Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013376.1 Corchorus capsularis cultivar CVL-1 contig13397, 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: 94299
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:216 original size:21 final size:20
Alignment explanation
Indices: 181--232 Score: 88
Period size: 21 Copynumber: 2.6 Consensus size: 20
171 AAAAATTATA
181 AAAAGGGGGG-GTATTTAGC
1 AAAAGGGGGGCGTATTTAGC
200 AAAAGGGGGGCGTTATTTAGC
1 AAAAGGGGGGCG-TATTTAGC
221 AAAAGGGGGGCG
1 AAAAGGGGGGCG
233 GTAAATAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 10 0.32
20 1 0.03
21 20 0.65
ACGTcount: A:0.31, C:0.08, G:0.44, T:0.17
Consensus pattern (20 bp):
AAAAGGGGGGCGTATTTAGC
Found at i:244 original size:21 final size:21
Alignment explanation
Indices: 199--244 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
189 GGGTATTTAG
* ** *
199 CAAAAGGGGGGCGTTATTTAG
1 CAAAAGGGGGGCGGTAAATAA
220 CAAAAGGGGGGCGGTAAATAA
1 CAAAAGGGGGGCGGTAAATAA
241 CAAA
1 CAAA
245 CCCCAATAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.11, G:0.35, T:0.15
Consensus pattern (21 bp):
CAAAAGGGGGGCGGTAAATAA
Found at i:696 original size:28 final size:28
Alignment explanation
Indices: 617--697 Score: 117
Period size: 29 Copynumber: 2.8 Consensus size: 28
607 AAATTGCAAG
617 TTTAGGGTACAAAATGTTCAAAATTAAAA
1 TTTAGGGTACAAAATG-TCAAAATTAAAA
* * *
646 TTTAGGGAACAAAATATCTAAAATTAAAT
1 TTTAGGGTACAAAATGTC-AAAATTAAAA
675 TTTAGGGTACAAAATGTCAAAAT
1 TTTAGGGTACAAAATGTCAAAAT
698 CATACAAGTT
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
28 7 0.15
29 39 0.85
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (28 bp):
TTTAGGGTACAAAATGTCAAAATTAAAA
Found at i:1717 original size:24 final size:25
Alignment explanation
Indices: 1683--1746 Score: 80
Period size: 24 Copynumber: 2.7 Consensus size: 25
1673 CTTGCAAAGT
1683 GAGTCGGAGGTTG-AGAGACAGAAG
1 GAGTCGGAGGTTGTAGAGACAGAAG
* * *
1707 GAGTCGAAGG-TGTAGAGGCGGAAG
1 GAGTCGGAGGTTGTAGAGACAGAAG
1731 GAGTCGGAGG-TGTAGA
1 GAGTCGGAGGTTGTAGA
1747 TTCACGCCCA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 2 0.06
24 33 0.94
ACGTcount: A:0.30, C:0.08, G:0.48, T:0.14
Consensus pattern (25 bp):
GAGTCGGAGGTTGTAGAGACAGAAG
Found at i:3131 original size:28 final size:28
Alignment explanation
Indices: 3089--3159 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
3079 CCAGGACGTC
* * *
3089 TCCCTCTGGTGTATCAGGTGGCAAATCT
1 TCCCTCTGGTATATCAGGCGGAAAATCT
3117 TCCCTCTGGTATATCAGGCGGAAAATCT
1 TCCCTCTGGTATATCAGGCGGAAAATCT
*
3145 TCCCTCTGGTCTATC
1 TCCCTCTGGTATATC
3160 CAGCATTGGG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.18, C:0.28, G:0.21, T:0.32
Consensus pattern (28 bp):
TCCCTCTGGTATATCAGGCGGAAAATCT
Found at i:4172 original size:15 final size:15
Alignment explanation
Indices: 4152--4190 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 15
4142 GCTAGTAAGG
4152 GAAGTCGGAGGGACA
1 GAAGTCGGAGGGACA
4167 GAAGTCGTGGAGGGACA
1 GAAGTC--GGAGGGACA
4184 GAAGTCG
1 GAAGTCG
4191 TAGTCTGGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 7 0.32
17 15 0.68
ACGTcount: A:0.31, C:0.13, G:0.46, T:0.10
Consensus pattern (15 bp):
GAAGTCGGAGGGACA
Found at i:4180 original size:17 final size:17
Alignment explanation
Indices: 4158--4191 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
4148 AAGGGAAGTC
4158 GGAGGGACAGAAGTCGT
1 GGAGGGACAGAAGTCGT
4175 GGAGGGACAGAAGTCGT
1 GGAGGGACAGAAGTCGT
4192 AGTCTGGCCT
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:0.29, C:0.12, G:0.47, T:0.12
Consensus pattern (17 bp):
GGAGGGACAGAAGTCGT
Found at i:5870 original size:43 final size:44
Alignment explanation
Indices: 5804--5890 Score: 142
Period size: 43 Copynumber: 2.0 Consensus size: 44
5794 TAACTTATTA
*
5804 TTGTTACCTACTCTTTTTATAAAATTTATTGCTATAC-AACAAC
1 TTGTTACCAACTCTTTTTATAAAATTTATTGCTATACGAACAAC
5847 TTGTTACCAACTC-TTTTATTAAAATTTATTGCTATACGAACAAC
1 TTGTTACCAACTCTTTTTA-TAAAATTTATTGCTATACGAACAAC
5891 CCAGCAGAGA
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
42 5 0.12
43 30 0.73
44 6 0.15
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.43
Consensus pattern (44 bp):
TTGTTACCAACTCTTTTTATAAAATTTATTGCTATACGAACAAC
Found at i:6346 original size:31 final size:31
Alignment explanation
Indices: 6304--6399 Score: 120
Period size: 31 Copynumber: 3.0 Consensus size: 31
6294 TGAACAAAGC
*
6304 CCGGTCACGATCCGCGTGCGACCCACCATGG
1 CCGGTCACGATCCACGTGCGACCCACCATGG
* *
6335 CCGGTCGCGATCCACGTGCGACTGGCACCATGG
1 CCGGTCACGATCCACGTGCGAC--CCACCATGG
** *
6368 TAGGTCACAATCCACGTGCGACCCACCATGG
1 CCGGTCACGATCCACGTGCGACCCACCATGG
6399 C
1 C
6400 TCGGGTCGCG
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
31 28 0.52
33 26 0.48
ACGTcount: A:0.19, C:0.39, G:0.28, T:0.15
Consensus pattern (31 bp):
CCGGTCACGATCCACGTGCGACCCACCATGG
Found at i:6994 original size:30 final size:30
Alignment explanation
Indices: 6958--7018 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
6948 CCACATATTA
6958 GGCTTTATTGATGCTAGGGGGGCATGAGTT
1 GGCTTTATTGATGCTAGGGGGGCATGAGTT
*
6988 GGCTTTATTGATGTTAGGGGGGCATGAGTT
1 GGCTTTATTGATGCTAGGGGGGCATGAGTT
7018 G
1 G
7019 CTAGTTTATC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.16, C:0.08, G:0.41, T:0.34
Consensus pattern (30 bp):
GGCTTTATTGATGCTAGGGGGGCATGAGTT
Found at i:9461 original size:29 final size:29
Alignment explanation
Indices: 9426--9482 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
9416 TTTGTTTTTT
*
9426 AAAGTTAAGAGGCCAATTTGTCACAAAAA
1 AAAGTTAAGAGGCCAATTTATCACAAAAA
* * *
9455 AAAGTTAAGGGGTCAATTTATCCCAAAA
1 AAAGTTAAGAGGCCAATTTATCACAAAA
9483 TGGATAGTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.46, C:0.14, G:0.18, T:0.23
Consensus pattern (29 bp):
AAAGTTAAGAGGCCAATTTATCACAAAAA
Found at i:12827 original size:2 final size:2
Alignment explanation
Indices: 12820--12847 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12810 AGCTATTATG
12820 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12848 GGACTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18188 original size:98 final size:95
Alignment explanation
Indices: 18068--18256 Score: 324
Period size: 98 Copynumber: 2.0 Consensus size: 95
18058 TTGTTCTATA
18068 CAAAATAAAATTTAGAGGAGCCAAATTGAAATTTTTAAGGTGTAGTTGCATATAGATACACAATT
1 CAAAATAAAATTTAGAGGAGCCAAATTGAAATTTTTAAGGTGTAGTTGCATATAGATACACAA-T
18133 AATTACCAAGGGGATTTTCTAATTTTTGGTATG
65 --TTACCAAGGGGATTTTCTAATTTTTGGTATG
* * *
18166 CAAAATTAAATTTGGAGGAGCCAATTTGAAATTTTTAAGGTGTAGTTGCATATAGATACACAATT
1 CAAAATAAAATTTAGAGGAGCCAAATTGAAATTTTTAAGGTGTAGTTGCATATAGATACACAATT
18231 TACCAAGGGGATTTTCTAATTTTTGG
66 TACCAAGGGGATTTTCTAATTTTTGG
18257 GAGGCATGGC
Statistics
Matches: 88, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
95 27 0.31
97 1 0.01
98 60 0.68
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.35
Consensus pattern (95 bp):
CAAAATAAAATTTAGAGGAGCCAAATTGAAATTTTTAAGGTGTAGTTGCATATAGATACACAATT
TACCAAGGGGATTTTCTAATTTTTGGTATG
Found at i:37674 original size:11 final size:11
Alignment explanation
Indices: 37660--37697 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
37650 ATCCATAACA
37660 AATTTATAATT
1 AATTTATAATT
37671 AATTTATAATT
1 AATTTATAATT
37682 -ATTTGATAATT
1 AATTT-ATAATT
*
37693 TATTT
1 AATTT
37698 TATATATAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:52346 original size:25 final size:25
Alignment explanation
Indices: 52297--52347 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
52287 TTAGTAGAAT
*
52297 AATTGTAAAAGTTTATTTCTAAAAA
1 AATTGTAAAAGTATATTTCTAAAAA
52322 AATTGTAAAAGAATATATTT-TAAAAA
1 AATTGTAAAAG--TATATTTCTAAAAA
52348 TTCTAATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 11 0.48
26 6 0.26
27 6 0.26
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (25 bp):
AATTGTAAAAGTATATTTCTAAAAA
Found at i:59003 original size:45 final size:45
Alignment explanation
Indices: 58937--59026 Score: 137
Period size: 45 Copynumber: 2.0 Consensus size: 45
58927 GATTACTTCT
58937 CCAGCTCATCATTAACCCGGGGTA-GGGATCTTTCAGTAATTCCAC
1 CCAGCTCATCATTAACCCGGGGTATGGG-TCTTTCAGTAATTCCAC
** *
58982 CCAGCTCATCATTAATTCGGGGTATGGGTCTTTTAGTAATTCCAC
1 CCAGCTCATCATTAACCCGGGGTATGGGTCTTTCAGTAATTCCAC
59027 TACTCTATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
45 38 0.93
46 3 0.07
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.31
Consensus pattern (45 bp):
CCAGCTCATCATTAACCCGGGGTATGGGTCTTTCAGTAATTCCAC
Found at i:66010 original size:17 final size:17
Alignment explanation
Indices: 65988--66021 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
65978 AATTGATTAA
65988 TGCAAACCATATAGTAT
1 TGCAAACCATATAGTAT
66005 TGCAAACCATATAGTAT
1 TGCAAACCATATAGTAT
66022 ATCATTTAAA
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:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (17 bp):
TGCAAACCATATAGTAT
Found at i:70314 original size:2 final size:2
Alignment explanation
Indices: 70307--70339 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
70297 GACGGAGACT
*
70307 GA GA GA GA GA GA GA GA GA GA GA GA AA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
70340 TTTTAGGGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:79144 original size:79 final size:79
Alignment explanation
Indices: 79013--79191 Score: 304
Period size: 79 Copynumber: 2.3 Consensus size: 79
79003 AACAAACAAT
* * *
79013 GGATAAACTTCAAGGTTATAGATGAGTATAGAACAAGATTTTACCCTCAATGTTGCCATCATTCA
1 GGATAAAATTCAAGGTTATAGAAGAGTATAGAACAAGATTTTACCCCCAATGTTGCCATCATTCA
*
79078 GATTTATATTCGCA
66 GATTTATATTCACA
79092 GGATAAAATTCAAGGTTATAGAAGAGTATAGAACAAGATTTTACCCCCAATGTTGCCATCATTCA
1 GGATAAAATTCAAGGTTATAGAAGAGTATAGAACAAGATTTTACCCCCAATGTTGCCATCATTCA
* *
79157 GATTTATATTTATA
66 GATTTATATTCACA
79171 GGATAAAATTCAAGGTTATAG
1 GGATAAAATTCAAGGTTATAG
79192 CCTCACACCA
Statistics
Matches: 94, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 94 1.00
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (79 bp):
GGATAAAATTCAAGGTTATAGAAGAGTATAGAACAAGATTTTACCCCCAATGTTGCCATCATTCA
GATTTATATTCACA
Found at i:83944 original size:2 final size:2
Alignment explanation
Indices: 83937--83966 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
83927 GAATTGCAAA
83937 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
83967 TTTAAACAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:86791 original size:13 final size:13
Alignment explanation
Indices: 86773--86797 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
86763 TGTTGTTATT
86773 TTGTAGATCTAAG
1 TTGTAGATCTAAG
86786 TTGTAGATCTAA
1 TTGTAGATCTAA
86798 AATTATGTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (13 bp):
TTGTAGATCTAAG
Found at i:87222 original size:22 final size:22
Alignment explanation
Indices: 87191--87236 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
87181 TTAAAAGTGT
87191 AAAAAATGAGACAATGTTTAGC
1 AAAAAATGAGACAATGTTTAGC
* **
87213 AAAAACTGAGACGGTGTTTAGC
1 AAAAAATGAGACAATGTTTAGC
87235 AA
1 AA
87237 CACCATAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.46, C:0.11, G:0.22, T:0.22
Consensus pattern (22 bp):
AAAAAATGAGACAATGTTTAGC
Found at i:90021 original size:14 final size:15
Alignment explanation
Indices: 89981--90023 Score: 79
Period size: 15 Copynumber: 2.9 Consensus size: 15
89971 TCATATTCAT
89981 GAATCAATTATTTGG
1 GAATCAATTATTTGG
89996 GAATCAATTATTTGG
1 GAATCAATTATTTGG
90011 GAATC-ATTATTTG
1 GAATCAATTATTTG
90024 TTTAGGGTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
14 8 0.29
15 20 0.71
ACGTcount: A:0.33, C:0.07, G:0.19, T:0.42
Consensus pattern (15 bp):
GAATCAATTATTTGG
Done.