Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019369.1 Corchorus olitorius cultivar O-4 contig19402, 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: 106105
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:15307 original size:9 final size:9
Alignment explanation
Indices: 15293--15323 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
15283 AATAAGTAAG
15293 CACCGAATC
1 CACCGAATC
15302 CACCGAATC
1 CACCGAATC
*
15311 CACCGAATG
1 CACCGAATC
15320 CACC
1 CACC
15324 AAAATAAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.32, C:0.45, G:0.13, T:0.10
Consensus pattern (9 bp):
CACCGAATC
Found at i:22458 original size:170 final size:166
Alignment explanation
Indices: 22058--22538 Score: 626
Period size: 170 Copynumber: 2.8 Consensus size: 166
22048 GGTTGTTGCA
* * *
22058 AAGATATTAATGCAGAGATTTTTGAAGGGGAAATCGGCAATAAATCCGTGGAAGTTGATTTGGTT
1 AAGATATTAATGTAGAGATTTTTGAAGGGGAAATCGGCAATAAATCTGTGGAAGCTGATTTGG-T
22123 GTGAATAATTTGAATTC-ATATAGGAGTGATGTTGCTAATGGAGATTTGGTTATTTATGATAGCA
65 GTGAATAATTTGAATTCAAT-TAGGAGTGATGTTGCTAATGGAGATTTGGTTATTTATGATAGCA
* *
22187 TTGACTCTAGAAACGAGGAGTTTGTTACAGAATCTACTG
129 TTGACTCTA-AAACGAGGAATTTGTTACAGAATCTAATG
* * *
22226 ATGATATTAATGTAGAGATTTTTGAAGGGTAAATCGGTAATAAATCTGTGGAAGCTGATTTGGTG
1 AAGATATTAATGTAGAGATTTTTGAAGGGGAAATCGGCAATAAATCTGTGGAAGCTGATTTGGTG
22291 ATGAATAATTTGAATTCAATTAGGAGTGATGTTGCTAATGGAGATTAATTTGGTTATTTATGATA
66 -TGAATAATTTGAATTCAATTAGGAGTGATGTTGCTAATGGAG----ATTTGGTTATTTATGATA
* *
22356 GCATTGACTCGT-AAA-GAGGAATTTGTTGCATAATCTAATG
126 GCATTGACTC-TAAAACGAGGAATTTGTTACAGAATCTAATG
* ** *
22396 AAGATATTAATGTAGAGATTTTCGAAGGGGAAATCAACATTAAATCTGTGGAAGCTGATTTGGTG
1 AAGATATTAATGTAGAGATTTTTGAAGGGGAAATCGGCAATAAATCTGTGGAAGCTGATTTGGT-
* * * * *
22461 GTGAATAATTTGAATTCAATTAATTAGGAGTAATGTTGCTAATGGAAATCTGGCTAATTATGATA
65 GTGAATAATTTGAATTC----AATTAGGAGTGATGTTGCTAATGGAGATTTGGTTATTTATGATA
* *
22526 CCTTTGACTCTAA
126 GCATTGACTCTAA
22539 TAAAGAGGTG
Statistics
Matches: 276, Mismatches: 24, Indels: 24
0.85 0.07 0.07
Matches are distributed among these distances:
167 2 0.01
168 96 0.35
169 3 0.01
170 118 0.43
171 4 0.01
172 28 0.10
173 1 0.00
174 24 0.09
ACGTcount: A:0.33, C:0.08, G:0.24, T:0.35
Consensus pattern (166 bp):
AAGATATTAATGTAGAGATTTTTGAAGGGGAAATCGGCAATAAATCTGTGGAAGCTGATTTGGTG
TGAATAATTTGAATTCAATTAGGAGTGATGTTGCTAATGGAGATTTGGTTATTTATGATAGCATT
GACTCTAAAACGAGGAATTTGTTACAGAATCTAATG
Found at i:27023 original size:19 final size:20
Alignment explanation
Indices: 26993--27055 Score: 74
Period size: 21 Copynumber: 3.1 Consensus size: 20
26983 TTGACACTGT
26993 TTAGCAACTGTACAGATGAGA
1 TTAGC-ACTGTACAGATGAGA
*
27014 TTA-CACTGTACAGATTAGA
1 TTAGCACTGTACAGATGAGA
* *
27033 TTAGGTACTGTACATATGAGA
1 TTA-GCACTGTACAGATGAGA
27054 TT
1 TT
27056 CTTAGAGCAG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 17 0.47
20 1 0.03
21 18 0.50
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.32
Consensus pattern (20 bp):
TTAGCACTGTACAGATGAGA
Found at i:30462 original size:2 final size:2
Alignment explanation
Indices: 30457--30490 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
30447 TTGCTGGAAC
30457 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
30491 CTTATTATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:33079 original size:25 final size:26
Alignment explanation
Indices: 33045--33093 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
33035 CATTTCCCAC
* *
33045 CATAAACATACAATTAAA-CTAAAAA
1 CATAAACATAAAAATAAACCTAAAAA
*
33070 CATAACCATAAAAATAAACCTAAA
1 CATAAACATAAAAATAAACCTAAA
33094 TTTGAAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 15 0.75
26 5 0.25
ACGTcount: A:0.63, C:0.18, G:0.00, T:0.18
Consensus pattern (26 bp):
CATAAACATAAAAATAAACCTAAAAA
Found at i:34129 original size:25 final size:25
Alignment explanation
Indices: 34101--34160 Score: 102
Period size: 25 Copynumber: 2.4 Consensus size: 25
34091 TAATCCAATA
34101 TTGAATTCTATTGAACCAAATAGTG
1 TTGAATTCTATTGAACCAAATAGTG
*
34126 TTGAATTCTATTGAACCAAATTGTG
1 TTGAATTCTATTGAACCAAATAGTG
34151 TTGAAGTTCT
1 TTGAA-TTCT
34161 TTTAAAGTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 29 0.88
26 4 0.12
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.40
Consensus pattern (25 bp):
TTGAATTCTATTGAACCAAATAGTG
Found at i:34308 original size:101 final size:101
Alignment explanation
Indices: 34129--34317 Score: 254
Period size: 101 Copynumber: 1.9 Consensus size: 101
34119 AATAGTGTTG
* * **
34129 AATTCTATTGAACCAAATTGTGTTGAAGTTCTTTTAAAGTCTATTTCTCATTCACATGATTAGGA
1 AATTCTATTGAACCAAATAGTGTTGAAGTTCTTTTAAAGCCTATTTCTCATTCACATGATTAAAA
* *
34194 CTCGAGATGTTGCTTAACGAGACTAATCCAATATTA
66 CCCGAGATATTGCTTAACGAGACTAATCCAATATTA
** * * *
34230 AATTCTATTGAATTAGATAGTGTTGGAGTTCTTTTATAA-CCTATTTCTCGTTCACATGATTAAA
1 AATTCTATTGAACCAAATAGTGTTGAAGTTCTTTTA-AAGCCTATTTCTCATTCACATGATTAAA
*
34294 ACCCGAGATATTGCTTAATGAGAC
65 ACCCGAGATATTGCTTAACGAGAC
34318 ATCAAAGCCT
Statistics
Matches: 75, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
101 73 0.97
102 2 0.03
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (101 bp):
AATTCTATTGAACCAAATAGTGTTGAAGTTCTTTTAAAGCCTATTTCTCATTCACATGATTAAAA
CCCGAGATATTGCTTAACGAGACTAATCCAATATTA
Found at i:38582 original size:9 final size:9
Alignment explanation
Indices: 38568--38603 Score: 72
Period size: 9 Copynumber: 4.0 Consensus size: 9
38558 GTATAATACT
38568 ATATCGTTA
1 ATATCGTTA
38577 ATATCGTTA
1 ATATCGTTA
38586 ATATCGTTA
1 ATATCGTTA
38595 ATATCGTTA
1 ATATCGTTA
38604 CAAGGTGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (9 bp):
ATATCGTTA
Found at i:38954 original size:11 final size:11
Alignment explanation
Indices: 38911--38948 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
38901 TTCCTATATA
*
38911 AAATAAATTAT
1 AAATTAATTAT
38922 CAAA-TAATTAT
1 -AAATTAATTAT
38933 AAATTAATTAT
1 AAATTAATTAT
38944 AAATT
1 AAATT
38949 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:41160 original size:29 final size:29
Alignment explanation
Indices: 41118--41173 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
41108 ACTTTGCCTT
*
41118 AAATCTCAAATAAGGGTTCAAACTTTTAA
1 AAATCTCAAATAAGGGTCCAAACTTTTAA
* *
41147 AAATGTCAAATAAGGGTCCCAACTTTT
1 AAATCTCAAATAAGGGTCCAAACTTTT
41174 TGGAAAGGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.30
Consensus pattern (29 bp):
AAATCTCAAATAAGGGTCCAAACTTTTAA
Found at i:41830 original size:2 final size:2
Alignment explanation
Indices: 41817--41860 Score: 79
Period size: 2 Copynumber: 21.5 Consensus size: 2
41807 GTTTCAAATA
41817 AT AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41860 A
1 A
41861 AGTAATAGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 39 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:43022 original size:2 final size:2
Alignment explanation
Indices: 43015--43055 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
43005 CTAGAGATGA
43015 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT A
43056 AGACTTTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:46818 original size:22 final size:22
Alignment explanation
Indices: 46776--46824 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
46766 ACATATGTGG
* *
46776 TTTAATTAAACTTTAAAAAATC
1 TTTAATTAAACTTGAAAAAATA
*
46798 TTTAATTAGAAC-TGAACAAATA
1 TTTAATTA-AACTTGAAAAAATA
46820 TTTAA
1 TTTAA
46825 ATAATGTACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.49, C:0.08, G:0.04, T:0.39
Consensus pattern (22 bp):
TTTAATTAAACTTGAAAAAATA
Found at i:52347 original size:15 final size:15
Alignment explanation
Indices: 52327--52359 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
52317 TTAATGAGTT
52327 AAAATAAAA-AAATGA
1 AAAATAAAAGAAAT-A
52342 AAAATAAAAGAAATA
1 AAAATAAAAGAAATA
52357 AAA
1 AAA
52360 TTGAAAGACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (15 bp):
AAAATAAAAGAAATA
Found at i:58230 original size:69 final size:69
Alignment explanation
Indices: 58106--58240 Score: 209
Period size: 69 Copynumber: 2.0 Consensus size: 69
58096 GCTTGAAATG
* * *
58106 CATTGTCTTTATATGTAATTTTAGCATTTGGATGTAATTAATGGAATTCCTACCATTTTTTCCTT
1 CATTATCTTTATATGTAATTTTAGCATTTGGATGTAATTAATGGAACTCCCACCATTTTTTCCTT
58171 AATA
66 AATA
**
58175 CATTATCTTTATATGTAATTTTAGCA-TTGAGATGTAATTAATGGTGCTCCCACCATTTTTTCCT
1 CATTATCTTTATATGTAATTTTAGCATTTG-GATGTAATTAATGGAACTCCCACCATTTTTTCCT
58239 TA
65 TA
58241 GTTGTTAGTC
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
68 3 0.05
69 57 0.95
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.47
Consensus pattern (69 bp):
CATTATCTTTATATGTAATTTTAGCATTTGGATGTAATTAATGGAACTCCCACCATTTTTTCCTT
AATA
Found at i:58366 original size:2 final size:2
Alignment explanation
Indices: 58361--58398 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
58351 CCCGCGCGCG
58361 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
58399 AAGCCTTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:59716 original size:30 final size:30
Alignment explanation
Indices: 59658--59721 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
59648 TCCTTCTAAC
* *
59658 AAAAGAAATTTGCTTATGGTCCTCTTTGAA
1 AAAAGAAATTTACTTATGATCCTCTTTGAA
*
59688 AAAAGAAATTTACTTATGAAT-CTTTTTGAA
1 AAAAGAAATTTACTTATG-ATCCTCTTTGAA
59718 AAAA
1 AAAA
59722 AATTGATACC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 29 0.97
31 1 0.03
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.36
Consensus pattern (30 bp):
AAAAGAAATTTACTTATGATCCTCTTTGAA
Found at i:77036 original size:24 final size:24
Alignment explanation
Indices: 76981--77056 Score: 80
Period size: 24 Copynumber: 3.2 Consensus size: 24
76971 ATGCCATGTT
* * *
76981 TCACTTTTTGAAACACATGGCATG
1 TCACTTTTTGATACACATGACGTG
*
77005 CCACTTTTTGATACACATGACGTG
1 TCACTTTTTGATACACATGACGTG
* * * *
77029 TCATTTTTTGGTATACGTGACGTG
1 TCACTTTTTGATACACATGACGTG
77053 TCAC
1 TCAC
77057 AGGTCGTTTT
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (24 bp):
TCACTTTTTGATACACATGACGTG
Found at i:79721 original size:29 final size:29
Alignment explanation
Indices: 79667--79722 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
79657 GACACAACTT
*
79667 AATTAATTGAGACCACCTTGTTTAAAAAA
1 AATTAATTGAGACCACCTTGTATAAAAAA
79696 AATTAATTGAGACCACCATT-TATAAAA
1 AATTAATTGAGACCACC-TTGTATAAAA
79723 TTTAATGCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 23 0.92
30 2 0.08
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.30
Consensus pattern (29 bp):
AATTAATTGAGACCACCTTGTATAAAAAA
Found at i:81540 original size:25 final size:25
Alignment explanation
Indices: 81494--81563 Score: 70
Period size: 25 Copynumber: 2.7 Consensus size: 25
81484 AGAAAAAGTC
* *
81494 AATTTGGTCCCTCTATTAAAAAATT-
1 AATTTAGTCCCTCTACT-AAAAATTG
*
81519 AATTTAGTCCCTCTACTCAAAATTG
1 AATTTAGTCCCTCTACTAAAAATTG
81544 ATCACTTTAGTCCCTCTACT
1 A--A-TTTAGTCCCTCTACT
81564 TATAGGTTTG
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
24 6 0.16
25 16 0.42
27 1 0.03
28 15 0.39
ACGTcount: A:0.30, C:0.24, G:0.07, T:0.39
Consensus pattern (25 bp):
AATTTAGTCCCTCTACTAAAAATTG
Found at i:83171 original size:52 final size:52
Alignment explanation
Indices: 83094--83217 Score: 248
Period size: 52 Copynumber: 2.4 Consensus size: 52
83084 CACCTACCAT
83094 TTTTGTCTAACCAATAACCATTAATAAATAGAGTATGATATTTATGTGATTA
1 TTTTGTCTAACCAATAACCATTAATAAATAGAGTATGATATTTATGTGATTA
83146 TTTTGTCTAACCAATAACCATTAATAAATAGAGTATGATATTTATGTGATTA
1 TTTTGTCTAACCAATAACCATTAATAAATAGAGTATGATATTTATGTGATTA
83198 TTTTGTCTAACCAATAACCA
1 TTTTGTCTAACCAATAACCA
83218 CAAATCAATA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (52 bp):
TTTTGTCTAACCAATAACCATTAATAAATAGAGTATGATATTTATGTGATTA
Found at i:88620 original size:7 final size:7
Alignment explanation
Indices: 88608--88634 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
88598 TTTAGCTGAT
88608 ATATATC
1 ATATATC
88615 ATATATC
1 ATATATC
88622 ATATATC
1 ATATATC
88629 ATATAT
1 ATATAT
88635 ATAGTTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (7 bp):
ATATATC
Found at i:89399 original size:61 final size:60
Alignment explanation
Indices: 89304--89539 Score: 318
Period size: 56 Copynumber: 3.9 Consensus size: 60
89294 AAAATAAAAT
* *
89304 TTTAGCTTACTTAAGAACCTAAAAATAAAATTTTGTATTAAAAAAAATGAAATAAGCTATA
1 TTTAGCTTACTTAAGAACCTGAAAATAAAATTTTGTATT-AAAAAAATGAAATAAGATATA
* *
89365 TTTAGCTTACTTAAGAATCTGAAAATAAAATTTTGTATTAAAAAAATGAAATAAGTTATA
1 TTTAGCTTACTTAAGAACCTGAAAATAAAATTTTGTATTAAAAAAATGAAATAAGATATA
*
89425 TTTAGCTTAC-T---AACCTGAAAATAAAATTTTGTATTAAGAAAATGAAATAAGATATATTCA
1 TTTAGCTTACTTAAGAACCTGAAAATAAAATTTTGTATTAAAAAAATGAAATAAG--ATA-T-A
*
89485 TTATATAGCTTACTTAAGAACTTGAAAATAAAATTTTGTATTAAAAAAATGAAAT
1 -T-T-TAGCTTACTTAAGAACCTGAAAATAAAATTTTGTATTAAAAAAATGAAAT
89540 GAGGCTTTAT
Statistics
Matches: 156, Mismatches: 8, Indels: 16
0.87 0.04 0.09
Matches are distributed among these distances:
56 38 0.24
58 2 0.01
59 2 0.01
60 31 0.20
61 38 0.24
62 1 0.01
63 8 0.05
64 1 0.01
67 35 0.22
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (60 bp):
TTTAGCTTACTTAAGAACCTGAAAATAAAATTTTGTATTAAAAAAATGAAATAAGATATA
Found at i:89513 original size:123 final size:117
Alignment explanation
Indices: 89319--89539 Score: 329
Period size: 123 Copynumber: 1.8 Consensus size: 117
89309 CTTACTTAAG
*
89319 AACCTAAAAATAAAATTTTGTATTAAAAAAAATGAAATAAGCTATATTTAGCTTACTTAAGAATC
1 AACCTAAAAATAAAATTTTGTATTAAAAAAAATGAAATAAGATATATTTAGCTTACTTAAGAATC
89384 TGAAAATAAAATTTTGTATTAAAAAAATGAAATAAGTTATATTTAGCTTACT
66 TGAAAATAAAATTTTGTATTAAAAAAATGAAATAAGTTATATTTAGCTTACT
* *
89436 AACCTGAAAATAAAATTTTGTATT-AAGAAAATGAAATAAGATATATTCATTATATAGCTTACTT
1 AACCTAAAAATAAAATTTTGTATTAAAAAAAATGAAATAAG--ATA-T-A-T-T-TAGCTTACTT
89500 AAGAA-CTTGAAAATAAAATTTTGTATTAAAAAAATGAAAT
59 AAGAATC-TGAAAATAAAATTTTGTATTAAAAAAATGAAAT
89540 GAGGCTTTAT
Statistics
Matches: 93, Mismatches: 3, Indels: 10
0.88 0.03 0.09
Matches are distributed among these distances:
116 15 0.16
117 23 0.25
118 2 0.02
119 1 0.01
120 1 0.01
121 1 0.01
122 2 0.02
123 48 0.52
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.34
Consensus pattern (117 bp):
AACCTAAAAATAAAATTTTGTATTAAAAAAAATGAAATAAGATATATTTAGCTTACTTAAGAATC
TGAAAATAAAATTTTGTATTAAAAAAATGAAATAAGTTATATTTAGCTTACT
Found at i:98497 original size:11 final size:11
Alignment explanation
Indices: 98481--98515 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
98471 TTGACAGCGC
*
98481 AACAAAAATAA
1 AACAAAAACAA
*
98492 AACAAAAACGA
1 AACAAAAACAA
98503 AACAAAAACAA
1 AACAAAAACAA
98514 AA
1 AA
98516 AACAGAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.80, C:0.14, G:0.03, T:0.03
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:100417 original size:107 final size:103
Alignment explanation
Indices: 100201--100480 Score: 364
Period size: 107 Copynumber: 2.7 Consensus size: 103
100191 TTTCTAACCC
* ** * * *
100201 TTAAAATAAAATTTTAATTTTAATTT-GGGCTTAACTTAGTGAATGAGTTATATATTTTATTTCT
1 TTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTAAATTAGTT-TATATTTTATTTCT
* * * *
100265 AAAGCCCTATAACAGTATTATTAATTATGGAATTTACCC
65 AAAACCCTATAACAATATTATTAATTATGAAATTTACCA
*
100304 TTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTAAAATTAGTTTAGTATTTTATTTA
1 TTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGT-AAATTAGTTTA-TATTTTATTTC
* *
100369 TAAAACCCTATAATAATAAATTATTAATTTTGAAATTTACCA
64 TAAAACCCTATAACAAT--ATTATTAATTATGAAATTTACCA
*
100411 TTAAAATAAAAACAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTC
1 TTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGT-AAATTAG-TTTATATTTTATTTC
100476 TAAAA
64 TAAAA
100481 ATCTATGATA
Statistics
Matches: 155, Mismatches: 16, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
103 23 0.15
104 15 0.10
105 31 0.20
107 82 0.53
108 4 0.03
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.42
Consensus pattern (103 bp):
TTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTAAATTAGTTTATATTTTATTTCTA
AAACCCTATAACAATATTATTAATTATGAAATTTACCA
Found at i:100513 original size:107 final size:107
Alignment explanation
Indices: 100216--100515 Score: 319
Period size: 107 Copynumber: 2.8 Consensus size: 107
100206 ATAAAATTTT
* * * * **
100216 AATTTTAATTT-GGGCTTAACTTAGT-GAATGAGTTATA-TATTTTATTTCTAAAGCCCTAT-A-
1 AATTTTAATTTGGGGCTAAACTTAGTAAAATTAGTT-TAGTATTTTATTTATAAAAACCTATAAT
* ** * * * * *
100276 ACAGTATTATTAATTATGGAATTTACCCTTAAAATAAAAATAA
65 AAAAAACTATTAATTTTGAAATTTACCATTAAAATAAAAACAA
*
100319 AATTTTAATTTGGGGCTAAACTTAGTAAAATTAGTTTAGTATTTTATTTATAAAACCCTATAATA
1 AATTTTAATTTGGGGCTAAACTTAGTAAAATTAGTTTAGTATTTTATTTATAAAAACCTATAATA
* *
100384 ATAAATTATTAATTTTGAAATTTACCATTAAAATAAAAACAA
66 AAAAACTATTAATTTTGAAATTTACCATTAAAATAAAAACAA
* * * *
100426 AATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTA-TATTTTATTTCTAAAAATCTATGAT
1 AATTTTAATTTGGGGCTAAACTTAGTAAAATTAG-TTTAGTATTTTATTTATAAAAACCTATAAT
100490 AAAAAACCT-TTAATTTT-ATAATTTAC
65 AAAAAA-CTATTAATTTTGA-AATTTAC
100516 TCTTAGAAAT
Statistics
Matches: 169, Mismatches: 20, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
103 11 0.07
104 15 0.09
105 27 0.16
106 2 0.01
107 109 0.64
108 5 0.03
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.42
Consensus pattern (107 bp):
AATTTTAATTTGGGGCTAAACTTAGTAAAATTAGTTTAGTATTTTATTTATAAAAACCTATAATA
AAAAACTATTAATTTTGAAATTTACCATTAAAATAAAAACAA
Found at i:100633 original size:17 final size:17
Alignment explanation
Indices: 100611--100644 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
100601 ACGTCAGGGG
100611 GAGACTAGGGGAGAGAT
1 GAGACTAGGGGAGAGAT
100628 GAGACTAGGGGAGAGAT
1 GAGACTAGGGGAGAGAT
100645 CTTGGAGGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.47, T:0.12
Consensus pattern (17 bp):
GAGACTAGGGGAGAGAT
Found at i:101511 original size:2 final size:2
Alignment explanation
Indices: 101504--101532 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
101494 AAACTCGTAA
101504 AT 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 AT A
101533 ACCCGTCTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:102263 original size:20 final size:21
Alignment explanation
Indices: 102226--102268 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
102216 AACCCGTTAA
*
102226 TTAAAGCGTGTCACTCGTGTC
1 TTAAAGCGTGTCAATCGTGTC
*
102247 TTAAA-CGTGTTAATCGTGTC
1 TTAAAGCGTGTCAATCGTGTC
102267 TT
1 TT
102269 GACATGATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.40
Consensus pattern (21 bp):
TTAAAGCGTGTCAATCGTGTC
Found at i:102334 original size:42 final size:43
Alignment explanation
Indices: 102256--102338 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 43
102246 CTTAAACGTG
* *
102256 TTAATCGTGTCTTGACATGATTAGGACACGAAACACGATAATC
1 TTAATCGTGTCCTGACACGATTAGGACACGAAACACGATAATC
*
102299 TTAATCGTGTCCT-ACACGATTCA-GACACGAGACACGATAA
1 TTAATCGTGTCCTGACACGATT-AGGACACGAAACACGATAA
102339 GTCAAACACG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
42 23 0.64
43 13 0.36
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (43 bp):
TTAATCGTGTCCTGACACGATTAGGACACGAAACACGATAATC
Found at i:102961 original size:56 final size:56
Alignment explanation
Indices: 102866--102979 Score: 201
Period size: 56 Copynumber: 2.0 Consensus size: 56
102856 TATCTGTTTC
*
102866 CTTTCACACAATAAATGTTATAATAAATCATATCCCCCTATTTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCATATCCCCCTATCTCTACTTAATTATT
* *
102922 CTTTCACACAATAAATGTTATAATAAATCCTATCTCCCTATCTCTACTTAATTATT
1 CTTTCACACAATAAATGTTATAATAAATCATATCCCCCTATCTCTACTTAATTATT
102978 CT
1 CT
102980 ATAAAATAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.34, C:0.23, G:0.02, T:0.41
Consensus pattern (56 bp):
CTTTCACACAATAAATGTTATAATAAATCATATCCCCCTATCTCTACTTAATTATT
Found at i:103092 original size:42 final size:42
Alignment explanation
Indices: 103045--103125 Score: 137
Period size: 42 Copynumber: 1.9 Consensus size: 42
103035 TAAAGATCAG
103045 GATTTGAGTTAAGTATTTCTTAATTTACA-AAGAATTTTCTAT
1 GATTTGAGTTAAGTATTTCTTAATTTACAGAA-AATTTTCTAT
*
103087 GATTTGAGTTGAGTATTTCTTAATTTACAGAAAATTTTC
1 GATTTGAGTTAAGTATTTCTTAATTTACAGAAAATTTTC
103126 AAGACTTAGC
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
42 35 0.95
43 2 0.05
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.47
Consensus pattern (42 bp):
GATTTGAGTTAAGTATTTCTTAATTTACAGAAAATTTTCTAT
Done.