Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021577.1 Corchorus olitorius cultivar O-4 contig21610, 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: 48377
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:2082 original size:56 final size:56
Alignment explanation
Indices: 1996--2126 Score: 156
Period size: 56 Copynumber: 2.3 Consensus size: 56
1986 TGTTAATAAT
* * * * *
1996 TCATAAATCATAAAAAACAAACAAAGAAATATAATAAATTGTATATTGATTTGTAA
1 TCATAAATCATAAAAAATAAACAAAGAAATATAATAAATCGCATAATAATTTGTAA
* * *
2052 TCATAAATCATAAAAAATATATAAATAAATATAATAAATCGCATAATAATTTGTAA
1 TCATAAATCATAAAAAATAAACAAAGAAATATAATAAATCGCATAATAATTTGTAA
* *
2108 T-ATAACATGAAAAAAAATA
1 TCATAA-ATCATAAAAAATA
2127 CAATCTTCAT
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
55 4 0.06
56 60 0.94
ACGTcount: A:0.58, C:0.07, G:0.05, T:0.30
Consensus pattern (56 bp):
TCATAAATCATAAAAAATAAACAAAGAAATATAATAAATCGCATAATAATTTGTAA
Found at i:2754 original size:23 final size:23
Alignment explanation
Indices: 2728--2775 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
2718 GTTAATGCTT
2728 TCCATAAATGTAGTAACTTTACA
1 TCCATAAATGTAGTAACTTTACA
2751 TCCATAAATGTAGTAACTTTACA
1 TCCATAAATGTAGTAACTTTACA
2774 TC
1 TC
2776 GTGAGTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.35
Consensus pattern (23 bp):
TCCATAAATGTAGTAACTTTACA
Found at i:3012 original size:29 final size:29
Alignment explanation
Indices: 2970--3032 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
2960 TAATCATTAA
* *
2970 AATTCCATCTACCAATATACGAGCTACAT
1 AATTCCATCAACCAATAAACGAGCTACAT
* * *
2999 AATTTCATCAACCAATAAACGTGTTACAT
1 AATTCCATCAACCAATAAACGAGCTACAT
3028 AATTC
1 AATTC
3033 TTTATTTTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.40, C:0.24, G:0.06, T:0.30
Consensus pattern (29 bp):
AATTCCATCAACCAATAAACGAGCTACAT
Found at i:7138 original size:24 final size:23
Alignment explanation
Indices: 7097--7142 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
7087 ATTATGTAAG
7097 AAAAGATGAAGAAAAAAATACATA
1 AAAAGATGAAGAAAAAAA-ACATA
*
7121 AAAAGAT-AAGAACGAAAAACAT
1 AAAAGATGAAGAA-AAAAAACAT
7143 TATGATAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.70, C:0.07, G:0.13, T:0.11
Consensus pattern (23 bp):
AAAAGATGAAGAAAAAAAACATA
Found at i:7173 original size:15 final size:17
Alignment explanation
Indices: 7147--7199 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 17
7137 AAACATTATG
7147 ATAA-TATA-ACTAATA
1 ATAATTATATACTAATA
*
7162 ATAATTTTACTACTAATA
1 ATAATTATA-TACTAATA
7180 ATAATTAT-TA-TAATA
1 ATAATTATATACTAATA
7195 ATAAT
1 ATAAT
7200 AAGAACTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 14 0.42
16 5 0.15
18 14 0.42
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (17 bp):
ATAATTATATACTAATA
Found at i:7178 original size:18 final size:18
Alignment explanation
Indices: 7155--7201 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
7145 TGATAATATA
7155 ACTAATAATAATT-TTACT
1 ACTAATAATAATTATTA-T
7173 ACTAATAATAATTATTAT
1 ACTAATAATAATTATTAT
*
7191 AATAATAATAA
1 ACTAATAATAA
7202 GAACTTTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 24 0.89
19 3 0.11
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.40
Consensus pattern (18 bp):
ACTAATAATAATTATTAT
Found at i:9980 original size:23 final size:23
Alignment explanation
Indices: 9952--10000 Score: 68
Period size: 20 Copynumber: 2.3 Consensus size: 23
9942 ATTTATGTCA
*
9952 TAATTATTATTACAATAGATTCT
1 TAATTATTAGTACAATAGATTCT
9975 T-A--ATTAGTACAATAGATTCT
1 TAATTATTAGTACAATAGATTCT
9995 TAATTA
1 TAATTA
10001 GTACAATGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
20 18 0.82
21 1 0.05
22 1 0.05
23 2 0.09
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (23 bp):
TAATTATTAGTACAATAGATTCT
Found at i:9985 original size:20 final size:20
Alignment explanation
Indices: 9957--10007 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
9947 TGTCATAATT
*
9957 ATTATTACAATAGATTCTTA
1 ATTAGTACAATAGATTCTTA
9977 ATTAGTACAATAGATTCTTA
1 ATTAGTACAATAGATTCTTA
9997 ATTAGTACAAT
1 ATTAGTACAAT
10008 GTCTTTTTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (20 bp):
ATTAGTACAATAGATTCTTA
Found at i:16054 original size:74 final size:74
Alignment explanation
Indices: 15932--16154 Score: 324
Period size: 74 Copynumber: 3.0 Consensus size: 74
15922 TACCCAAAAT
* * * * **
15932 AATTGTGAGTGCCCACCCCAATTGAATTAAACCATGTTAAGTGACCAATTTGTTCCATATGAAAC
1 AATTGTGAGTGTCCACCTCAATTGGATTAAACCATGTTAAGTGTCCAATTTGACCCATATGAAAC
15997 ATTAGTAAA
66 ATTAGTAAA
* * *
16006 AATTGTGAGTATCCACCTCAATTGGATTAAACCATGTTAAGTGTCCAATTGGGCCCATATGAAAC
1 AATTGTGAGTGTCCACCTCAATTGGATTAAACCATGTTAAGTGTCCAATTTGACCCATATGAAAC
16071 ATTAGTAAA
66 ATTAGTAAA
* *
16080 AATTGTGAGTGTCCACCTCAATTGGATTAAACAATATTAAGTGTCC-A-TTGACCCATATGAAAC
1 AATTGTGAGTGTCCACCTCAATTGGATTAAACCATGTTAAGTGTCCAATTTGACCCATATGAAAC
*
16143 ATTAATAAA
66 ATTAGTAAA
16152 AAT
1 AAT
16155 ATATGTATTT
Statistics
Matches: 135, Mismatches: 14, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
72 25 0.19
73 1 0.01
74 109 0.81
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.30
Consensus pattern (74 bp):
AATTGTGAGTGTCCACCTCAATTGGATTAAACCATGTTAAGTGTCCAATTTGACCCATATGAAAC
ATTAGTAAA
Found at i:20704 original size:24 final size:24
Alignment explanation
Indices: 20672--20719 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
20662 TGAATTGTTT
20672 TAATGCAAGAACCAAAATAAAACA
1 TAATGCAAGAACCAAAATAAAACA
20696 TAATGCAAGAACCAAAATAAAACA
1 TAATGCAAGAACCAAAATAAAACA
20720 GAACGTTCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.62, C:0.17, G:0.08, T:0.12
Consensus pattern (24 bp):
TAATGCAAGAACCAAAATAAAACA
Found at i:25305 original size:21 final size:21
Alignment explanation
Indices: 25281--25363 Score: 52
Period size: 21 Copynumber: 4.2 Consensus size: 21
25271 TTTTTATTAA
25281 TTTTAGTAACCTTATAAATCT
1 TTTTAGTAACCTTATAAATCT
* * *
25302 TTTTAATAA--TAATAAAT-A
1 TTTTAGTAACCTTATAAATCT
*
25320 TTTT-GTAACCTTATTGAA-CT
1 TTTTAGTAACCTTA-TAAATCT
* * *
25340 TTTCATTAACCATA-AAATCT
1 TTTTAGTAACCTTATAAATCT
25360 TTTT
1 TTTT
25364 TTTTTGTTTT
Statistics
Matches: 44, Mismatches: 12, Indels: 13
0.64 0.17 0.19
Matches are distributed among these distances:
17 3 0.07
18 4 0.09
19 11 0.25
20 11 0.25
21 15 0.34
ACGTcount: A:0.36, C:0.12, G:0.04, T:0.48
Consensus pattern (21 bp):
TTTTAGTAACCTTATAAATCT
Found at i:26195 original size:26 final size:26
Alignment explanation
Indices: 26166--26225 Score: 102
Period size: 26 Copynumber: 2.3 Consensus size: 26
26156 TTTTGGTAAC
*
26166 TTTATTAAGACACTGACCATGTTAAG
1 TTTATTAAGACACTAACCATGTTAAG
26192 TTTATTAAGACACTAACCATGTTAAG
1 TTTATTAAGACACTAACCATGTTAAG
*
26218 TTTTTTAA
1 TTTATTAA
26226 TAGCAATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (26 bp):
TTTATTAAGACACTAACCATGTTAAG
Found at i:26255 original size:20 final size:19
Alignment explanation
Indices: 26232--26282 Score: 50
Period size: 20 Copynumber: 2.7 Consensus size: 19
26222 TTAATAGCAA
26232 TATAAGCTTTTTAATAACCT
1 TATAAGCTTTTTAATAA-CT
* * *
26252 TATAAACATTTTCATAACT
1 TATAAGCTTTTTAATAACT
*
26271 TA-AAGTTTTTTA
1 TATAAGCTTTTTA
26283 CCTTATGAAC
Statistics
Matches: 24, Mismatches: 7, Indels: 2
0.73 0.21 0.06
Matches are distributed among these distances:
18 6 0.25
19 4 0.17
20 14 0.58
ACGTcount: A:0.37, C:0.12, G:0.04, T:0.47
Consensus pattern (19 bp):
TATAAGCTTTTTAATAACT
Found at i:26315 original size:21 final size:21
Alignment explanation
Indices: 26290--26331 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
26280 TTACCTTATG
26290 AACTTGTCAACAATCATATAA
1 AACTTGTCAACAATCATATAA
* * *
26311 AACTTTTCAATAATCTTATAA
1 AACTTGTCAACAATCATATAA
26332 GGATTTTAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.17, G:0.02, T:0.36
Consensus pattern (21 bp):
AACTTGTCAACAATCATATAA
Found at i:30706 original size:22 final size:24
Alignment explanation
Indices: 30680--30726 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
30670 TCATTCAAGG
*
30680 TTTTTA-TA-AAGTGATGTAATTT
1 TTTTTAGTAGAAGTAATGTAATTT
30702 TTTTTATGTAGAAGTAATGTAATTT
1 TTTTTA-GTAGAAGTAATGTAATTT
30727 CGAATTTCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
24 2 0.10
25 13 0.62
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (24 bp):
TTTTTAGTAGAAGTAATGTAATTT
Found at i:31139 original size:11 final size:11
Alignment explanation
Indices: 31115--31149 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
31105 TTGACAGCGC
31115 AACAAAAACAA
1 AACAAAAACAA
* *
31126 AACGAAAACGA
1 AACAAAAACAA
31137 AACAAAAACAA
1 AACAAAAACAA
31148 AA
1 AA
31150 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:31141 original size:16 final size:16
Alignment explanation
Indices: 31120--31178 Score: 50
Period size: 16 Copynumber: 3.7 Consensus size: 16
31110 AGCGCAACAA
31120 AAACAAAACGAAAACG
1 AAACAAAACGAAAACG
*
31136 AAACAAAAACAAAAAAC-
1 AAAC-AAAAC-GAAAACG
*
31153 AGA-AAAACGAAAACG
1 AAACAAAACGAAAACG
* *
31168 ATACCAAACGA
1 AAACAAAACGA
31179 CCCCTTACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
14 5 0.15
15 7 0.21
16 10 0.29
17 7 0.21
18 5 0.15
ACGTcount: A:0.69, C:0.19, G:0.10, T:0.02
Consensus pattern (16 bp):
AAACAAAACGAAAACG
Found at i:31781 original size:14 final size:14
Alignment explanation
Indices: 31762--31788 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
31752 GGAACAAATG
31762 AAGCATCTGTGTTT
1 AAGCATCTGTGTTT
31776 AAGCATCTGTGTT
1 AAGCATCTGTGTT
31789 CCAACATGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.41
Consensus pattern (14 bp):
AAGCATCTGTGTTT
Found at i:33131 original size:19 final size:18
Alignment explanation
Indices: 33107--33142 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
33097 TGAAGATTTA
33107 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
33126 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
33143 ATTATTTCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:33772 original size:18 final size:19
Alignment explanation
Indices: 33744--33780 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
33734 CTCTTCTTCT
33744 TTTTCTCTTCTAGTTTTAG
1 TTTTCTCTTCTAGTTTTAG
33763 TTTT-TCTTCTAGTTTTAG
1 TTTTCTCTTCTAGTTTTAG
33781 GGCTAGGGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.11, C:0.14, G:0.11, T:0.65
Consensus pattern (19 bp):
TTTTCTCTTCTAGTTTTAG
Found at i:39122 original size:12 final size:12
Alignment explanation
Indices: 39102--39136 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
39092 AACATGTTAA
39102 TTTTCTTTTTAT
1 TTTTCTTTTTAT
* *
39114 TTTTGTTTTTGT
1 TTTTCTTTTTAT
39126 TTTTCTTTTTA
1 TTTTCTTTTTA
39137 GGATTTCAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.06, C:0.06, G:0.06, T:0.83
Consensus pattern (12 bp):
TTTTCTTTTTAT
Found at i:39562 original size:3 final size:3
Alignment explanation
Indices: 39554--39579 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
39544 TCATCTCCAT
39554 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
39580 TTGCATTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:47094 original size:157 final size:157
Alignment explanation
Indices: 46808--47118 Score: 568
Period size: 157 Copynumber: 2.0 Consensus size: 157
46798 GTGTGTGTGT
46808 GTGTGAGCAATAACGACGTTATATAAAAATGTCACTTAAGTTAAGAAAGTGACATGATGAATATA
1 GTGTGAGCAATAACGACGTTATATAAAAATGTCACTTAAGTTAAGAAAGTGACATGATGAATATA
*
46873 GCCCTTGCGACATATATGATATATGTATCGCTTGAAATGTCACTAAAACTCCAAATATTAACAAC
66 GCCCTTGCGACATATATGATATATATATCGCTTGAAATGTCACTAAAACTCCAAATATTAACAAC
*
46938 GTTTGACACAAATGTCGTTATATAAAA
131 ATTTGACACAAATGTCGTTATATAAAA
*
46965 GTGTGAGCAATAGCGACGTTATATAAAAATGTCACTTAAGTTAAGAAAGTGACATGATGAATATA
1 GTGTGAGCAATAACGACGTTATATAAAAATGTCACTTAAGTTAAGAAAGTGACATGATGAATATA
*
47030 GCCCTTGCGACATATATGATATATATGTCGCTTGAAATGTCACTAAAACTCCAAATATTAACAAC
66 GCCCTTGCGACATATATGATATATATATCGCTTGAAATGTCACTAAAACTCCAAATATTAACAAC
* *
47095 ATTTGGCACAAATGTCGTTTTATA
131 ATTTGACACAAATGTCGTTATATA
47119 GTCATTTTTC
Statistics
Matches: 148, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
157 148 1.00
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (157 bp):
GTGTGAGCAATAACGACGTTATATAAAAATGTCACTTAAGTTAAGAAAGTGACATGATGAATATA
GCCCTTGCGACATATATGATATATATATCGCTTGAAATGTCACTAAAACTCCAAATATTAACAAC
ATTTGACACAAATGTCGTTATATAAAA
Done.