensus size: 20
98024 ATTTGGAAAA
*
98034 TCGCAACGCGATACTGACTA
1 TCGCAACGCGATACTGACTT
* **
98054 TCGCAACGCGATAAT-ACAAAA
1 TCGCAACGCGATACTGAC--TT
98075 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
*
98095 TCGCAACGCGATACTTACTT
1 TCGCAACGCGATACTGACTT
98115 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
98135 TCGCA
1 TCGCA
98140 GCGAGATAAT
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
19 2 0.03
20 57 0.75
21 15 0.20
22 2 0.03
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.23
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:98362 original size:22 final size:22
Alignment explanation
Indices: 98334--98377 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
98324 CACTCTCTCA
98334 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
98356 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
98378 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:98689 original size:20 final size:20
Alignment explanation
Indices: 98640--98698 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
98630 TTTATTCTCT
* **
98640 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
98660 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* *
98680 TGTTGCGATTTTCATTTTC
1 CGTTGCGATTGTCATTTTC
98699 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:98889 original size:25 final size:24
Alignment explanation
Indices: 98835--98889 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
98825 TGTTTATTAT
* *
98835 TGTTTTTGGTATATCTTCATAGTG
1 TGTTTTTGGTATATCTACATAGTA
*
98859 TAGTTTTTGGTATATCTAACTTAGTA
1 T-GTTTTTGGTATATCT-ACATAGTA
98885 TGTTT
1 TGTTT
98890 ATTATTTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 1 0.04
25 19 0.73
26 6 0.23
ACGTcount: A:0.20, C:0.07, G:0.18, T:0.55
Consensus pattern (24 bp):
TGTTTTTGGTATATCTACATAGTA
Found at i:100039 original size:18 final size:18
Alignment explanation
Indices: 100018--100065 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
100008 TCCACTTCGG
100018 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
100036 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
100054 GAGCCATCACCT
1 GAGCCATCACCT
100066 GATTGACCCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:100640 original size:20 final size:18
Alignment explanation
Indices: 100617--100661 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 18
100607 CGCAACACGA
100617 AAATGACTATCGCAATGCGG
1 AAATGA-TATCGCAATGC-G
100637 AAATGGATATCGCAATGCG
1 AAAT-GATATCGCAATGCG
100656 AAATGA
1 AAATGA
100662 AAATAGCAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 2 0.08
19 5 0.21
20 15 0.62
21 2 0.08
ACGTcount: A:0.40, C:0.16, G:0.24, T:0.20
Consensus pattern (18 bp):
AAATGATATCGCAATGCG
Found at i:100727 original size:19 final size:19
Alignment explanation
Indices: 100625--100718 Score: 99
Period size: 19 Copynumber: 5.2 Consensus size: 19
100615 GAAAATGACT
* *
100625 ATCGCAATGCGGAAATGGAT
1 ATCGCAATGC-GAAATGAAA
100645 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
100664 ATAGCAA--C--AA-CAAA
1 ATCGCAATGCGAAATGAAA
100678 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
100697 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
100716 ATC
1 ATC
100719 ACATTGCGAT
Statistics
Matches: 62, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
14 9 0.15
15 2 0.03
16 1 0.02
17 1 0.02
18 2 0.03
19 37 0.60
20 10 0.16
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:100766 original size:20 final size:20
Alignment explanation
Indices: 100732--100786 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
100722 TTGCGATTTT
*
100732 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
100751 CATTTCCGCGTTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
100771 CATTTCCGCGTTGCGA
1 CATTTCCGCGTTGCGA
100787 AAGTAAGTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 5 0.15
20 29 0.85
ACGTcount: A:0.16, C:0.29, G:0.24, T:0.31
Consensus pattern (20 bp):
CATTTCCGCGTTGCGATAGC
Found at i:101187 original size:21 final size:20
Alignment explanation
Indices: 101161--101229 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 20
101151 CTGTCATCCC
101161 TCAAGAGTCCCCTCCAATCGT
1 TCAAGAGTCCCCTCC-ATCGT
* * **
101182 TCAAGAGGCCCCTATCATCCC
1 TCAAGAGTCCCCT-CCATCGT
* *
101203 TCAAGAGTCCCCCCCACCGT
1 TCAAGAGTCCCCTCCATCGT
101223 TCAAGAG
1 TCAAGAG
101230 GCCACTGTCA
Statistics
Matches: 37, Mismatches: 10, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
20 10 0.27
21 26 0.70
22 1 0.03
ACGTcount: A:0.25, C:0.41, G:0.16, T:0.19
Consensus pattern (20 bp):
TCAAGAGTCCCCTCCATCGT
Found at i:101241 original size:41 final size:42
Alignment explanation
Indices: 101151--101241 Score: 139
Period size: 41 Copynumber: 2.2 Consensus size: 42
101141 CCCGACTCAC
* *
101151 CTGTCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCCC
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
* *
101193 CTATCATCCCTCAAGAGTCCCC-CCCACCGTTCAAGAGGCCA
1 CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
101234 CTGTCATC
1 CTGTCATC
101242 GTTGAAGAGG
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 23 0.52
42 21 0.48
ACGTcount: A:0.22, C:0.42, G:0.15, T:0.21
Consensus pattern (42 bp):
CTGTCATCCCTCAAGAGTCCCCTCCAACCGTTCAAGAGGCCA
Found at i:102683 original size:14 final size:14
Alignment explanation
Indices: 102649--102687 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
102639 TTGATTGTTT
102649 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
102663 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
102677 TGTTGATTTGT
1 AATTGATTTGT
102688 TTAATTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:102851 original size:19 final size:19
Alignment explanation
Indices: 102827--102891 Score: 86
Period size: 19 Copynumber: 3.7 Consensus size: 19
102817 GCAACGAGAG
102827 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
102846 AATCGCAATGCGAAATAAA
1 AATCGCAATGCGAAATGAA
102865 AATCGCAA--CG--A-GAA
1 AATCGCAATGCGAAATGAA
102879 AATCGCAATGCGA
1 AATCGCAATGCGA
102892 TTTTCATATC
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
14 10 0.24
15 1 0.02
16 2 0.05
17 2 0.05
19 26 0.63
ACGTcount: A:0.48, C:0.18, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:102935 original size:20 final size:20
Alignment explanation
Indices: 102910--102985 Score: 116
Period size: 20 Copynumber: 3.8 Consensus size: 20
102900 TCGCATTGCG
*
102910 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
*
102930 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
*
102950 ATTTTCGCGTTGCGATAGTC
1 ATTTTCGCGTTGCGATAGCC
*
102970 ATTTTCGCATTGCGAT
1 ATTTTCGCGTTGCGAT
102986 TTCCCCGTTG
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.16, C:0.22, G:0.21, T:0.41
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:102944 original size:34 final size:34
Alignment explanation
Indices: 102900--103001 Score: 96
Period size: 40 Copynumber: 2.8 Consensus size: 34
102890 GATTTTCATA
*
102900 TCGCATTGCGATTTTCTCGTTGCGATAGCCATTTT
1 TCGCATTGCGATTTTCCCGTTGCGATAGCCA-TTT
* * * *
102935 CTCGTTGCGATAGCCATTTTCGCGTTGCGATAGTCATTT
1 -TC---GC-ATTGCGATTTTCCCGTTGCGATAGCCATTT
*
102974 TCGCATTGCGATTTCCCCGTTGCGATAG
1 TCGCATTGCGATTTTCCCGTTGCGATAG
103002 TCAAATGAAT
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
34 20 0.37
35 2 0.04
36 2 0.04
38 2 0.04
39 5 0.09
40 23 0.43
ACGTcount: A:0.15, C:0.25, G:0.23, T:0.38
Consensus pattern (34 bp):
TCGCATTGCGATTTTCCCGTTGCGATAGCCATTT
Found at i:103301 original size:20 final size:20
Alignment explanation
Indices: 103208--103291 Score: 132
Period size: 20 Copynumber: 4.2 Consensus size: 20
103198 ATTGCGATTT
*
103208 TCAGAATCTCGTTGCGAAAG
1 TCAGAATCACGTTGCGAAAG
103228 TCAGAATCACGTTGCGAAAG
1 TCAGAATCACGTTGCGAAAG
**
103248 TCAGAATCGTGTTGCGAAAG
1 TCAGAATCACGTTGCGAAAG
*
103268 TCAGTATCACGTTGCGAAAG
1 TCAGAATCACGTTGCGAAAG
103288 TCAG
1 TCAG
103292 TAGCGCGTTG
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 58 1.00
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (20 bp):
TCAGAATCACGTTGCGAAAG
Found at i:103951 original size:18 final size:18
Alignment explanation
Indices: 103927--103970 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
103917 AACATAATTG
103927 TTAACCATAACACTCAAA
1 TTAACCATAACACTCAAA
* *
103945 TTGACCATAGCACTCAAA
1 TTAACCATAACACTCAAA
103963 TTAACCAT
1 TTAACCAT
103971 TCAATTCTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.43, C:0.27, G:0.05, T:0.25
Consensus pattern (18 bp):
TTAACCATAACACTCAAA
Found at i:104101 original size:19 final size:19
Alignment explanation
Indices: 104077--104125 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
104067 CAAAATAATC
*
104077 CAATTTCACATTCTAACAT
1 CAATTTCACATTCAAACAT
*
104096 CAATTTCAACACTCAAACAT
1 CAATTTC-ACATTCAAACAT
*
104116 TAATTT-ACAT
1 CAATTTCACAT
104126 CATAGTACAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 3 0.12
19 7 0.28
20 15 0.60
ACGTcount: A:0.41, C:0.24, G:0.00, T:0.35
Consensus pattern (19 bp):
CAATTTCACATTCAAACAT
Found at i:106399 original size:22 final size:20
Alignment explanation
Indices: 106356--106410 Score: 56
Period size: 22 Copynumber: 2.6 Consensus size: 20
106346 CATCCAAATG
* *
106356 AACTATGCAAATGTCCATCA
1 AACTATGCAAATATCCAACA
106376 AACTATGCATCAATATCCAACA
1 AACTATGCA--AATATCCAACA
* *
106398 AAATATGTAAATA
1 AACTATGCAAATA
106411 GTCTCAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 13 0.45
22 16 0.55
ACGTcount: A:0.47, C:0.20, G:0.07, T:0.25
Consensus pattern (20 bp):
AACTATGCAAATATCCAACA
Found at i:111397 original size:37 final size:37
Alignment explanation
Indices: 111344--111447 Score: 147
Period size: 36 Copynumber: 2.8 Consensus size: 37
111334 TATTTTCGTC
111344 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
111381 TTGCTAGGATTCAAACTCCT-AAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
111417 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
111448 CCACAAGCAC
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
36 31 0.53
37 27 0.47
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:115954 original size:20 final size:21
Alignment explanation
Indices: 115921--115960 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
115911 AAAGCGCAAA
*
115921 AACAAAAAAGAAAAA-AAAAG
1 AACAAAAAACAAAAAGAAAAG
*
115941 AACAAAAATCAAAAAGAAAA
1 AACAAAAAACAAAAAGAAAA
115961 AGGGACAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.82, C:0.07, G:0.07, T:0.03
Consensus pattern (21 bp):
AACAAAAAACAAAAAGAAAAG
Found at i:116638 original size:22 final size:22
Alignment explanation
Indices: 116564--116640 Score: 127
Period size: 22 Copynumber: 3.5 Consensus size: 22
116554 GCTACCTCAT
*
116564 CAAACCGTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
* *
116586 CAAACCTATGAGCATCACATGC
1 CAAACCTTTGAGCATCAAATGC
116608 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
116630 CAAACCTTTGA
1 CAAACCTTTGA
116641 CCAAACATAA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.36, C:0.29, G:0.14, T:0.21
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:117671 original size:106 final size:106
Alignment explanation
Indices: 117486--118403 Score: 1435
Period size: 106 Copynumber: 8.7 Consensus size: 106
117476 ACATAATTTT
* * * * * *
117486 AACTTCACAACGAAGGGACGGCTGGTTGTCAA-CAACAATTTTCCAATTTCGGAGCCAATTTTAA
1 AACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAA
*
117550 CTTCATAGCGAAGGATATTGGACTCCAGACAACGCAAGTTC
66 CTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTC
* * *
117591 AACTTCACGACGAAGAGACTGCTGGTTGTCAATAAACAATTTCCCAATTTCAGATCCAATTTCAA
1 AACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAA
* * *
117656 CTTCACAACGAAGGATATTAGACTCCAGACAACACAAGTTC
66 CTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTC
* *
117697 AACTTCACGACGAAGGGACCGCTGGTTGTTAATAAACAACTTT-CCAATTTCAGGGCCAATTTCA
1 AACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAA-TTTCCCAATTTCAGAGCCAATTTCA
*
117761 ACTTCACAGTGAAGGATATTGGACTCCAGACAACGCAAGTTC
65 ACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTC
* * * * *
117803 AACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAACTTCTCAATTTCAGGGCCAATTTCAA
1 AACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAA
117868 CTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTC
66 CTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTC
* * * *
117909 AACTTCACGACGAAGAGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAA
1 AACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAA
* *
117974 CTTCAAAACGAAGGATATTGGACTCCAGACAACGCAAGTTC
66 CTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTC
118015 AACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAA
1 AACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAA
118080 CTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTC
66 CTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTC
*
118121 AACTTCACGATGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAA
1 AACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAA
* *
118186 CTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTC
66 CTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTC
118227 AACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAA
1 AACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAA
* * * *
118292 CTTCATAGCAAAGGATATTGGACTCGAGACAACACAAGTTC
66 CTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTC
* * * * *** *
118333 AACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCTGGTTCCAGAGCCAATTTCAA
1 AACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAA
118398 CTTCAC
66 CTTCAC
118404 GATGGAGGAT
Statistics
Matches: 755, Mismatches: 55, Indels: 5
0.93 0.07 0.01
Matches are distributed among these distances:
105 31 0.04
106 721 0.95
107 3 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.24
Consensus pattern (106 bp):
AACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAA
CTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTC
Found at i:119173 original size:37 final size:37
Alignment explanation
Indices: 119120--119223 Score: 138
Period size: 36 Copynumber: 2.8 Consensus size: 37
119110 CCTTTTTATC
*
119120 CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
119157 TTGCTAGGATTCAAACTCCT-AAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
119193 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
119224 CCACAAGAAC
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
36 30 0.53
37 27 0.47
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:127241 original size:5 final size:5
Alignment explanation
Indices: 127230--127508 Score: 524
Period size: 5 Copynumber: 56.0 Consensus size: 5
127220 ATTCAGAGAT
* * *
127230 CAACA TAACA TAACA TAACA CAACA CAACA CAACA CAACA CAACA CAACA
1 CAACA CAACA CAACA CAACA CAACA CAACA CAACA CAACA CAACA CAACA
127280 CAACA CAACA CAACA CAACA CAACA CAACA CAACA CAACA CAACA CAACA
1 CAACA CAACA CAACA CAACA CAACA CAACA CAACA CAACA CAACA CAACA
127330 CAACA CAACA CAACA CAACA CAACA CAACA CAACA CAACA CAACA CAACA
1 CAACA CAACA CAACA CAACA CAACA CAACA CAACA CAACA CAACA CAACA
127380 CAACA CAACA CAACA CAACA CAACA CAACA CAA-A CAACA CAACA CAACA
1 CAACA CAACA CAACA CAACA CAACA CAACA CAACA CAACA CAACA CAACA
127429 CAACA CAACA CAACA CAACA CAACA CAACA CAACA CAACA CAACA CAACA
1 CAACA CAACA CAACA CAACA CAACA CAACA CAACA CAACA CAACA CAACA
127479 CAACA CAACA CAACA CAACA CAACA CAACA
1 CAACA CAACA CAACA CAACA CAACA CAACA
127509 GGAAAATATC
Statistics
Matches: 271, Mismatches: 2, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
4 4 0.01
5 267 0.99
ACGTcount: A:0.60, C:0.39, G:0.00, T:0.01
Consensus pattern (5 bp):
CAACA
Found at i:131448 original size:3 final size:3
Alignment explanation
Indices: 131427--131471 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
131417 TCTTTTCTGC
* *
131427 ATT ATC ATT ATC A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
131472 GAGAAAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
2 1 0.03
3 36 0.97
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:131708 original size:20 final size:21
Alignment explanation
Indices: 131683--131730 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
131673 CCCAATTCGT
*
131683 AATGCGAA-TAAGTAAATCGC
1 AATGCGAATTAAGAAAATCGC
**
131703 AATGCGAATTTGGAAAATCGC
1 AATGCGAATTAAGAAAATCGC
131724 AATGCGA
1 AATGCGA
131731 TACTAACTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.21
Consensus pattern (21 bp):
AATGCGAATTAAGAAAATCGC
Found at i:131730 original size:41 final size:41
Alignment explanation
Indices: 131683--131895 Score: 123
Period size: 41 Copynumber: 5.2 Consensus size: 41
131673 CCCAATTCGT
*
131683 AATGCGAATAAGTAAATCGCAATGCGAATTTGGAAAATCGC
1 AATGCGAATAAGTAAATCGCAATGCGAATTTCGAAAATCGC
* * * * *
131724 AATGCG-AT-ACTAACTATCGCATTGCGATTTTCCAAATTCGC
1 AATGCGAATAAGTAA--ATCGCAATGCGAATTTCGAAAATCGC
* * * * ** * *
131765 ATTGCGATTTACGT-ATTCGCGTTGCGATTTTC-ATAATTCGC
1 AATGCGA-ATAAGTAAATCGCAATGCGAATTTCGA-AAATCGC
* * * ** *
131806 ATTGCAAATACGTAAATCGCAATGCG-ATTAAGTAAATCGC
1 AATGCGAATAAGTAAATCGCAATGCGAATTTCGAAAATCGC
* * * *
131846 AATGCGAATTAGGAAAATCGCAATGCGAA-TACGTAAATCGC
1 AATGCGAA-TAAGTAAATCGCAATGCGAATTTCGAAAATCGC
131887 AATGCGAAT
1 AATGCGAAT
131896 CTTACTATCG
Statistics
Matches: 135, Mismatches: 27, Indels: 21
0.74 0.15 0.11
Matches are distributed among these distances:
39 4 0.03
40 23 0.17
41 104 0.77
42 1 0.01
43 2 0.01
44 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (41 bp):
AATGCGAATAAGTAAATCGCAATGCGAATTTCGAAAATCGC
Found at i:131766 original size:21 final size:20
Alignment explanation
Indices: 131740--131810 Score: 88
Period size: 21 Copynumber: 3.5 Consensus size: 20
131730 ATACTAACTA
131740 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTT-CAAAT
* **
131761 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTTCAAAT
*
131781 TCGCGTTGCGATTTTCATAAT
1 TCGCATTGCGATTTTCA-AAT
131802 TCGCATTGC
1 TCGCATTGC
131811 AAATACGTAA
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 17 0.41
21 24 0.59
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTTCAAAT
Found at i:131784 original size:20 final size:20
Alignment explanation
Indices: 131740--131810 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
131730 ATACTAACTA
* *
131740 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGA-TTTACATAT
*
131761 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACATAT
* *
131781 TCGCGTTGCGATTTTCATAAT
1 TCGCATTGCGATTTACAT-AT
131802 TCGCATTGC
1 TCGCATTGC
131811 AAATACGTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 21 0.50
21 21 0.50
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:131894 original size:20 final size:20
Alignment explanation
Indices: 131802--131913 Score: 127
Period size: 20 Copynumber: 5.5 Consensus size: 20
131792 TTTTCATAAT
* *
131802 TCGCATTGCAAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
131822 TCGCAATGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
* *
131842 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
131863 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
131883 TCGCAATGCGAAT-CTTACTA
1 TCGCAATGCGAATACGTA-AA
131903 TCGCAATGCGA
1 TCGCAATGCGA
131914 TTTACATAGC
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
19 3 0.04
20 58 0.73
21 18 0.23
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:132477 original size:19 final size:19
Alignment explanation
Indices: 132428--132498 Score: 90
Period size: 19 Copynumber: 3.7 Consensus size: 19
132418 TAGTTTCGAG
132428 AATGAAAATCGCAACGCGGA
1 AATGAAAATCGCAACGC-GA
*
132448 AAT-AACTATCGCAACGCGA
1 AATGAA-AATCGCAACGCGA
132467 AATGAAAATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
**
132486 AACCAAAATCGCA
1 AATGAAAATCGCA
132499 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
19 30 0.67
20 15 0.33
ACGTcount: A:0.46, C:0.24, G:0.18, T:0.11
Consensus pattern (19 bp):
AATGAAAATCGCAACGCGA
Found at i:132516 original size:19 final size:19
Alignment explanation
Indices: 132494--132686 Score: 113
Period size: 19 Copynumber: 11.1 Consensus size: 19
132484 GAAACCAAAA
*
132494 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
132513 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
132527 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
132546 TAGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
132560 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
132579 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
132593 TCTCGTTGCGATAGTT-ATT
1 TCGCGTTGCGAT-TTTCATT
132612 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
132626 TCTCATTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
132645 TCCGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
*
132665 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
132685 TC
1 TC
132687 AACCAAAAGA
Statistics
Matches: 133, Mismatches: 17, Indels: 48
0.67 0.09 0.24
Matches are distributed among these distances:
14 38 0.29
16 10 0.08
17 11 0.08
19 42 0.32
20 31 0.23
21 1 0.01
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:132535 original size:14 final size:14
Alignment explanation
Indices: 132516--132604 Score: 70
Period size: 14 Copynumber: 5.6 Consensus size: 14
132506 TTTCATTTCG
132516 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
132530 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
132547 AGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
*
132563 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
132582 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
132596 CGTTGCGAT
1 CGTTGCGAT
132605 AGTTATTTCG
Statistics
Matches: 61, Mismatches: 4, Indels: 20
0.72 0.05 0.24
Matches are distributed among these distances:
14 27 0.44
16 8 0.13
17 8 0.13
19 18 0.30
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:132541 original size:33 final size:33
Alignment explanation
Indices: 132499--132686 Score: 252
Period size: 33 Copynumber: 5.5 Consensus size: 33
132489 CAAAATCGCA
132499 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
132532 TTGCGATTTTCATTTAGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
132565 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
132598 TTGCGATAGTT-ATTTCGCGTTGCGATTCTCTCA
1 TTGCGAT-TTTCATTTCGCGTTGCGATTCTCTCG
**
132631 TTGCGATAGTCATTTCCGCGTTGCGATTTTCATTATCTCG
1 TTGCGATTTTCATTT-CGCGTTGCGA--TTC----TCTCG
132671 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
132687 AACCAAAAGA
Statistics
Matches: 137, Mismatches: 9, Indels: 12
0.87 0.06 0.08
Matches are distributed among these distances:
32 1 0.01
33 103 0.75
34 12 0.09
36 3 0.02
39 1 0.01
40 17 0.12
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:132663 original size:20 final size:20
Alignment explanation
Indices: 132640--132686 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
132630 ATTGCGATAG
132640 TCATTTCCGCGTTGCGATTT
1 TCATTTCCGCGTTGCGATTT
*
132660 TCATTAT-CTCGTTGCGATTT
1 TCATT-TCCGCGTTGCGATTT
132680 TCATTTC
1 TCATTTC
132687 AACCAAAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 1 0.04
20 22 0.92
21 1 0.04
ACGTcount: A:0.13, C:0.23, G:0.15, T:0.49
Consensus pattern (20 bp):
TCATTTCCGCGTTGCGATTT
Found at i:134861 original size:21 final size:21
Alignment explanation
Indices: 134837--134903 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
134827 TCATTCCTCG
134837 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
134858 AGAGACCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
134879 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
134900 AGAG
1 AGAG
134904 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.25, C:0.36, G:0.19, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:136273 original size:14 final size:14
Alignment explanation
Indices: 136254--136289 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
136244 ATTGTTTAAT
136254 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
136268 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
136282 TGATTTGT
1 TGATTTGT
136290 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:136418 original size:19 final size:19
Alignment explanation
Indices: 136396--136520 Score: 102
Period size: 19 Copynumber: 7.4 Consensus size: 19
136386 AAAAATTACT
136396 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
136415 ATCGCAA--CG--AT-ATA
1 ATCGCAATGCGAAATGAAA
136429 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
136448 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
136462 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
136481 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
136495 ATCGCAATGCGAAACT-AAA
1 ATCGCAATGCGAAA-TGAAA
136514 ATCGCAA
1 ATCGCAA
136521 CACGAAACTA
Statistics
Matches: 85, Mismatches: 5, Indels: 32
0.70 0.04 0.26
Matches are distributed among these distances:
14 29 0.34
15 4 0.05
16 6 0.07
17 6 0.07
18 4 0.05
19 36 0.42
ACGTcount: A:0.46, C:0.20, G:0.19, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:136438 original size:33 final size:33
Alignment explanation
Indices: 136396--136521 Score: 200
Period size: 33 Copynumber: 3.8 Consensus size: 33
136386 AAAAATTACT
* *
136396 ATCGCAATGCGAAATGAAAATCGCAACGATATA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
136429 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
136462 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
136495 ATCGCAATGCGAAACT-AAAATCGCAAC
1 ATCGCAATGCGAAA-TGAAAATCGCAAC
136522 ACGAAACTAA
Statistics
Matches: 88, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
33 87 0.99
34 1 0.01
ACGTcount: A:0.46, C:0.21, G:0.19, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:136526 original size:19 final size:19
Alignment explanation
Indices: 136492--136537 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
136482 TCGCAACGAC
**
136492 AAAATCGCAATGCGAAACT
1 AAAATCGCAACACGAAACT
136511 AAAATCGCAACACGAAACT
1 AAAATCGCAACACGAAACT
*
136530 AAATTCGC
1 AAAATCGC
136538 GTTGCGATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.48, C:0.24, G:0.13, T:0.15
Consensus pattern (19 bp):
AAAATCGCAACACGAAACT
Found at i:136555 original size:19 final size:19
Alignment explanation
Indices: 136533--136683 Score: 89
Period size: 19 Copynumber: 8.7 Consensus size: 19
136523 CGAAACTAAA
136533 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
136552 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
136567 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
136585 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
136600 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
136618 TTCGCATTGCGA--TT-A-
1 TTCGCGTTGCGATTTTCAT
*
136633 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
136651 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
136670 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
136684 AGACATTAAG
Statistics
Matches: 97, Mismatches: 19, Indels: 31
0.66 0.13 0.21
Matches are distributed among these distances:
14 26 0.27
16 9 0.09
17 9 0.09
19 43 0.44
20 10 0.10
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:136579 original size:33 final size:33
Alignment explanation
Indices: 136537--136663 Score: 227
Period size: 33 Copynumber: 3.8 Consensus size: 33
136527 ACTAAATTCG
* *
136537 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
136570 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
136603 CGTTGCGATTTTCATTTCGCATTGCGATTATCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
136636 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
136664 AGTAATTTCC
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 91 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:136610 original size:14 final size:14
Alignment explanation
Indices: 136558--136645 Score: 50
Period size: 14 Copynumber: 5.6 Consensus size: 14
136548 TCATTTCGCT
*
136558 TTGCGATTCCCTCG
1 TTGCGATTCTCTCG
*
136572 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
136589 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
*
136605 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
*
136622 CATTGCGATTATCTCG
1 --TTGCGATTCTCTCG
136638 TTGCGATT
1 TTGCGATT
136646 TTCATTTCGC
Statistics
Matches: 58, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 20 0.34
16 14 0.24
17 12 0.21
19 12 0.21
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:139009 original size:12 final size:12
Alignment explanation
Indices: 138992--139016 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
138982 TCTTCGGGGA
138992 CTTTTTCTTCTT
1 CTTTTTCTTCTT
139004 CTTTTTCTTCTT
1 CTTTTTCTTCTT
139016 C
1 C
139017 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:139225 original size:24 final size:24
Alignment explanation
Indices: 139191--139244 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
139181 CTGAAACATC
*
139191 ATCAAAATCCGAGTATTAACCAAT
1 ATCAAAATCCGAGTATTAACCAAG
* * *
139215 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
139239 ATCAAA
1 ATCAAA
139245 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTAACCAAG
Found at i:140081 original size:20 final size:20
Alignment explanation
Indices: 140048--140126 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 20
140038 GAATAAGTAA
* *
140048 ATCGCAATGCGATACTGACT
1 ATCGCAACGAGATACTGACT
* *
140068 ATCGCAACGAGATAAT-ACAAA
1 ATCGCAACGAGATACTGAC--T
*
140089 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATACTGACT
* *
140109 TTCGCAACGAGATTCTGA
1 ATCGCAACGAGATACTGA
140127 AAATCGCAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
19 2 0.04
20 30 0.62
21 14 0.29
22 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGAGATACTGACT
Found at i:140133 original size:20 final size:20
Alignment explanation
Indices: 140086--140135 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
140076 GAGATAATAC
140086 AAAATCGCAACGAGATTCTG
1 AAAATCGCAACGAGATTCTG
***
140106 ACTTTCGCAACGAGATTCTG
1 AAAATCGCAACGAGATTCTG
140126 AAAATCGCAA
1 AAAATCGCAA
140136 TCATCTTCAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (20 bp):
AAAATCGCAACGAGATTCTG
Found at i:140444 original size:20 final size:20
Alignment explanation
Indices: 140349--140436 Score: 124
Period size: 20 Copynumber: 4.4 Consensus size: 20
140339 CAACGGGGAA
140349 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
140369 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
* ***
140389 ATCGCAATGCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
140409 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
140429 ATCGCAAC
1 ATCGCAAC
140437 TAGAAAATTG
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
19 5 0.09
20 48 0.83
21 5 0.09
ACGTcount: A:0.39, C:0.24, G:0.23, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:140504 original size:19 final size:19
Alignment explanation
Indices: 140482--140526 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
140472 GATTTTCTCT
140482 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
140501 TTGCGATTTTCATTTTGCA
1 TTGCGATTTTCATTTCGCA
140520 TTGCGAT
1 TTGCGAT
140527 ATTCTCTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.16, C:0.18, G:0.18, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:142160 original size:40 final size:42
Alignment explanation
Indices: 142116--142206 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 42
142106 CCTCTTCAAC
* *
142116 GATGACAGTGGCCTCTTGAACG-GTG-GGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGAAGGGGACTCTTGAGG
* *
142156 GATGATAGGGGCCTCTTGAACGATTGAAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGAAGGGGACTCTTGAGG
*
142198 AATGACAGG
1 GATGACAGG
142207 TGAGTCGGGC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
40 20 0.47
41 2 0.05
42 21 0.49
ACGTcount: A:0.23, C:0.15, G:0.40, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGAGTGAAGGGGACTCTTGAGG
Found at i:142171 original size:21 final size:20
Alignment explanation
Indices: 142142--142202 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
142132 TGAACGGTGG
142142 GGGGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGA-A
* **
142163 GGGGCCTCTTGAACGATTGAA
1 GGGGACTCTTGAGGGA-TGAA
*
142184 GGGGACTCTTGAGGAATGA
1 GGGGACTCTTGAGGGATGA
142203 CAGGTGAGTC
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
20 3 0.09
21 26 0.81
22 3 0.09
ACGTcount: A:0.25, C:0.13, G:0.39, T:0.23
Consensus pattern (20 bp):
GGGGACTCTTGAGGGATGAA
Found at i:142572 original size:20 final size:20
Alignment explanation
Indices: 142547--142585 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
142537 GAAGAATAGT
142547 TTACTTTCGCAACACGAAAC
1 TTACTTTCGCAACACGAAAC
*
142567 TTACTTTCGCAACGCGAAA
1 TTACTTTCGCAACACGAAA
142586 ATGACTATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (20 bp):
TTACTTTCGCAACACGAAAC
Found at i:142609 original size:20 final size:20
Alignment explanation
Indices: 142573--142648 Score: 91
Period size: 20 Copynumber: 3.9 Consensus size: 20
142563 AAACTTACTT
* *
142573 TCGCAACGCGAAAATGACTA
1 TCGCAATGCGGAAATGACTA
*
142593 TCGTAATGCGGAAATGACTA
1 TCGCAATGCGGAAATGACTA
* * *
142613 TTGCAACGCGGAAATGGCTA
1 TCGCAATGCGGAAATGACTA
142633 TCGCAATGC-GAAATGA
1 TCGCAATGCGGAAATGA
142649 AAATCGCAAC
Statistics
Matches: 46, Mismatches: 10, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
19 6 0.13
20 40 0.87
ACGTcount: A:0.36, C:0.20, G:0.25, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGGAAATGACTA
Found at i:142654 original size:19 final size:19
Alignment explanation
Indices: 142632--142690 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
142622 GGAAATGGCT
142632 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
142651 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
142665 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
142684 ATCGCAA
1 ATCGCAA
142691 CGACAAAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.52
ACGTcount: A:0.47, C:0.20, G:0.19, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:142667 original size:14 final size:14
Alignment explanation
Indices: 142648--142706 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
142638 ATGCGAAATG
142648 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
142662 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
142681 AAAATCGCAACGAC
1 AAAATCGCAACGAC
142695 AAAATCGCAACG
1 AAAATCGCAACG
142707 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.49, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:142722 original size:33 final size:33
Alignment explanation
Indices: 142632--142711 Score: 151
Period size: 33 Copynumber: 2.4 Consensus size: 33
142622 GGAAATGGCT
142632 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
142665 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
142698 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
142712 CACAAATCGC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:142740 original size:19 final size:18
Alignment explanation
Indices: 142718--142814 Score: 66
Period size: 19 Copynumber: 5.6 Consensus size: 18
142708 GAAACACAAA
142718 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGATTTTCATT
*
142737 TCGCGTTGCGA-TTT--TG
1 TCGC-TTGCGATTTTCATT
142753 TCG-TTGCGATTTTCATT
1 TCGCTTGCGATTTTCATT
* * *
142770 TTGCGTTACGA-TTT--TG
1 TCGC-TTGCGATTTTCATT
142786 TCG-TTGCGATTTTCATT
1 TCGCTTGCGATTTTCATT
142803 TCGCATTGCGAT
1 TCGC-TTGCGAT
142815 AGCCATTTCC
Statistics
Matches: 59, Mismatches: 9, Indels: 20
0.67 0.10 0.23
Matches are distributed among these distances:
14 11 0.19
15 6 0.10
16 7 0.12
17 7 0.12
18 6 0.10
19 22 0.37
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (18 bp):
TCGCTTGCGATTTTCATT
Found at i:142759 original size:14 final size:14
Alignment explanation
Indices: 142740--142798 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
142730 TTTCATTTCG
142740 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
142754 CGTTGCGATTTTCATTTT
1 CGTTGCGA--TT--TTGT
*
142772 GCGTTACGATTTTGT
1 -CGTTGCGATTTTGT
142787 CGTTGCGATTTT
1 CGTTGCGATTTT
142799 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
14 19 0.53
15 3 0.08
16 2 0.06
17 2 0.06
18 3 0.08
19 7 0.19
ACGTcount: A:0.10, C:0.15, G:0.24, T:0.51
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:142765 original size:33 final size:33
Alignment explanation
Indices: 142723--142814 Score: 157
Period size: 33 Copynumber: 2.8 Consensus size: 33
142713 ACAAATCGCA
142723 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
* *
142756 TTGCGATTTTCATTTTGCGTTACGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
142789 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
142815 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:142821 original size:19 final size:20
Alignment explanation
Indices: 142799--142842 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
142789 TTGCGATTTT
142799 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
* *
142818 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCATTGCGATAGC
142838 CATTT
1 CATTT
142843 TCGTGCTGCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (20 bp):
CATTTCCGCATTGCGATAGC
Found at i:142852 original size:20 final size:20
Alignment explanation
Indices: 142809--142853 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
142799 CATTTCGCAT
*
142809 TGCGATAGCCATTTCCGCGT
1 TGCGATAGCCATTTCCGCGC
* * *
142829 TGCGATAGTCATTTTCGTGC
1 TGCGATAGCCATTTCCGCGC
142849 TGCGA
1 TGCGA
142854 AAGTAAACTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.27, T:0.33
Consensus pattern (20 bp):
TGCGATAGCCATTTCCGCGC
Found at i:143417 original size:18 final size:18
Alignment explanation
Indices: 143390--143430 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
143380 GGTCGATCAA
*
143390 GTGATGGCTCTGGGTGAG
1 GTGATAGCTCTGGGTGAG
143408 GTGATAGCTCTGGGTGAG
1 GTGATAGCTCTGGGTGAG
143426 GTGAT
1 GTGAT
143431 GACTCCCGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.15, C:0.10, G:0.46, T:0.29
Consensus pattern (18 bp):
GTGATAGCTCTGGGTGAG
Found at i:145291 original size:18 final size:18
Alignment explanation
Indices: 145264--145317 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
145254 TGCGAAAGTC
*
145264 AGTATTGAGTTGCGATTA
1 AGTATCGAGTTGCGATTA
* *
145282 AGTATCGAGTTGCGAAGTC
1 AGTATCGAGTTGCG-ATTA
*
145301 AGTATCGCGTTGCGATT
1 AGTATCGAGTTGCGATT
145318 TGTATTATCG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
18 15 0.50
19 15 0.50
ACGTcount: A:0.24, C:0.13, G:0.30, T:0.33
Consensus pattern (18 bp):
AGTATCGAGTTGCGATTA
Found at i:145306 original size:19 final size:19
Alignment explanation
Indices: 145252--145315 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
145242 GTATTATCTC
*
145252 GTTGCGAAAGTCAGTATTGA
1 GTTGCG-AAGTCAGTATCGA
* *
145272 GTTGCG-ATTAAGTATCGA
1 GTTGCGAAGTCAGTATCGA
*
145290 GTTGCGAAGTCAGTATCGC
1 GTTGCGAAGTCAGTATCGA
145309 GTTGCGA
1 GTTGCGA
145316 TTTGTATTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
18 15 0.41
19 16 0.43
20 6 0.16
ACGTcount: A:0.25, C:0.14, G:0.31, T:0.30
Consensus pattern (19 bp):
GTTGCGAAGTCAGTATCGA
Found at i:145328 original size:20 final size:21
Alignment explanation
Indices: 145303--145343 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
145293 GCGAAGTCAG
*
145303 TATCGCGTTGCGA-TTTGTAT
1 TATCGCATTGCGATTTTGTAT
145323 TATCGCATTGCGATTTTGTAT
1 TATCGCATTGCGATTTTGTAT
145344 CGCGCAATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.17, C:0.15, G:0.22, T:0.46
Consensus pattern (21 bp):
TATCGCATTGCGATTTTGTAT
Found at i:145627 original size:9 final size:9
Alignment explanation
Indices: 145613--145649 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
145603 TTATTTTCTC
145613 TTATTATTT
1 TTATTATTT
*
145622 TTATTATTA
1 TTATTATTT
145631 TTATTATTT
1 TTATTATTT
145640 TTATTATTT
1 TTATTATTT
145649 T
1 T
145650 GAAATTTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (9 bp):
TTATTATTT
Found at i:145628 original size:3 final size:3
Alignment explanation
Indices: 145613--145647 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
145603 TTATTTTCTC
* *
145613 TTA TTA TTT TTA TTA TTA TTA TTA TTT TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
145648 TTGAAATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (3 bp):
TTA
Found at i:148529 original size:21 final size:21
Alignment explanation
Indices: 148505--148561 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
148495 TCAGCGTAGC
*
148505 CGATTCAGATACCACAATCGT
1 CGATTCAGATGCCACAATCGT
*
148526 CGATTCAGATGCCACTATCGT
1 CGATTCAGATGCCACAATCGT
148547 CGATTCAGATGCCAC
1 CGATTCAGATGCCAC
148562 CACCGTATGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.25
Consensus pattern (21 bp):
CGATTCAGATGCCACAATCGT
Found at i:151646 original size:15 final size:16
Alignment explanation
Indices: 151628--151659 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
151618 AAATGTCACG
151628 AAATA-AAAAAAAACT
1 AAATACAAAAAAAACT
151643 AAATACAAAAAAAACT
1 AAATACAAAAAAAACT
151659 A
1 A
151660 TAAAAACCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.78, C:0.09, G:0.00, T:0.12
Consensus pattern (16 bp):
AAATACAAAAAAAACT
Found at i:151942 original size:2 final size:2
Alignment explanation
Indices: 151935--151964 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
151925 ATGTGAGGTG
151935 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
151965 GTATTTAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:152178 original size:13 final size:15
Alignment explanation
Indices: 152148--152213 Score: 64
Period size: 15 Copynumber: 4.3 Consensus size: 15
152138 AAAATAAATA
152148 ATAAAATATATACAT
1 ATAAAATATATACAT
*
152163 ATAAAATAT-TA-GT
1 ATAAAATATATACAT
*
152176 ATAATATATATATATAT
1 ATAA-A-ATATATACAT
*
152193 ATATATATATATACAT
1 ATA-AAATATATACAT
152209 ATAAA
1 ATAAA
152214 TAAAATATTA
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
13 5 0.12
14 3 0.07
15 14 0.34
16 14 0.34
17 4 0.10
18 1 0.02
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (15 bp):
ATAAAATATATACAT
Found at i:152186 original size:2 final size:2
Alignment explanation
Indices: 152153--152211 Score: 61
Period size: 2 Copynumber: 30.5 Consensus size: 2
152143 AAATAATAAA
* *
152153 AT AT AT AC AT AT A- AA AT AT -T AGT AT A- AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
*
152193 AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT A
152212 AATAAAATAT
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
1 3 0.06
2 43 0.90
3 2 0.04
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (2 bp):
AT
Found at i:152247 original size:15 final size:15
Alignment explanation
Indices: 152227--152260 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
152217 AATATTAGGG
152227 AAAAGAAAAAAAAGA
1 AAAAGAAAAAAAAGA
* *
152242 AAAAGAAAATAAATA
1 AAAAGAAAAAAAAGA
152257 AAAA
1 AAAA
152261 ATGAATAATA
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:0.85, C:0.00, G:0.09, T:0.06
Consensus pattern (15 bp):
AAAAGAAAAAAAAGA
Found at i:154309 original size:85 final size:85
Alignment explanation
Indices: 154187--155018 Score: 992
Period size: 85 Copynumber: 9.8 Consensus size: 85
154177 ATGTGTCATC
* * * * * * ** * * * *
154187 GAGCTGAATGGAATTGAACTCGAAAG-CTTTAGTTGACATATAGCTTTTCTCGACTTAAGTTGTG
1 GAGCTGAGTGTAATCGAACTCGAAGGTC-TTGGTTGACAGATAGCCCTTCTCGCCTTGAGCTATG
* * * *
154251 CTGCAAATTTGACATACCCTT
65 CTGTAAATTTGATATGCCTTT
* *
154272 GAGCT-ATGTGTAATCGAACTCGAATGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
1 GAGCTGA-GTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAGCCCTTCTCGCCTTGAGCTATG
*
154336 TTGTAAATTTGATATGCCTTT
65 CTGTAAATTTGATATGCCTTT
* * *
154357 GAGCTGAGTGTAATCGAACTCGAAGGT-TTTGTTGACAGATAGCCCTTCCCGCCTTGAGCTATGG
1 GAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
*
154421 TGTGAA-TTGAATATGCCTTT
66 TGTAAATTTG-ATATGCCTTT
* * * *
154441 GAGTTGAGTGTAATCGAACTTGAAGGTCTT-GTTGACAGATAGCCCTTCTCGTCTTGAGCTATGT
1 GAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
*
154505 TGTAAATTGGATATGCCTTT
66 TGTAAATTTGATATGCCTTT
* * * * *
154525 GAGCTGAGTGTAATCGAACTCGAAGATCTTGGTTGATAGATAACTCTTCTCGCCTTGAGTTATGC
1 GAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
*
154590 TGTAAATTGGATATGCCTTT
66 TGTAAATTTGATATGCCTTT
* * * *
154610 AAGCTGATTGTAATCGAACTCGAAGGTCCTGGTTGACAAATAGCCCTTCTCGCCTTGAGCTATGC
1 GAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
* * *
154675 TGTAAATTGGACATGTCTTT
66 TGTAAATTTGATATGCCTTT
* * * * * * *
154695 GAGCTGATTGTAATCGAACTCAAAGGTTTTTCGTTAACAGATTGCCTTTCTCGCCTTGAGCTATG
1 GAGCTGAGTGTAATCGAACTCGAAGG-TCTTGGTTGACAGATAGCCCTTCTCGCCTTGAGCTATG
* *
154760 TTGTAAATTTGATGTGCCTTT
65 CTGTAAATTTGATATGCCTTT
* * * *
154781 GAGTTGAGTGTAATCGAACTCAAATGTCTTGGTTGACAGATAGCCCATCTCGCCTTGAGCTATGC
1 GAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
*
154846 TGCAAATTTGATATGCCTTT
66 TGTAAATTTGATATGCCTTT
* * *
154866 GAGCTGAATGTAATCGAACTCGAAGGTCTTTGTT-AGCAGATAGCCCTTCTCTCCTTGAGCTATG
1 GAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGA-CAGATAGCCCTTCTCGCCTTGAGCTATG
*
154930 CTGTAATTTTGATATGCCTTT
65 CTGTAAATTTGATATGCCTTT
* * * * * *
154951 GAGCTGAGTGTAATCGAACTCAAAGGTCTTGGTTAACAAATAACCATTCTCGCCTTGAGTTATGC
1 GAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
155016 TGT
66 TGT
155019 CAATAGTTCC
Statistics
Matches: 643, Mismatches: 94, Indels: 20
0.85 0.12 0.03
Matches are distributed among these distances:
83 3 0.00
84 148 0.23
85 419 0.65
86 73 0.11
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (85 bp):
GAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
TGTAAATTTGATATGCCTTT
Found at i:154834 original size:256 final size:254
Alignment explanation
Indices: 154270--155106 Score: 1052
Period size: 256 Copynumber: 3.2 Consensus size: 254
154260 TGACATACCC
154270 TTGAGCT-ATGTGTAATCGAACTCGAATGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGCTA
1 TTGAGCTGA-GTGTAATCGAACTCGAATGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGCTA
* *
154334 TGTTGTAAATTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGT-TTTGTTGACAGATA
65 TGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATA
* * * * * **
154398 GCCCTTCCCGCCTTGAGCTATGGTGTGAATTGAATATGCCTTTGAGTTGAGTGTAATCGAACTTG
130 GCCCTTCTCGCCTTGAGCTATGCTGTAAATTGGATATGCCTTTGAGCTGAGTGTAATCGAACTCA
* * *
154463 AAGGTCTTGTTGACAGATAGCCCTTCTCGTCTTGAGCTATGTTGTAAATTGGATATGCCT
195 AAGGTCTTGTTAACAGATAGCCATTCTCGCCTTGAGCTATGTTGTAAATTGGATATGCCT
* * *
154523 TTGAGCTGAGTGTAATCGAACTCGAA-GATCTTGGTTGATAGATAACTCTTCTCGCCTTGAGTTA
1 TTGAGCTGAGTGTAATCGAACTCGAATG-TCTTGGTTGACAGATAACCCTTCTCGCCTTGAGCTA
* * * * * *
154587 TGCTGTAAATTGGATATGCCTTTAAGCTGATTGTAATCGAACTCGAAGGTCCTGGTTGACAAATA
65 TGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATA
* * *
154652 GCCCTTCTCGCCTTGAGCTATGCTGTAAATTGGACATGTCTTTGAGCTGATTGTAATCGAACTCA
130 GCCCTTCTCGCCTTGAGCTATGCTGTAAATTGGATATGCCTTTGAGCTGAGTGTAATCGAACTCA
* * * * *
154717 AAGGTTTTTCGTTAACAGATTGCCTTTCTCGCCTTGAGCTATGTTGTAAATTTGATGTGCCT
195 AAGG-TCTT-GTTAACAGATAGCCATTCTCGCCTTGAGCTATGTTGTAAATTGGATATGCCT
* * * *
154779 TTGAGTTGAGTGTAATCGAACTCAAATGTCTTGGTTGACAGATAGCCCATCTCGCCTTGAGCTAT
1 TTGAGCTGAGTGTAATCGAACTCGAATGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGCTAT
*
154844 GCTGCAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTT-AGCAGATA
66 GCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGA-CAGATA
* * *
154908 GCCCTTCTCTCCTTGAGCTATGCTGTAATTTTGATATGCCTTTGAGCTGAGTGTAATCGAACTCA
130 GCCCTTCTCGCCTTGAGCTATGCTGTAAATTGGATATGCCTTTGAGCTGAGTGTAATCGAACTCA
* * * *
154973 AAGGTCTTGGTTAACAAATAACCATTCTCGCCTTGAGTTATGCTGTCAATAGTTCCTTTAAGTGA
195 AAGGTCTT-GTTAACAGATAGCCATTCTCGCCTTGAGCTATGTTGT-AA-A------TT--G-G-
*
155038 AAAATGCCT
247 -ATATGCCT
* * * * *
155047 TTGAACTGAGTGTAATCGAACTCGTAGGTCTTGGTGGACATATAACCCTTCTCGCCTTGA
1 TTGAGCTGAGTGTAATCGAACTCGAATGTCTTGGTTGACAGATAACCCTTCTCGCCTTGA
155107 CTTATGTTGC
Statistics
Matches: 497, Mismatches: 67, Indels: 25
0.84 0.11 0.04
Matches are distributed among these distances:
252 1 0.00
253 103 0.21
254 71 0.14
255 38 0.08
256 222 0.45
257 2 0.00
263 2 0.00
266 1 0.00
268 57 0.11
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (254 bp):
TTGAGCTGAGTGTAATCGAACTCGAATGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGCTAT
GCTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAG
CCCTTCTCGCCTTGAGCTATGCTGTAAATTGGATATGCCTTTGAGCTGAGTGTAATCGAACTCAA
AGGTCTTGTTAACAGATAGCCATTCTCGCCTTGAGCTATGTTGTAAATTGGATATGCCT
Found at i:154947 original size:341 final size:338
Alignment explanation
Indices: 154279--155018 Score: 1052
Period size: 341 Copynumber: 2.2 Consensus size: 338
154269 CTTGAGCTAT
* * *
154279 GTGTAATCGAACTCGAATGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGCTATGTTGTAAAT
1 GTGTAATCGAACTCGAAGGTCTTGGTTGACAAATAACCCTTCTCGCCTTGAGCTATGCTGTAAAT
* * * *
154344 TTGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTTTTGTTGACAGATAGCCCTTCCCGC
66 TGGACATGCCTTTGAGCTGAGTGTAATCGAACTCAAAGGTTTTGTTAACAGATAGCCCTTCCCGC
* **
154409 CTTGAGCTATGGTGTGAATTGAATATGCCTTTGAGTTGAGTGTAATCGAACTTGAAGGTCTTGTT
131 CTTGAGCTATGGTGTAAATTGAATATGCCTTTGAGTTGAGTGTAATCGAACTCAAAGGTCTTGTT
* * * * *
154474 GACAGATAGCCCTTCTCGTCTTGAGCTATGTTGTAAATTGGATATGCCTTTGAGCTGAGTGTAAT
196 GACAGATAGCCCATCTCGCCTTGAGCTATGCTGCAAATTGGATATGCCTTTGAGCTGAATGTAAT
* * *
154539 CGAACTCGAAGATCTTGGTTGATAGATAACTCTTCTCGCCTTGAGTTATGCTGTAAATTGGATAT
261 CGAACTCGAAGATCTTGGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTGGATAT
154604 GCCTTTAAGCTGA
326 GCCTTTAAGCTGA
* * *
154617 TTGTAATCGAACTCGAAGGTCCTGGTTGACAAATAGCCCTTCTCGCCTTGAGCTATGCTGTAAAT
1 GTGTAATCGAACTCGAAGGTCTTGGTTGACAAATAACCCTTCTCGCCTTGAGCTATGCTGTAAAT
* * * * *
154682 TGGACATGTCTTTGAGCTGATTGTAATCGAACTCAAAGGTTTTTCGTTAACAGATTGCCTTTCTC
66 TGGACATGCCTTTGAGCTGAGTGTAATCGAACTCAAAGG-TTTT-GTTAACAGATAGCCCTTCCC
* * *
154747 GCCTTGAGCTATGTTGTAAATTTG-ATGTGCCTTTGAGTTGAGTGTAATCGAACTCAAATGTCTT
129 GCCTTGAGCTATGGTGTAAA-TTGAATATGCCTTTGAGTTGAGTGTAATCGAACTCAAAGGTCTT
*
154811 GGTTGACAGATAGCCCATCTCGCCTTGAGCTATGCTGCAAATTTGATATGCCTTTGAGCTGAATG
193 -GTTGACAGATAGCCCATCTCGCCTTGAGCTATGCTGCAAATTGGATATGCCTTTGAGCTGAATG
* * * * * *
154876 TAATCGAACTCGAAGGTCTTTGTT-AGCAGATAGCCCTTCTCTCCTTGAGCTATGCTGTAATTTT
257 TAATCGAACTCGAAGATCTTGGTTGA-CAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTG
*
154940 GATATGCCTTTGAGCTGA
321 GATATGCCTTTAAGCTGA
* * * *
154958 GTGTAATCGAACTCAAAGGTCTTGGTTAACAAATAACCATTCTCGCCTTGAGTTATGCTGT
1 GTGTAATCGAACTCGAAGGTCTTGGTTGACAAATAACCCTTCTCGCCTTGAGCTATGCTGT
155019 CAATAGTTCC
Statistics
Matches: 353, Mismatches: 44, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
338 93 0.26
339 4 0.01
340 71 0.20
341 185 0.52
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.35
Consensus pattern (338 bp):
GTGTAATCGAACTCGAAGGTCTTGGTTGACAAATAACCCTTCTCGCCTTGAGCTATGCTGTAAAT
TGGACATGCCTTTGAGCTGAGTGTAATCGAACTCAAAGGTTTTGTTAACAGATAGCCCTTCCCGC
CTTGAGCTATGGTGTAAATTGAATATGCCTTTGAGTTGAGTGTAATCGAACTCAAAGGTCTTGTT
GACAGATAGCCCATCTCGCCTTGAGCTATGCTGCAAATTGGATATGCCTTTGAGCTGAATGTAAT
CGAACTCGAAGATCTTGGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTGGATAT
GCCTTTAAGCTGA
Done.