Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013858.1 Corchorus capsularis cultivar CVL-1 contig13879, 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: 31818
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:871 original size:46 final size:46
Alignment explanation
Indices: 801--989 Score: 236
Period size: 46 Copynumber: 4.1 Consensus size: 46
791 TATGCGTTGC
* * *
801 AAGAGGCTACCGTATAGAG-AATTCTTTCTGGAGATGGGTGCTCATAT
1 AAGA-GCTACCGTATAGAGTAA-TCTTTCTGAAGAAGGGTGCTCACAT
* * * *
848 AAGAGCTACCATGTAGAGTATTCTTTCTGAAGAAGTGTGCTCACAT
1 AAGAGCTACCGTATAGAGTAATCTTTCTGAAGAAGGGTGCTCACAT
** *
894 AAGAGCTATTGTATAGAGTAATCTTTCTGAAGAAGTGTGCTCACAT
1 AAGAGCTACCGTATAGAGTAATCTTTCTGAAGAAGGGTGCTCACAT
** *
940 AAGAGCTATTGTATAAAGTAATCTTTCTGAAGAAGGGTGCTCACAT
1 AAGAGCTACCGTATAGAGTAATCTTTCTGAAGAAGGGTGCTCACAT
986 AAGA
1 AAGA
990 TGCATCTCCT
Statistics
Matches: 127, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
46 122 0.96
47 5 0.04
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.30
Consensus pattern (46 bp):
AAGAGCTACCGTATAGAGTAATCTTTCTGAAGAAGGGTGCTCACAT
Found at i:1196 original size:36 final size:36
Alignment explanation
Indices: 1151--1271 Score: 165
Period size: 36 Copynumber: 3.4 Consensus size: 36
1141 AAAGGCTAGT
*
1151 GGCATTATAGCCAAATATTGGGCGAC-TATGGCCAAC
1 GGCATTATAGCCAAATATTGGGCGACTTA-GGCCATC
* *
1187 GGCTTTATAG-CAAATTTTTGGGCGACTTAGGCCATC
1 GGCATTATAGCCAAA-TATTGGGCGACTTAGGCCATC
* *
1223 GGCATTATAGCCAAGTATTAGGCGACTTAGGCCATC
1 GGCATTATAGCCAAATATTGGGCGACTTAGGCCATC
1259 GGCATTATAGCCA
1 GGCATTATAGCCA
1272 GAAACAGAGC
Statistics
Matches: 75, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
35 4 0.05
36 66 0.88
37 5 0.07
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.26
Consensus pattern (36 bp):
GGCATTATAGCCAAATATTGGGCGACTTAGGCCATC
Found at i:1719 original size:20 final size:17
Alignment explanation
Indices: 1685--1718 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1675 GGAAGAGCTG
1685 TCACCATATGGGAAGAA
1 TCACCATATGGGAAGAA
*
1702 TCACCATATTGGAAGAA
1 TCACCATATGGGAAGAA
1719 GGAGTCAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.41, C:0.18, G:0.21, T:0.21
Consensus pattern (17 bp):
TCACCATATGGGAAGAA
Found at i:1751 original size:37 final size:37
Alignment explanation
Indices: 1705--1793 Score: 142
Period size: 37 Copynumber: 2.4 Consensus size: 37
1695 GGAAGAATCA
* * *
1705 CCATATTGGAAGAAGGAGTCAGTAGAAAGCGCTATCC
1 CCATGTTGGAAGAAGAAGTCAGCAGAAAGCGCTATCC
*
1742 CCATGTTGGAAGAAGAAGTCAGCAGAAAGCGCTATTC
1 CCATGTTGGAAGAAGAAGTCAGCAGAAAGCGCTATCC
1779 CCATGTTGGAAGAAG
1 CCATGTTGGAAGAAG
1794 TATAAATTCT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (37 bp):
CCATGTTGGAAGAAGAAGTCAGCAGAAAGCGCTATCC
Found at i:1859 original size:45 final size:44
Alignment explanation
Indices: 1794--1986 Score: 181
Period size: 45 Copynumber: 4.2 Consensus size: 44
1784 TTGGAAGAAG
* * **
1794 TATAAATTCTCTCTGTTGGAAGCGTTAGCATCATGTTGGAAGTGCA
1 TATAAATTTTGTC-GTTGGAAGCGCCA-CATCATGTTGGAAGTGCA
* * * * *
1840 TATAAATTTTATCGCTGGAAGCGCCACCCTCATGCTGGAAGAGCA
1 TATAAATTTTGTCGTTGGAAGCGCCA-CATCATGTTGGAAGTGCA
* **
1885 TATAAATTTTGT-GATTGGAGGCGCCACAATCATGTTGGAAGTGGG
1 TATAAATTTTGTCG-TTGGAAGCGCCAC-ATCATGTTGGAAGTGCA
* * *
1930 TATAAATTTTGTCTATTGGAAGCGCCAACACCATGTTGGAAGTGCG
1 TATAAATTTTGTC-GTTGGAAGCGCC-ACATCATGTTGGAAGTGCA
1976 TATAAATTTTG
1 TATAAATTTTG
1987 ACAATTTTGT
Statistics
Matches: 121, Mismatches: 21, Indels: 10
0.80 0.14 0.07
Matches are distributed among these distances:
44 2 0.02
45 70 0.58
46 47 0.39
47 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (44 bp):
TATAAATTTTGTCGTTGGAAGCGCCACATCATGTTGGAAGTGCA
Found at i:2601 original size:65 final size:65
Alignment explanation
Indices: 2495--2646 Score: 196
Period size: 65 Copynumber: 2.3 Consensus size: 65
2485 AGAGTGAATA
* * * *
2495 TAGGCGTTGTAAGCCCTTTTTAAAGCTACATAGGCTATAGTAGGCGTTGCAAAGCTGCATAAATT
1 TAGGCGTAGTAAG-CCTTTTTTAAGCTACATAGACTATAGTAGACGTTGCAAAGCTGCATAAATT
2560 G
65 G
* * * * **
2561 TAGGCGTCGTAAGCCTTTTTTAAGCTGCATAGACTGTAGTAGACGTTGTAAAGCTGCATAGGTTG
1 TAGGCGTAGTAAGCCTTTTTTAAGCTACATAGACTATAGTAGACGTTGCAAAGCTGCATAAATTG
*
2626 TAGGCATAGTAAGCCTTTTTT
1 TAGGCGTAGTAAGCCTTTTTT
2647 TTTAAAGTTG
Statistics
Matches: 75, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
65 63 0.84
66 12 0.16
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (65 bp):
TAGGCGTAGTAAGCCTTTTTTAAGCTACATAGACTATAGTAGACGTTGCAAAGCTGCATAAATTG
Found at i:2821 original size:104 final size:108
Alignment explanation
Indices: 2671--2872 Score: 272
Period size: 104 Copynumber: 1.9 Consensus size: 108
2661 GCTAGAAGCG
* * * * * *
2671 TCAATAAGGAGGGGCACTCTTGGAGGTGCAATCAATGCAACACTCCTA-AGGGTGCAC-CTGCTC
1 TCAACAAGGAAGGGCACTCCTAGAGGTGCAACCAATGCAACACTCCTATA-GGTGCACTC-ACTC
2734 CAAGTC-AA-A-A-ATTTTTTAATGGGCTACATAGGTCAGAATCA
64 CAAGTCAAATATAGATTTTTTAATGGGCTACATAGGTCAGAATCA
*
2775 TCAACAAGGAAGGGCACTCCTAGAGGTGCAACCAGTGCAACACTCCTATAGGTGCACTCACTCCA
1 TCAACAAGGAAGGGCACTCCTAGAGGTGCAACCAATGCAACACTCCTATAGGTGCACTCACTCCA
2840 AGTCAAAATATAGATTTTTTAATGGGCTACATA
66 AGTC-AAATATAGATTTTTTAATGGGCTACATA
2873 AGCCAGATTC
Statistics
Matches: 84, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
104 58 0.69
105 2 0.02
106 2 0.02
107 1 0.01
108 1 0.01
109 20 0.24
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (108 bp):
TCAACAAGGAAGGGCACTCCTAGAGGTGCAACCAATGCAACACTCCTATAGGTGCACTCACTCCA
AGTCAAATATAGATTTTTTAATGGGCTACATAGGTCAGAATCA
Found at i:2968 original size:68 final size:68
Alignment explanation
Indices: 2858--2990 Score: 187
Period size: 68 Copynumber: 2.0 Consensus size: 68
2848 TATAGATTTT
** *
2858 TTAATGGGCTACATAAGCCAGATTCAACAAAAGGAAAGACACTTTTGGCTACGATCCTTGCTGAA
1 TTAATGGGCTACATAAGCCAGAAGCAACAAAAGGAAAGACACTTATGGCTACGATCCTTGCTGAA
2923 ATC
66 ATC
* * **
2926 TTAATTGGCTACATAAGCCAGAAGCATCACAAAGGAAA-ACACTTATGGCTGTGATCCTTGCTGA
1 TTAATGGGCTACATAAGCCAGAAGCAACA-AAAGGAAAGACACTTATGGCTACGATCCTTGCTGA
2990 A
65 A
2991 TATGGAATCT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
68 49 0.86
69 8 0.14
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (68 bp):
TTAATGGGCTACATAAGCCAGAAGCAACAAAAGGAAAGACACTTATGGCTACGATCCTTGCTGAA
ATC
Found at i:3910 original size:46 final size:46
Alignment explanation
Indices: 3843--3934 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
3833 TACGGTGAAA
*
3843 CTGATTTAAGGCGTCAATCATGGGATTTATGGTAAGAAGGAAATAT
1 CTGATATAAGGCGTCAATCATGGGATTTATGGTAAGAAGGAAATAT
3889 CTGATATAAGGCGTCAATCATGGGATTTATGGTAAGAAGGAAATAT
1 CTGATATAAGGCGTCAATCATGGGATTTATGGTAAGAAGGAAATAT
3935 TCAAGGAAGA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.36, C:0.09, G:0.26, T:0.29
Consensus pattern (46 bp):
CTGATATAAGGCGTCAATCATGGGATTTATGGTAAGAAGGAAATAT
Found at i:5007 original size:19 final size:19
Alignment explanation
Indices: 4971--5007 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4961 AAAAATATGA
**
4971 GTAAAAAATAATTTAAAAT
1 GTAAAAAATAATAAAAAAT
4990 GTAAAAAATAATAAAAAA
1 GTAAAAAATAATAAAAAA
5008 AAGTCACGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.24
Consensus pattern (19 bp):
GTAAAAAATAATAAAAAAT
Found at i:8563 original size:26 final size:27
Alignment explanation
Indices: 8528--8598 Score: 90
Period size: 26 Copynumber: 2.7 Consensus size: 27
8518 CGTCACGTAG
**
8528 GGGCATTTTGGTCATTTTTGCA-CTAA
1 GGGCATTTTGGTCATTTTCACATCTAA
* *
8554 GGGCATTTTGGTCATTTACACATTTAA
1 GGGCATTTTGGTCATTTTCACATCTAA
*
8581 GGGCATTTTGGTCGTTTT
1 GGGCATTTTGGTCATTTT
8599 GAGTCTACTT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
26 19 0.50
27 19 0.50
ACGTcount: A:0.18, C:0.14, G:0.24, T:0.44
Consensus pattern (27 bp):
GGGCATTTTGGTCATTTTCACATCTAA
Found at i:24155 original size:33 final size:34
Alignment explanation
Indices: 24129--24192 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
24119 TTTCAATGCT
*
24129 ATGATCATCCAAAACAGA-TTTGTTTTCATCACA
1 ATGAGCATCCAAAACAGATTTTGTTTTCATCACA
*
24162 ATTAGCATCCAAAACAGATTTTG-TTTCATCA
1 ATGAGCATCCAAAACAGATTTTGTTTTCATCA
24193 TAAACAACAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 24 0.86
34 4 0.14
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.34
Consensus pattern (34 bp):
ATGAGCATCCAAAACAGATTTTGTTTTCATCACA
Found at i:24209 original size:33 final size:33
Alignment explanation
Indices: 24172--24276 Score: 104
Period size: 33 Copynumber: 3.2 Consensus size: 33
24162 ATTAGCATCC
* * *
24172 AAAACAGATTTTGTTTCATCATAAACAACACCT
1 AAAACAGATTTAGTGTCATCACAAACAACACCT
*
24205 AAAACAGATTTAGTGTCATCGCAAACAACA-CT
1 AAAACAGATTTAGTGTCATCACAAACAACACCT
** * * * *
24237 CAAATTAGGTTTAGTATCATCGCAAACAACATCT
1 -AAAACAGATTTAGTGTCATCACAAACAACACCT
24271 AAAACA
1 AAAACA
24277 CTCTTTGCAA
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
32 2 0.03
33 56 0.93
34 2 0.03
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.26
Consensus pattern (33 bp):
AAAACAGATTTAGTGTCATCACAAACAACACCT
Found at i:25789 original size:10 final size:10
Alignment explanation
Indices: 25776--25801 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
25766 TCAATTTCAC
25776 TCAATTCCTT
1 TCAATTCCTT
25786 TCAATTCCTT
1 TCAATTCCTT
25796 TCAATT
1 TCAATT
25802 AGGGCTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.23, C:0.27, G:0.00, T:0.50
Consensus pattern (10 bp):
TCAATTCCTT
Found at i:31036 original size:15 final size:15
Alignment explanation
Indices: 31018--31048 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
31008 TTACTTTTAC
*
31018 TACTTTTATCATTTT
1 TACTTTTACCATTTT
31033 TACTTTTACCATTTT
1 TACTTTTACCATTTT
31048 T
1 T
31049 CTTACTCTTT
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:0.19, C:0.16, G:0.00, T:0.65
Consensus pattern (15 bp):
TACTTTTACCATTTT
Found at i:31048 original size:24 final size:25
Alignment explanation
Indices: 31005--31075 Score: 72
Period size: 24 Copynumber: 2.8 Consensus size: 25
30995 TGATTACCAT
* *
31005 TTTTTACTTTTACTACTTTTATCA-
1 TTTTTACTTTTACCATTTTTATCAC
* *
31029 TTTTTACTTTTACCATTTTTCTTAC
1 TTTTTACTTTTACCATTTTTATCAC
*
31054 TCTTTTACTTAATACCATTTTT
1 T-TTTTACTT-TTACCATTTTT
31076 GTTTAATACC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
24 20 0.51
25 1 0.03
26 8 0.21
27 10 0.26
ACGTcount: A:0.20, C:0.18, G:0.00, T:0.62
Consensus pattern (25 bp):
TTTTTACTTTTACCATTTTTATCAC
Found at i:31159 original size:16 final size:16
Alignment explanation
Indices: 31056--31159 Score: 61
Period size: 16 Copynumber: 6.2 Consensus size: 16
31046 TTTCTTACTC
31056 TTTTACTTAATACCAT
1 TTTTACTTAATACCAT
**
31072 TTTTGTTTAATACCAT
1 TTTTACTTAATACCAT
*
31088 CTCTTAC-TAGATACCAT
1 -TTTTACTTA-ATACCAT
*
31105 TTTTGACCCTTAACACCAT
1 TTTT-A--CTTAATACCAT
* **
31124 TTTTAATTCTTTA-C-T
1 TTTTACTT-AATACCAT
31139 CTTTTACTTAATACCAT
1 -TTTTACTTAATACCAT
31156 TTTT
1 TTTT
31160 TAATCTACAC
Statistics
Matches: 64, Mismatches: 14, Indels: 20
0.65 0.14 0.20
Matches are distributed among these distances:
15 3 0.05
16 34 0.53
17 13 0.20
18 1 0.02
19 11 0.17
20 2 0.03
ACGTcount: A:0.26, C:0.21, G:0.03, T:0.50
Consensus pattern (16 bp):
TTTTACTTAATACCAT
Found at i:31245 original size:14 final size:14
Alignment explanation
Indices: 31226--31274 Score: 64
Period size: 14 Copynumber: 3.5 Consensus size: 14
31216 ATTTTGACCC
31226 TCTTACTGATTACT
1 TCTTACTGATTACT
*
31240 TCTTACTAATTACT
1 TCTTACTGATTACT
31254 T-TTACCTGATTACT
1 TCTTA-CTGATTACT
*
31268 TTTTACT
1 TCTTACT
31275 ACTATTTGCC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 3 0.10
14 25 0.81
15 3 0.10
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (14 bp):
TCTTACTGATTACT
Found at i:31312 original size:14 final size:13
Alignment explanation
Indices: 31289--31326 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
31279 TTTGCCATTT
31289 TTACTTTTTACTGA
1 TTAC-TTTTACTGA
31303 TTACTCTTTACTGA
1 TTACT-TTTACTGA
31317 TTACTTTTAC
1 TTACTTTTAC
31327 CTTTTTACTG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.26
14 17 0.74
ACGTcount: A:0.21, C:0.18, G:0.05, T:0.55
Consensus pattern (13 bp):
TTACTTTTACTGA
Found at i:31634 original size:32 final size:32
Alignment explanation
Indices: 31572--31658 Score: 120
Period size: 32 Copynumber: 2.7 Consensus size: 32
31562 TTCTTAATTA
* *
31572 TTAATTTACTGATTAGTCCTTTTTAGTTCCTTTC
1 TTAA-TTACTGATTAAT-CTTTTTACTTCCTTTC
31606 TTAATTACTGATTAATCTTTTTACTTCCTTTC
1 TTAATTACTGATTAATCTTTTTACTTCCTTTC
* *
31638 TTAATTACTTATTACTCTTTT
1 TTAATTACTGATTAATCTTTT
31659 ACTCTCTCCT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 34 0.69
33 11 0.22
34 4 0.08
ACGTcount: A:0.21, C:0.17, G:0.05, T:0.57
Consensus pattern (32 bp):
TTAATTACTGATTAATCTTTTTACTTCCTTTC
Found at i:31788 original size:38 final size:37
Alignment explanation
Indices: 31669--31818 Score: 119
Period size: 38 Copynumber: 4.0 Consensus size: 37
31659 ACTCTCTCCT
* * *
31669 TTAAGTATCAATTTACTGATTA--A-TCCATTGACTC
1 TTAATTATCAATTTACTGATTATTATTACTTTGACTC
* * *
31703 TTAATTA-CTGATTTACTGATTACTATTTTTACCTTGACTC
1 TTAATTATC-AATTTACTGA-T--TATTATTACTTTGACTC
* *
31743 TTGATTATCAATTTTACTGATTATTCTTACTTTGACTC
1 TTAATTATCAA-TTTACTGATTATTATTACTTTGACTC
* * *
31781 TTAATTATCAACTTTACTGACTACTAATACTTTGACTC
1 TTAATTATCAA-TTTACTGATTATTATTACTTTGACTC
Statistics
Matches: 92, Mismatches: 15, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
33 1 0.01
34 15 0.16
35 1 0.01
37 2 0.02
38 47 0.51
40 17 0.18
41 9 0.10
ACGTcount: A:0.28, C:0.18, G:0.07, T:0.47
Consensus pattern (37 bp):
TTAATTATCAATTTACTGATTATTATTACTTTGACTC
Done.