Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012131.1 Corchorus capsularis cultivar CVL-1 contig12152, 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: 62814
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2410 original size:30 final size:30
Alignment explanation
Indices: 2374--2441 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
2364 AAGGGTCCAT
*
2374 TGGCCGGTTGT-GCGCGG-ATGGCCCATGCGA
1 TGGCCGGTTGTGGC-CGGTA-GCCCCATGCGA
2404 TGGCCGGTTGTGGCCGGTAGCCCCATGCGA
1 TGGCCGGTTGTGGCCGGTAGCCCCATGCGA
2434 TGGCCGGT
1 TGGCCGGT
2442 CAAGTGGCCG
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
30 32 0.91
31 3 0.09
ACGTcount: A:0.09, C:0.28, G:0.43, T:0.21
Consensus pattern (30 bp):
TGGCCGGTTGTGGCCGGTAGCCCCATGCGA
Found at i:6316 original size:18 final size:17
Alignment explanation
Indices: 6289--6324 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
6279 TTTCTCTTCA
6289 TCTATTTTTCTTCTAGT
1 TCTATTTTTCTTCTAGT
6306 TCTAGTTTTTCTTCTAGT
1 TCTA-TTTTTCTTCTAGT
6324 T
1 T
6325 TTAGGTTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.11, C:0.17, G:0.08, T:0.64
Consensus pattern (17 bp):
TCTATTTTTCTTCTAGT
Found at i:9032 original size:9 final size:9
Alignment explanation
Indices: 9018--9044 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
9008 AACATATCTC
9018 TTCAAAGAT
1 TTCAAAGAT
9027 TTCAAAGAT
1 TTCAAAGAT
9036 TTCAAAGAT
1 TTCAAAGAT
9045 GATAATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (9 bp):
TTCAAAGAT
Found at i:9163 original size:2 final size:2
Alignment explanation
Indices: 9156--9185 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
9146 AAATGCTTAG
9156 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9186 ACAATGTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:12882 original size:2 final size:2
Alignment explanation
Indices: 12877--12905 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12867 CACGTGTGTG
12877 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12906 CTGATACCAG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13254 original size:55 final size:54
Alignment explanation
Indices: 13170--13278 Score: 200
Period size: 55 Copynumber: 2.0 Consensus size: 54
13160 ATTGAAAACA
13170 TTTTGCAGACATTCCCTCCATGATGAGGATAACTTTGCAGAGCATTATTTTCTTC
1 TTTTGCAGACATTCCCTCCATGATGAGGATAACTTTGCAGAGCATTA-TTTCTTC
*
13225 TTTTGCAGAGATTCCCTCCATGATGAGGATAACTTTGCAGAGCATTATTTCTTC
1 TTTTGCAGACATTCCCTCCATGATGAGGATAACTTTGCAGAGCATTATTTCTTC
13279 AACTTTGCAG
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
54 7 0.13
55 46 0.87
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (54 bp):
TTTTGCAGACATTCCCTCCATGATGAGGATAACTTTGCAGAGCATTATTTCTTC
Found at i:13287 original size:24 final size:25
Alignment explanation
Indices: 13255--13308 Score: 101
Period size: 24 Copynumber: 2.2 Consensus size: 25
13245 TGATGAGGAT
13255 AACTTTGCAGAGCATTAT-TTCTTC
1 AACTTTGCAGAGCATTATCTTCTTC
13279 AACTTTGCAGAGCATTATCTTCTTC
1 AACTTTGCAGAGCATTATCTTCTTC
13304 AACTT
1 AACTT
13309 CTGACTTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 18 0.62
25 11 0.38
ACGTcount: A:0.26, C:0.22, G:0.11, T:0.41
Consensus pattern (25 bp):
AACTTTGCAGAGCATTATCTTCTTC
Found at i:18407 original size:19 final size:21
Alignment explanation
Indices: 18378--18419 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
18368 ATAAACTATG
18378 AACTAAAATTGAAA-TAATTA
1 AACTAAAATTGAAAGTAATTA
18398 AACT-AAATTGAAAGTAATTA
1 AACTAAAATTGAAAGTAATTA
18418 AA
1 AA
18420 ATAGAAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.60, C:0.05, G:0.07, T:0.29
Consensus pattern (21 bp):
AACTAAAATTGAAAGTAATTA
Found at i:21731 original size:13 final size:13
Alignment explanation
Indices: 21699--21747 Score: 52
Period size: 12 Copynumber: 4.1 Consensus size: 13
21689 ACCCAAATCA
21699 AATTAT-TAAAAC
1 AATTATATAAAAC
*
21711 CATT-TATAAAAC
1 AATTATATAAAAC
21723 AATTATATAAAAC
1 AATTATATAAAAC
*
21736 GA-TA-ATAAAAC
1 AATTATATAAAAC
21747 A
1 A
21748 GTTCCTCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
11 8 0.26
12 14 0.45
13 9 0.29
ACGTcount: A:0.59, C:0.10, G:0.02, T:0.29
Consensus pattern (13 bp):
AATTATATAAAAC
Found at i:21743 original size:24 final size:24
Alignment explanation
Indices: 21699--21747 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
21689 ACCCAAATCA
*
21699 AATTATTAAAACCATTTATAAAAC
1 AATTATTAAAACCATTAATAAAAC
*
21723 AATTATATAAAACGA-TAATAAAAC
1 AATTAT-TAAAACCATTAATAAAAC
21747 A
1 A
21748 GTTCCTCAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.59, C:0.10, G:0.02, T:0.29
Consensus pattern (24 bp):
AATTATTAAAACCATTAATAAAAC
Found at i:25547 original size:20 final size:20
Alignment explanation
Indices: 25509--25548 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
25499 ACTTCCAACA
* *
25509 CAATTAATTTCTTCAAAAAT
1 CAATGAATTTCATCAAAAAT
*
25529 CAATGAATTTCATCCAAAAT
1 CAATGAATTTCATCAAAAAT
25549 TGGTCTCTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.17, G:0.03, T:0.35
Consensus pattern (20 bp):
CAATGAATTTCATCAAAAAT
Found at i:27077 original size:21 final size:21
Alignment explanation
Indices: 27051--27099 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
27041 GCACTGGAGG
* * *
27051 ACATGGGTCGCGAGGCAAACC
1 ACATGGGGCGCCAAGCAAACC
*
27072 ACATGGGGCGCCAAGCATACC
1 ACATGGGGCGCCAAGCAAACC
27093 ACATGGG
1 ACATGGG
27100 CCCCCAGTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.29, C:0.29, G:0.33, T:0.10
Consensus pattern (21 bp):
ACATGGGGCGCCAAGCAAACC
Found at i:30230 original size:61 final size:62
Alignment explanation
Indices: 30119--30250 Score: 139
Period size: 62 Copynumber: 2.2 Consensus size: 62
30109 AAAAATCGAA
* **
30119 ATTAGGG-TTTGAGGGGGATGAAATCACAAAAATTGAAAGAAGGGAAAAGGG-AATTTTGCG
1 ATTAGGGTTTTGAGGGGGATCAAATCACAAAAATTGAAAGAAGCAAAAAGGGTAATTTTGCG
* **
30179 ATTAGGGTTTATGAGGGGG-TCAAATCGCAAAAATT-AAA-AAGCAAACGAAGGGTGGTTTTGCG
1 ATTAGGGTTT-TGAGGGGGATCAAATCACAAAAATTGAAAGAAGCAAA--AAGGGTAATTTTGCG
*
30241 ATTTGGGTTT
1 ATTAGGGTTT
30251 GAAAAATCAA
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
59 5 0.08
60 10 0.17
61 21 0.35
62 24 0.40
ACGTcount: A:0.36, C:0.07, G:0.32, T:0.26
Consensus pattern (62 bp):
ATTAGGGTTTTGAGGGGGATCAAATCACAAAAATTGAAAGAAGCAAAAAGGGTAATTTTGCG
Found at i:35195 original size:2 final size:2
Alignment explanation
Indices: 35190--35224 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
35180 TAAATATATA
35190 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
35225 TAAATAAATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:37022 original size:30 final size:30
Alignment explanation
Indices: 36956--37024 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 30
36946 ATATTTATTT
*
36956 AGGGACTTTAGTATAGGTGCCTCTGTGTTT
1 AGGGACTTTAGTATAGGTGCCTCTGTGTTG
36986 AGGGACTTTAGTAT-GGATGCC-CTTGTGCTTG
1 AGGGACTTTAGTATAGG-TGCCTC-TGTG-TTG
37017 A-GGACTTT
1 AGGGACTTT
37025 TGGGGAGAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
29 3 0.09
30 29 0.83
31 3 0.09
ACGTcount: A:0.17, C:0.14, G:0.30, T:0.38
Consensus pattern (30 bp):
AGGGACTTTAGTATAGGTGCCTCTGTGTTG
Found at i:41554 original size:106 final size:106
Alignment explanation
Indices: 41406--41623 Score: 348
Period size: 106 Copynumber: 2.0 Consensus size: 106
41396 CGCCTGTCCT
* * * *
41406 TTATAGTCATTTGTTATGTGAGAAAAGATAGAAATAGGACAGGTCTCTGGCTCCATAGCAAAAGT
1 TTATAGTCATTTGCTATGTGAGAAAAGACAGAAATAGAACAGGTCTCTAGCTCCATAGCAAAAGT
*
41471 TAGGTGGAGCTTTTAGTAATTTTAGTAGGGGTTACAAATTA
66 TAGGTGGAGCTTTTAGTAATTTTAGTAGGGATTACAAATTA
*
41512 TTATAGTCATTTGCTATGTGAGAAAAGACA-AAAGTAGAACAGGTCTCTAGCTTCATAGCAAAAG
1 TTATAGTCATTTGCTATGTGAGAAAAGACAGAAA-TAGAACAGGTCTCTAGCTCCATAGCAAAAG
*
41576 TTAGGTGGAGCTTTTAGTAATTTTGGTAGGGATTACAAATTA
65 TTAGGTGGAGCTTTTAGTAATTTTAGTAGGGATTACAAATTA
41618 TGTATA
1 T-TATA
41624 ATATAAAAAT
Statistics
Matches: 103, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
105 3 0.03
106 96 0.93
107 4 0.04
ACGTcount: A:0.34, C:0.10, G:0.23, T:0.33
Consensus pattern (106 bp):
TTATAGTCATTTGCTATGTGAGAAAAGACAGAAATAGAACAGGTCTCTAGCTCCATAGCAAAAGT
TAGGTGGAGCTTTTAGTAATTTTAGTAGGGATTACAAATTA
Found at i:41737 original size:40 final size:40
Alignment explanation
Indices: 41685--41760 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 40
41675 TGGAAAATAA
* *
41685 TTAAAAGAAAAACCTAATATTAATTATATAATTTTTTAAT
1 TTAAAAGAAAAACCTAATAATAATTATATAAATTTTTAAT
*
41725 TTAAAAGGAAAACCTAATAATAATTATATAAATTTT
1 TTAAAAGAAAAACCTAATAATAATTATATAAATTTT
41761 CTAAAATTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.39
Consensus pattern (40 bp):
TTAAAAGAAAAACCTAATAATAATTATATAAATTTTTAAT
Found at i:44740 original size:42 final size:42
Alignment explanation
Indices: 44693--44774 Score: 164
Period size: 42 Copynumber: 2.0 Consensus size: 42
44683 TTGTATGTGA
44693 TTTCCCTTAATTTTGTTTAGCATTTGTACAGTTTCCTTAATT
1 TTTCCCTTAATTTTGTTTAGCATTTGTACAGTTTCCTTAATT
44735 TTTCCCTTAATTTTGTTTAGCATTTGTACAGTTTCCTTAA
1 TTTCCCTTAATTTTGTTTAGCATTTGTACAGTTTCCTTAA
44775 ATAATGTTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.20, C:0.17, G:0.10, T:0.54
Consensus pattern (42 bp):
TTTCCCTTAATTTTGTTTAGCATTTGTACAGTTTCCTTAATT
Found at i:46853 original size:4 final size:4
Alignment explanation
Indices: 46846--46871 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
46836 AAATTAATTA
46846 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
46872 TAATAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:50061 original size:4 final size:4
Alignment explanation
Indices: 50052--50078 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
50042 CCTATCGCCA
50052 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
50079 ATAGCAACTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:56720 original size:40 final size:40
Alignment explanation
Indices: 56665--56745 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
56655 AATTGTTCCT
56665 TCCACTGTTCTGTCTATTACTAAAGAGATAGATAGATAGA
1 TCCACTGTTCTGTCTATTACTAAAGAGATAGATAGATAGA
56705 TCCACTGTTCTGTCTATTACTAAAGAGATAGATAGATAGA
1 TCCACTGTTCTGTCTATTACTAAAGAGATAGATAGATAGA
56745 T
1 T
56746 AGATAGATAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (40 bp):
TCCACTGTTCTGTCTATTACTAAAGAGATAGATAGATAGA
Found at i:56739 original size:4 final size:4
Alignment explanation
Indices: 56730--56759 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
56720 ATTACTAAAG
56730 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AG
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AG
56760 CACTTTCCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.27, T:0.23
Consensus pattern (4 bp):
AGAT
Found at i:59670 original size:16 final size:15
Alignment explanation
Indices: 59649--59684 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
59639 CACCTGAAAT
59649 ATAATAAAATAAATAA
1 ATAATAAAATAAA-AA
*
59665 ATAATATAATAAAAA
1 ATAATAAAATAAAAA
59680 ATAAT
1 ATAAT
59685 TGTACAACGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
ATAATAAAATAAAAA
Found at i:59843 original size:7 final size:7
Alignment explanation
Indices: 59831--59861 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
59821 CTGCTTCTAG
59831 TTTTGTC
1 TTTTGTC
59838 TTTTGTC
1 TTTTGTC
59845 TTTTGTC
1 TTTTGTC
59852 TTTTGTC
1 TTTTGTC
59859 TTT
1 TTT
59862 GACGGAACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.00, C:0.13, G:0.13, T:0.74
Consensus pattern (7 bp):
TTTTGTC
Found at i:60350 original size:53 final size:53
Alignment explanation
Indices: 60254--60407 Score: 238
Period size: 53 Copynumber: 2.9 Consensus size: 53
60244 CATTTATAAG
* * *
60254 TCCCTAAACACAGAGGCAATTCTATATCAAAAGACCTCGAACACAAGGGTGTTCA
1 TCCCTAAACACAGAGGC-A-TCTATATCAAAAGTCCTCAAACACAAGGGTATTCA
60309 TCCCTAAACACAGAGGCATCTATATCAAAAGTCCTCAAACACAAGGGTATTCA
1 TCCCTAAACACAGAGGCATCTATATCAAAAGTCCTCAAACACAAGGGTATTCA
* *
60362 TCCCTAAACACAGAGGCATCTACATC-AAAGTCCTCAAGCACAAGGG
1 TCCCTAAACACAGAGGCATCTATATCAAAAGTCCTCAAACACAAGGG
60408 CATCCATACT
Statistics
Matches: 94, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
52 19 0.20
53 57 0.61
54 1 0.01
55 17 0.18
ACGTcount: A:0.38, C:0.27, G:0.16, T:0.19
Consensus pattern (53 bp):
TCCCTAAACACAGAGGCATCTATATCAAAAGTCCTCAAACACAAGGGTATTCA
Found at i:60422 original size:30 final size:30
Alignment explanation
Indices: 60388--60464 Score: 79
Period size: 30 Copynumber: 2.5 Consensus size: 30
60378 CATCTACATC
60388 AAAGTCCTCAAGCACA-AG-GGCATCCATACT
1 AAAGTCC-CAA-CACATAGAGGCATCCATACT
*
60418 AAAGTCCCTAA-ACATAGAGGCATCTATACT
1 AAAGTCCC-AACACATAGAGGCATCCATACT
60448 AAAGTCCCCAAACACAT
1 AAAGT-CCC-AACACAT
60465 GTAACACAGG
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
28 3 0.08
29 3 0.08
30 25 0.62
31 5 0.12
32 4 0.10
ACGTcount: A:0.40, C:0.29, G:0.13, T:0.18
Consensus pattern (30 bp):
AAAGTCCCAACACATAGAGGCATCCATACT
Done.