Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013400.1 Corchorus capsularis cultivar CVL-1 contig13421, 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: 70506
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2388 original size:16 final size:16
Alignment explanation
Indices: 2348--2457 Score: 134
Period size: 16 Copynumber: 6.8 Consensus size: 16
2338 TTGGTGACCT
2348 CACCAGGTGAGTATTG
1 CACCAGGTGAGTATTG
* **
2364 TACTGGGTGAGTATCT-
1 CACCAGGTGAGTAT-TG
2380 CACCAGGTGAGTATCT-
1 CACCAGGTGAGTAT-TG
2396 CACCAGGTGAGTATTG
1 CACCAGGTGAGTATTG
2412 CACCAGGTGAGTATTG
1 CACCAGGTGAGTATTG
*
2428 CACCAGGTGAGTGTTTG
1 CACCAGGTGAGT-ATTG
*
2445 TACCAGGTGAGTA
1 CACCAGGTGAGTA
2458 GGGTAAGAAC
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
15 1 0.01
16 66 0.80
17 15 0.18
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (16 bp):
CACCAGGTGAGTATTG
Found at i:5697 original size:156 final size:155
Alignment explanation
Indices: 5310--5697 Score: 390
Period size: 156 Copynumber: 2.5 Consensus size: 155
5300 CCAAACCTCT
*
5310 CACCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTTTATTCTAAGTCTGAATGAGCTG
1 CACCTCAAACTGTCCTTAAATGAAAAACTAGCATAAG-TTTTTCATTCTAAGTCTGAATGAGCTG
** * * *
5375 AAATTTTGCCAAGGGACTTAGATTATCTCCATGAGACTATGGAAAAAATTCTAAGTAAAACTGAG
65 AAATTTCACC-AGAGACTTAGATTATCCCCATAAGACTATGGAAAAAATTCTAAGTAAAACTGAG
* * * ** *
5440 CTCCCCTTGATGGTTAACTAGGTTTCT
129 ATCCCCTAGATAGAGAACTAGGTTTCA
* ** * *
5467 CTCC-CTAAGTTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTC-CAACGAGGCT
1 CACCTC-AAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGA-GCT
* * *
5530 G-ATTTTCCACCAGTAGACTTAGATTATCCCCATAAGGCTATGGGAAAAATTCTAAGTAAAAAC-
64 GAAATTT-CACCAG-AGACTTAGATTATCCCCATAAGACTATGGAAAAAATTCTAAGT-AAAACT
* * * *
5593 GA-ATCCTCTAGCATAGAGAAGTTGGTTTGA
126 GAGATCCCCTAG-ATAGAGAACTAGGTTTCA
* * * * ** *
5623 CACCTCAAACTGTCCTTAATTGAAAAACTAGTATAAGTTTTTCATACGAAGTCTGTTTGAGATGA
1 CACCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGAGCTGA
5688 AATTTCACCA
66 AATTTCACCA
5698 AGATGATCTA
Statistics
Matches: 185, Mismatches: 37, Indels: 19
0.77 0.15 0.08
Matches are distributed among these distances:
155 16 0.09
156 125 0.68
157 44 0.24
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (155 bp):
CACCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGAGCTGA
AATTTCACCAGAGACTTAGATTATCCCCATAAGACTATGGAAAAAATTCTAAGTAAAACTGAGAT
CCCCTAGATAGAGAACTAGGTTTCA
Found at i:6815 original size:16 final size:16
Alignment explanation
Indices: 6794--6878 Score: 57
Period size: 16 Copynumber: 5.3 Consensus size: 16
6784 GTTCGGGTCA
*
6794 TCGGGTTTATTCGGGT
1 TCGGGTTAATTCGGGT
*
6810 TCGGGTTAAATTTGGG-
1 TCGGGTT-AATTCGGGT
** *
6826 TCATGTTGATTCGGGT
1 TCGGGTTAATTCGGGT
* *
6842 TCGGGTCAATTTTGGG-
1 TCGGGTTAA-TTCGGGT
* *
6858 TCAGATTAATTCGGGT
1 TCGGGTTAATTCGGGT
6874 TCGGG
1 TCGGG
6879 CTTGGATTGG
Statistics
Matches: 48, Mismatches: 17, Indels: 8
0.66 0.23 0.11
Matches are distributed among these distances:
15 11 0.23
16 26 0.54
17 11 0.23
ACGTcount: A:0.14, C:0.12, G:0.35, T:0.39
Consensus pattern (16 bp):
TCGGGTTAATTCGGGT
Found at i:6840 original size:32 final size:32
Alignment explanation
Indices: 6802--6878 Score: 111
Period size: 32 Copynumber: 2.4 Consensus size: 32
6792 CATCGGGTTT
* *
6802 ATTCGGGTTCGGGTTAAATTTGGGTCATG-TTG
1 ATTCGGGTTCGGGTCAAATTTGGGTCA-GATTA
*
6834 ATTCGGGTTCGGGTCAATTTTGGGTCAGATTA
1 ATTCGGGTTCGGGTCAAATTTGGGTCAGATTA
6866 ATTCGGGTTCGGG
1 ATTCGGGTTCGGG
6879 CTTGGATTGG
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
31 1 0.02
32 40 0.98
ACGTcount: A:0.16, C:0.12, G:0.35, T:0.38
Consensus pattern (32 bp):
ATTCGGGTTCGGGTCAAATTTGGGTCAGATTA
Found at i:7053 original size:20 final size:20
Alignment explanation
Indices: 7020--7058 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
7010 CATAGATGGA
*
7020 ATTTTCAGAAATTATTATTT
1 ATTTTCAGAAATTAGTATTT
7040 ATTTTCA-AATATTAGTATT
1 ATTTTCAGAA-ATTAGTATT
7059 GAATTCAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (20 bp):
ATTTTCAGAAATTAGTATTT
Found at i:7112 original size:16 final size:15
Alignment explanation
Indices: 7093--7143 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 15
7083 GTTTTTCCGC
7093 GTTTCAGATTTTTCGG
1 GTTT-AGATTTTTCGG
*
7109 GTTTTGATTTTTTCGG
1 GTTTAGA-TTTTTCGG
*
7125 GTTTGAGTTTTTTCGG
1 GTTT-AGATTTTTCGG
7141 GTT
1 GTT
7144 CGAATTTGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 2 0.07
16 27 0.90
17 1 0.03
ACGTcount: A:0.08, C:0.08, G:0.27, T:0.57
Consensus pattern (15 bp):
GTTTAGATTTTTCGG
Found at i:7119 original size:15 final size:16
Alignment explanation
Indices: 7101--7143 Score: 70
Period size: 16 Copynumber: 2.7 Consensus size: 16
7091 GCGTTTCAGA
7101 TTTTTCGGGTTTTGAT
1 TTTTTCGGGTTTTGAT
7117 TTTTTCGGG-TTTGAGT
1 TTTTTCGGGTTTTGA-T
7133 TTTTTCGGGTT
1 TTTTTCGGGTT
7144 CGAATTTGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.20
16 19 0.76
17 1 0.04
ACGTcount: A:0.05, C:0.07, G:0.28, T:0.60
Consensus pattern (16 bp):
TTTTTCGGGTTTTGAT
Found at i:8873 original size:16 final size:16
Alignment explanation
Indices: 8852--8882 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
8842 TTCATAATTA
8852 ATTGAAGGTAGAACTG
1 ATTGAAGGTAGAACTG
*
8868 ATTGAAGGTGGAACT
1 ATTGAAGGTAGAACT
8883 TTTTGGTTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.32, T:0.26
Consensus pattern (16 bp):
ATTGAAGGTAGAACTG
Found at i:24136 original size:2 final size:2
Alignment explanation
Indices: 24129--24165 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
24119 AGTTTGGGTG
24129 TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA CTA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA T
24166 GAGTTGAAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 30 0.91
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:24153 original size:19 final size:19
Alignment explanation
Indices: 24129--24165 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
24119 AGTTTGGGTG
24129 TATATATATATAATATATA
1 TATATATATATAATATATA
*
24148 TATATATATATACTATAT
1 TATATATATATAATATAT
24166 GAGTTGAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
TATATATATATAATATATA
Found at i:25942 original size:81 final size:81
Alignment explanation
Indices: 25803--25965 Score: 317
Period size: 81 Copynumber: 2.0 Consensus size: 81
25793 TCTTCTTGGA
25803 GCCGCACTCCCTAGCTAGCTTTAGTTACTTTGATATCGCCTTTTTGTCCTTAAATGAACAAAATG
1 GCCGCACTCCCTAGCTAGCTTTAGTTACTTTGATATCGCCTTTTTGTCCTTAAATGAACAAAATG
25868 CAAATTTGACTCCCGG
66 CAAATTTGACTCCCGG
*
25884 GCCGCACTCCCTAGCTAGCTTTAGTTACTTTGATATCGCCTTTTTGTCCTTAAGTGAACAAAATG
1 GCCGCACTCCCTAGCTAGCTTTAGTTACTTTGATATCGCCTTTTTGTCCTTAAATGAACAAAATG
25949 CAAATTTGACTCCCGG
66 CAAATTTGACTCCCGG
25965 G
1 G
25966 GGAGTGCTAC
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 81 1.00
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (81 bp):
GCCGCACTCCCTAGCTAGCTTTAGTTACTTTGATATCGCCTTTTTGTCCTTAAATGAACAAAATG
CAAATTTGACTCCCGG
Found at i:28007 original size:19 final size:19
Alignment explanation
Indices: 27983--28045 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 19
27973 GATGTGGTGG
27983 AATTGATGGTGGTCGGGAC
1 AATTGATGGTGGTCGGGAC
* *
28002 AATTGATGATATGT-GGTGA-
1 AATTGATGGT-GGTCGG-GAC
*
28021 AATTGGT-GTGGTCGGGAC
1 AATTGATGGTGGTCGGGAC
28039 AATTGAT
1 AATTGAT
28046 AATAATTTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 9
0.69 0.12 0.18
Matches are distributed among these distances:
17 4 0.12
18 9 0.26
19 17 0.50
20 4 0.12
ACGTcount: A:0.25, C:0.06, G:0.37, T:0.32
Consensus pattern (19 bp):
AATTGATGGTGGTCGGGAC
Found at i:28032 original size:37 final size:38
Alignment explanation
Indices: 27974--28045 Score: 119
Period size: 37 Copynumber: 1.9 Consensus size: 38
27964 ATCATGAATG
*
27974 ATGTGGTGGAATTGATGGTGGTCGGGACAATTGATGAT
1 ATGTGGTGAAATTGATGGTGGTCGGGACAATTGATGAT
*
28012 ATGTGGTGAAATTGGT-GTGGTCGGGACAATTGAT
1 ATGTGGTGAAATTGATGGTGGTCGGGACAATTGAT
28046 AATAATTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
37 18 0.56
38 14 0.44
ACGTcount: A:0.24, C:0.06, G:0.39, T:0.32
Consensus pattern (38 bp):
ATGTGGTGAAATTGATGGTGGTCGGGACAATTGATGAT
Found at i:29511 original size:26 final size:26
Alignment explanation
Indices: 29475--29528 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
29465 CTAACTTTAG
*
29475 AGTTAGGACTAGCATCAAGAATGTGC
1 AGTTAGGACTAACATCAAGAATGTGC
*
29501 AGTTAGGACTAACATGAAGAATGTGC
1 AGTTAGGACTAACATCAAGAATGTGC
29527 AG
1 AG
29529 CAGCGGTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.37, C:0.13, G:0.28, T:0.22
Consensus pattern (26 bp):
AGTTAGGACTAACATCAAGAATGTGC
Found at i:29618 original size:12 final size:13
Alignment explanation
Indices: 29601--29632 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
29591 TTTCTCCCAT
29601 GGACTTCA-TCAA
1 GGACTTCACTCAA
29613 GGACTT-ACTCAA
1 GGACTTCACTCAA
29625 GGACTTCA
1 GGACTTCA
29633 ACTTTGACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 1 0.06
12 16 0.89
13 1 0.06
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (13 bp):
GGACTTCACTCAA
Found at i:39519 original size:17 final size:17
Alignment explanation
Indices: 39494--39530 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
39484 TAATTACCAA
39494 AAAATTGAATGG-AAAG
1 AAAATTGAATGGAAAAG
39510 AAAATATGAATGGAAAAG
1 AAAAT-TGAATGGAAAAG
39528 AAA
1 AAA
39531 TGAAAGTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.26
17 7 0.37
18 7 0.37
ACGTcount: A:0.62, C:0.00, G:0.22, T:0.16
Consensus pattern (17 bp):
AAAATTGAATGGAAAAG
Found at i:52390 original size:33 final size:33
Alignment explanation
Indices: 52353--52436 Score: 134
Period size: 33 Copynumber: 2.5 Consensus size: 33
52343 TGCGGAGTCT
* *
52353 CCCCACAGGGGCGGCTTCACCATGGGCA-GGCTG
1 CCCCACTGGGGCGGCTTCACAATGGGCAGGGC-G
52386 CCCCACTGGGGCGGCTTCACAATGGGCAGGGCG
1 CCCCACTGGGGCGGCTTCACAATGGGCAGGGCG
52419 CCCCACTGGGGCGGCTTC
1 CCCCACTGGGGCGGCTTC
52437 GCCACGGTAG
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
33 45 0.94
34 3 0.06
ACGTcount: A:0.13, C:0.37, G:0.37, T:0.13
Consensus pattern (33 bp):
CCCCACTGGGGCGGCTTCACAATGGGCAGGGCG
Found at i:52564 original size:31 final size:32
Alignment explanation
Indices: 52520--52584 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 32
52510 AAAATAGCCG
*
52520 AGCCGCCCCACCGGAACGGTCTGCCGTGGCGA
1 AGCCGCCCCACCGGAACGGCCTGCCGTGGCGA
*
52552 AGCCG-CCCACCGGGACGGCCTGCCGTGGCGA
1 AGCCGCCCCACCGGAACGGCCTGCCGTGGCGA
52583 AG
1 AG
52585 GGGCGGCCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 26 0.84
32 5 0.16
ACGTcount: A:0.15, C:0.40, G:0.37, T:0.08
Consensus pattern (32 bp):
AGCCGCCCCACCGGAACGGCCTGCCGTGGCGA
Found at i:57565 original size:169 final size:169
Alignment explanation
Indices: 57286--57603 Score: 636
Period size: 169 Copynumber: 1.9 Consensus size: 169
57276 GTATTAGTTG
57286 CATACACCTATATGTGTTCATGTCATCATCATCGTCATGCGTATAGATGTGACTCTGTTTATAAA
1 CATACACCTATATGTGTTCATGTCATCATCATCGTCATGCGTATAGATGTGACTCTGTTTATAAA
57351 ATGGGAAATATTTGTTATCAATATACTATTTTTCTTTTGATGCCTTTTTGTAAAAATGTATTATT
66 ATGGGAAATATTTGTTATCAATATACTATTTTTCTTTTGATGCCTTTTTGTAAAAATGTATTATT
57416 ATGTGTAAGGACAGTTGTAATATTTGTTTTTTCCTTACA
131 ATGTGTAAGGACAGTTGTAATATTTGTTTTTTCCTTACA
57455 CATACACCTATATGTGTTCATGTCATCATCATCGTCATGCGTATAGATGTGACTCTGTTTATAAA
1 CATACACCTATATGTGTTCATGTCATCATCATCGTCATGCGTATAGATGTGACTCTGTTTATAAA
57520 ATGGGAAATATTTGTTATCAATATACTATTTTTCTTTTGATGCCTTTTTGTAAAAATGTATTATT
66 ATGGGAAATATTTGTTATCAATATACTATTTTTCTTTTGATGCCTTTTTGTAAAAATGTATTATT
57585 ATGTGTAAGGACAGTTGTA
131 ATGTGTAAGGACAGTTGTA
57604 TACATTATAG
Statistics
Matches: 149, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
169 149 1.00
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.43
Consensus pattern (169 bp):
CATACACCTATATGTGTTCATGTCATCATCATCGTCATGCGTATAGATGTGACTCTGTTTATAAA
ATGGGAAATATTTGTTATCAATATACTATTTTTCTTTTGATGCCTTTTTGTAAAAATGTATTATT
ATGTGTAAGGACAGTTGTAATATTTGTTTTTTCCTTACA
Found at i:58793 original size:78 final size:78
Alignment explanation
Indices: 58640--58795 Score: 197
Period size: 78 Copynumber: 2.0 Consensus size: 78
58630 CGGGAGGCAA
* * *
58640 GTCGACAATAGAAAGCCAAGGGTGGAGATGGCTCATGGTGACCCTATTGAAAAACCTGTATCTGT
1 GTCGACAATAGAAAGCCAAGGGTGGAAATAGCTCATGGTGACCCTATTGAAAAACCTGTAACTGT
*
58705 TTGCAAAAATCCT
66 TCGCAAAAATCCT
* * * * *
58718 GTCGACAATAGAAAGCTAGGGGTGGAAATAGCTCGTGGTGGCCCTATTGAAAGACCTG-AACATG
1 GTCGACAATAGAAAGCCAAGGGTGGAAATAGCTCATGGTGACCCTATTGAAAAACCTGTAAC-TG
* *
58782 TTCGTAGAAATCCT
65 TTCGCAAAAATCCT
58796 ATCTTTGATA
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
77 2 0.03
78 64 0.97
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (78 bp):
GTCGACAATAGAAAGCCAAGGGTGGAAATAGCTCATGGTGACCCTATTGAAAAACCTGTAACTGT
TCGCAAAAATCCT
Found at i:60200 original size:64 final size:64
Alignment explanation
Indices: 60099--60226 Score: 256
Period size: 64 Copynumber: 2.0 Consensus size: 64
60089 TTATTACTAC
60099 TATTATAATCATTATTATATTATTATTTTTATATCCTAATTAATAGTATTTGCTAAGGGAGAAA
1 TATTATAATCATTATTATATTATTATTTTTATATCCTAATTAATAGTATTTGCTAAGGGAGAAA
60163 TATTATAATCATTATTATATTATTATTTTTATATCCTAATTAATAGTATTTGCTAAGGGAGAAA
1 TATTATAATCATTATTATATTATTATTTTTATATCCTAATTAATAGTATTTGCTAAGGGAGAAA
60227 AGTAATGTTA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (64 bp):
TATTATAATCATTATTATATTATTATTTTTATATCCTAATTAATAGTATTTGCTAAGGGAGAAA
Found at i:68641 original size:31 final size:28
Alignment explanation
Indices: 68606--68669 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
68596 AAAAAGGTTA
*
68606 ATTTGGCCAAAATTTGGAGTTCAAGGGACTT
1 ATTTGG-CAAAA-TTGAAGTTCAAGGG-CTT
* *
68637 ATTTGGCGAAATTGAAGTTTAAGGGCTT
1 ATTTGGCAAAATTGAAGTTCAAGGGCTT
68665 ATTTG
1 ATTTG
68670 ACCGTTACCA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 8 0.27
29 12 0.40
30 4 0.13
31 6 0.20
ACGTcount: A:0.28, C:0.09, G:0.27, T:0.36
Consensus pattern (28 bp):
ATTTGGCAAAATTGAAGTTCAAGGGCTT
Done.