Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015098.1 Corchorus capsularis cultivar CVL-1 contig15119, 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: 12300
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Found at i:797 original size:4 final size:4
Alignment explanation
Indices: 788--818 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
778 CTTTATCTCA
788 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
819 CCTCAATTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:3020 original size:441 final size:440
Alignment explanation
Indices: 2200--3269 Score: 1474
Period size: 441 Copynumber: 2.4 Consensus size: 440
2190 ATTTAGGCAT
* * * * *
2200 TTCATGAAAGTTGTAAATCATTAAATTACCTTTCAATAGACACTTGAATCACCTTGATCCGACAA
1 TTCATGAAAGTTGTAGATCATGAAATTACCTTTAAATAGACACTTGAATCATCTTGATCGGACAA
* * * *
2265 ATAGAACAAAAAATACAAAAAATAAAAGCCGACATGTTAAATCGTCCAACCCATAATTGTAAACG
66 ATAGAACAAAAAATAC-AAAAATAAAAGCCAACACGTTAAATCGTCCAACCAATAATTGTAAAGG
* **
2330 ATTAAATAGCATAAA--ATATAAAAGTATGAGGGTCATTTGATAAATAATCCAG-GGAAAAAATA
130 ATTAAATAGCATAAAGCATA-AAAAGTATGAGGATCATTTGATAAATAATCCAGCAAAAAAAATA
* * * *
2392 TTTGTTTATGAAGACGAAACATAAAAATTACCTCTTGAACTCTCCACGAAACTCATTAGTCAAAT
194 TTTGTTTATGAAGACCAAACATAAAAATTACCTCTCGAACCCTCCACGAAACTCATTAATCAAAT
* * * *
2457 TCAGCTTTCAGACCCTTGGCGAAAGTCGTAGCTAACACAATAACCTTTCAACCGACACTTGAACA
259 TCAGCTTTCAGACCCTCGACGAAAGTCGTAGATAACACAATAACCTTTCAACCGACACTTAAACA
* * *
2522 ACCTCAATCGGACAAGTGGACCGAAAATTATACAATATTAGATAGACCGACAATCGAGACCACAA
324 ACCTCAATCGGACAAGTGGAACAAAAATTATACAATATTAGAGAGACCGACAATCGAGACCACAA
* * * *
2587 AATTTTAGAAGCATTTTTTAGAATCAAAACATCAAAATTGGCTTTTGAGTCC
389 AATTTCAGAAGCATTTTTTAGAATCAAAACATCAAAATTGACTTCTAAGTCC
* * *
2639 TTCATGAAAGTTGTAGACCATGAAATTACCTTTAAATAGAAACCTGAATCATCTTGATCGGACAA
1 TTCATGAAAGTTGTAGATCATGAAATTACCTTTAAATAGACACTTGAATCATCTTGATCGGACAA
* *
2704 ATAGAACAAAAAATACAAAAATAAAAGCCAACGCGTTAAATCGTCCAACTAATAATTGTAAAGGA
66 ATAGAACAAAAAATACAAAAATAAAAGCCAACACGTTAAATCGTCCAACCAATAATTGTAAAGGA
*
2769 TTAAATAGCATAAAGCATAAAAAGTGTGAGGATCATTTGATAAATAATCCAGCAAAAAAAATATT
131 TTAAATAGCATAAAGCATAAAAAGTATGAGGATCATTTGATAAATAATCCAGCAAAAAAAATATT
2834 TGTTTAT-AGAGACCAAACATAAAAATT-CTCTCTCGAACCCTCCACGAAACTCATTTAATCAAA
196 TGTTTATGA-AGACCAAACATAAAAATTAC-CTCTCGAACCCTCCACGAAACTCA-TTAATCAAA
* * * *
2897 TTCAGCTTTCAGGCCCTCGACGAAAGTCGTAGATCACACGATAACCTTTTAACCGACACTTAAAC
258 TTCAGCTTTCAGACCCTCGACGAAAGTCGTAGATAACACAATAACCTTTCAACCGACACTTAAAC
* *
2962 AATCTCAATCGGACAAGTGGAACAAAAATTATACGATATTAGAGAGACCGACAATCGAGACCACA
323 AACCTCAATCGGACAAGTGGAACAAAAATTATACAATATTAGAGAGACCGACAATCGAGACCACA
*
3027 AAATTTCAGAAGCATTTTTTAGAATCAAAACATTAAAATTGACTTCTAAGTCC
388 AAATTTCAGAAGCATTTTTTAGAATCAAAACATCAAAATTGACTTCTAAGTCC
* *
3080 TTCATGGAAGTTGTAGATCATGAAATTACCTTTTAATAGACACTTGAATCATCTTGATCGGACAA
1 TTCATGAAAGTTGTAGATCATGAAATTACCTTTAAATAGACACTTGAATCATCTTGATCGGACAA
** * * * * * * * ***
3145 GCAAAACAAAAAATATAAGAATTAAAGTCGAA-ACGTTCAATCTTCCAACCCAA-AACTTGTGGG
66 ATAGAACAAAAAATACAAAAATAAAAG-CCAACACGTTAAATCGTCCAA-CCAATAA-TTGTAAA
* * * *
3208 GGACTAAATAGCATAAAGCAT-AAAAGTAT-AGGGATCATTTGATAAATACTCTAACAAAAAAA
128 GGATTAAATAGCATAAAGCATAAAAAGTATGA-GGATCATTTGATAAATAATCCAGCAAAAAAA
3270 TTTTTTTTAT
Statistics
Matches: 557, Mismatches: 64, Indels: 18
0.87 0.10 0.03
Matches are distributed among these distances:
438 57 0.10
439 106 0.19
440 60 0.11
441 304 0.55
442 30 0.05
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.26
Consensus pattern (440 bp):
TTCATGAAAGTTGTAGATCATGAAATTACCTTTAAATAGACACTTGAATCATCTTGATCGGACAA
ATAGAACAAAAAATACAAAAATAAAAGCCAACACGTTAAATCGTCCAACCAATAATTGTAAAGGA
TTAAATAGCATAAAGCATAAAAAGTATGAGGATCATTTGATAAATAATCCAGCAAAAAAAATATT
TGTTTATGAAGACCAAACATAAAAATTACCTCTCGAACCCTCCACGAAACTCATTAATCAAATTC
AGCTTTCAGACCCTCGACGAAAGTCGTAGATAACACAATAACCTTTCAACCGACACTTAAACAAC
CTCAATCGGACAAGTGGAACAAAAATTATACAATATTAGAGAGACCGACAATCGAGACCACAAAA
TTTCAGAAGCATTTTTTAGAATCAAAACATCAAAATTGACTTCTAAGTCC
Found at i:7686 original size:2 final size:2
Alignment explanation
Indices: 7679--7711 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
7669 ATTACAATAC
7679 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
7712 GTCATGCCCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8246 original size:35 final size:35
Alignment explanation
Indices: 8200--8270 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
8190 GTACAGGTCA
8200 TCAGAATGCCACATAAGCATTAATAGACAGTTTTT
1 TCAGAATGCCACATAAGCATTAATAGACAGTTTTT
8235 TCAGAATGCCACATAAGCATTAATAGACAGTTTTT
1 TCAGAATGCCACATAAGCATTAATAGACAGTTTTT
8270 T
1 T
8271 AGTACATTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (35 bp):
TCAGAATGCCACATAAGCATTAATAGACAGTTTTT
Found at i:9708 original size:2 final size:2
Alignment explanation
Indices: 9695--9729 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
9685 TTTGGGATTA
*
9695 AT AT AG AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9730 AACAAGGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:11622 original size:21 final size:21
Alignment explanation
Indices: 11597--11668 Score: 85
Period size: 21 Copynumber: 3.4 Consensus size: 21
11587 ATCACCCTTT
11597 ACTCTTACTAATTACTATTTG
1 ACTCTTACTAATTACTATTTG
11618 ACTCTTACTAATTA-TCACTTTG
1 ACTCTTACTAATTACT-A-TTTG
** *
11640 -CTCTTACTGGTTACTATTTT
1 ACTCTTACTAATTACTATTTG
11660 ACTCTTACT
1 ACTCTTACT
11669 GGTTATCTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
20 4 0.09
21 35 0.80
22 5 0.11
ACGTcount: A:0.24, C:0.22, G:0.06, T:0.49
Consensus pattern (21 bp):
ACTCTTACTAATTACTATTTG
Found at i:11669 original size:21 final size:20
Alignment explanation
Indices: 11594--11682 Score: 79
Period size: 21 Copynumber: 4.3 Consensus size: 20
11584 CTGATCACCC
11594 TTTACTCTTACTAATTACTAT
1 TTTACTCTTACTAATTA-TAT
* *
11615 TTGACTCTTACTAATTATCAC
1 TTTACTCTTACTAATTAT-AT
* **
11636 TTTGCTCTTACTGGTTACTAT
1 TTTACTCTTACTAATTA-TAT
** *
11657 TTTACTCTTACTGGTTATCT
1 TTTACTCTTACTAATTATAT
11677 TTTACT
1 TTTACT
11683 GATTACTATT
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
20 9 0.16
21 47 0.82
22 1 0.02
ACGTcount: A:0.21, C:0.20, G:0.07, T:0.52
Consensus pattern (20 bp):
TTTACTCTTACTAATTATAT
Found at i:11682 original size:35 final size:37
Alignment explanation
Indices: 11641--11719 Score: 117
Period size: 35 Copynumber: 2.2 Consensus size: 37
11631 ATCACTTTGC
* * *
11641 TCTTACTGGTTACTATTTTACTC-TTACTGGTTATCT
1 TCTTACTGATTACTATTTTACTCTTTACTGATTACCT
11677 T-TTACTGATTACTATTTTACTCTTTACTGATTACCT
1 TCTTACTGATTACTATTTTACTCTTTACTGATTACCT
11713 TCTTACT
1 TCTTACT
11720 TTTTACTGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
35 20 0.53
36 13 0.34
37 5 0.13
ACGTcount: A:0.19, C:0.20, G:0.08, T:0.53
Consensus pattern (37 bp):
TCTTACTGATTACTATTTTACTCTTTACTGATTACCT
Found at i:11703 original size:22 final size:22
Alignment explanation
Indices: 11677--12036 Score: 164
Period size: 22 Copynumber: 16.5 Consensus size: 22
11667 CTGGTTATCT
11677 TTTACTGATTACTATTTTACTC
1 TTTACTGATTACTATTTTACTC
* *
11699 TTTACTGATTACCT-TCTTACTT
1 TTTACTGATTA-CTATTTTACTC
*
11721 TTTACTGATTACCATTTTACTC
1 TTTACTGATTACTATTTTACTC
* *
11743 TTTTACTGATTACCATTTTCTGCTCCC
1 -TTTACTGATTACTA-TTT-TACT--C
* *
11770 TTTTTTACTGATTACTCTTTTACTT
1 ---TTTACTGATTACTATTTTACTC
* * *
11795 TTTACTGATT-GTCTTTT--GC
1 TTTACTGATTACTATTTTACTC
* *
11814 TTTACTGATTACCT-TTTTATTT
1 TTTACTGATTA-CTATTTTACTC
11836 TTTACTGATTAGCT-TTTTACTC
1 TTTACTGATTA-CTATTTTACTC
* *
11858 -TTACTGATTTC-CTTTTACT-
1 TTTACTGATTACTATTTTACTC
*
11877 TCTTACTTG-TTACTTTTTTACTC
1 T-TTAC-TGATTACTATTTTACTC
* *
11900 -TTACTGATTAATATTTTACTTTT
1 TTTACTGATTACTATTTTAC--TC
* * *
11923 TTTACTGACTATTATTTCACTC
1 TTTACTGATTACTATTTTACTC
* *
11945 TTGT--TGATTACCT-TCTTACTT
1 TT-TACTGATTA-CTATTTTACTC
* *
11966 TTTAATGATTAC-CTTTTACTC
1 TTTACTGATTACTATTTTACTC
* * * *
11987 -TTACTAACTACCATTTTACCC
1 TTTACTGATTACTATTTTACTC
* *
12008 TTT-CAGA-TACT-TTTTACTT
1 TTTACTGATTACTATTTTACTC
12027 TTTACTGATT
1 TTTACTGATT
12037 GCATGCTATT
Statistics
Matches: 259, Mismatches: 47, Indels: 65
0.70 0.13 0.18
Matches are distributed among these distances:
19 19 0.07
20 29 0.11
21 67 0.26
22 84 0.32
23 18 0.07
24 19 0.07
25 3 0.01
27 4 0.02
28 3 0.01
29 13 0.05
ACGTcount: A:0.19, C:0.20, G:0.06, T:0.55
Consensus pattern (22 bp):
TTTACTGATTACTATTTTACTC
Found at i:11755 original size:15 final size:15
Alignment explanation
Indices: 11737--11793 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 15
11727 GATTACCATT
11737 TTACTCTTTTACTGA
1 TTACTCTTTTACTGA
*
11752 TTAC-CATTTT-CTGC
1 TTACTC-TTTTACTGA
** *
11766 TCCCTTTTTTACTGA
1 TTACTCTTTTACTGA
11781 TTACTCTTTTACT
1 TTACTCTTTTACT
11794 TTTTACTGAT
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
14 10 0.32
15 21 0.68
ACGTcount: A:0.16, C:0.25, G:0.05, T:0.54
Consensus pattern (15 bp):
TTACTCTTTTACTGA
Found at i:11796 original size:21 final size:21
Alignment explanation
Indices: 11772--11922 Score: 125
Period size: 21 Copynumber: 7.2 Consensus size: 21
11762 CTGCTCCCTT
11772 TTTTACTGATTACTCTTTTAC
1 TTTTACTGATTACTCTTTTAC
* *
11793 TTTTTACTGATT-GTCTTTTGC
1 -TTTTACTGATTACTCTTTTAC
*
11814 -TTTACTGATTAC-CTTTTTATT
1 TTTTACTGATTACTC-TTTTA-C
11835 TTTTACTGATTAGCT-TTTTAC
1 TTTTACTGATTA-CTCTTTTAC
* *
11856 TCTTACTGATTTC-CTTTTAC
1 TTTTACTGATTACTCTTTTAC
*
11876 TTCTTACTTG-TTACTTTTTTAC
1 TT-TTAC-TGATTACTCTTTTAC
* * *
11898 TCTTACTGATTAATATTTTAC
1 TTTTACTGATTACTCTTTTAC
11919 TTTT
1 TTTT
11923 TTTACTGACT
Statistics
Matches: 103, Mismatches: 15, Indels: 23
0.73 0.11 0.16
Matches are distributed among these distances:
19 11 0.11
20 14 0.14
21 41 0.40
22 36 0.35
23 1 0.01
ACGTcount: A:0.17, C:0.17, G:0.07, T:0.60
Consensus pattern (21 bp):
TTTTACTGATTACTCTTTTAC
Found at i:11844 original size:63 final size:64
Alignment explanation
Indices: 11770--11923 Score: 167
Period size: 63 Copynumber: 2.4 Consensus size: 64
11760 TTCTGCTCCC
*
11770 TTTTTTACTGATTACTCTTTTACTTTTTACTGATTGT-CTTTTGC-T-TTAC-TGATTACCTTTT
1 TTTTTTACTGATTACT-TTTTACTTTTTACTGATT-TCCTTTTACTTCTTACTTG-TTACCTTTT
11831 TA
63 TA
* *
11833 TTTTTTACTGATTAGCTTTTTAC-TCTTACTGATTTCCTTTTACTTCTTACTTGTTACTTTTTTA
1 TTTTTTACTGATTA-CTTTTTACTTTTTACTGATTTCCTTTTACTTCTTACTTGTTACCTTTTTA
* * *
11897 -CTCTTACTGATTAATATTTTACTTTTT
1 TTTTTTACTGATTACT-TTTTACTTTTT
11924 TTACTGACTA
Statistics
Matches: 77, Mismatches: 7, Indels: 13
0.79 0.07 0.13
Matches are distributed among these distances:
61 1 0.01
62 17 0.22
63 38 0.49
64 19 0.25
65 2 0.03
ACGTcount: A:0.17, C:0.16, G:0.06, T:0.60
Consensus pattern (64 bp):
TTTTTTACTGATTACTTTTTACTTTTTACTGATTTCCTTTTACTTCTTACTTGTTACCTTTTTA
Found at i:11895 original size:42 final size:43
Alignment explanation
Indices: 11774--12005 Score: 153
Period size: 42 Copynumber: 5.4 Consensus size: 43
11764 GCTCCCTTTT
* *
11774 TTACTGATTA-CTCTTTTACTTTTTACTGATT-G-TCTTTTGCT-
1 TTACTGATTACCT-TTTTACTTCTTACTGATTAGCT-TTTTACTC
* *
11815 TTACTGATTACCTTTTTATTTTTTACTGATTAGCTTTTTACTC
1 TTACTGATTACCTTTTTACTTCTTACTGATTAGCTTTTTACTC
*
11858 TTACTGATTTCC-TTTTACTTCTTACTTG-TTA-CTTTTTTACTC
1 TTACTGATTACCTTTTTACTTCTTAC-TGATTAGC-TTTTTACTC
* * *
11900 TTACTGATTA-ATATTTTACTTTTTTTACTGACTA--TTATTTCACTC
1 TTACTGATTACCT-TTTTAC--TTCTTACTGATTAGCTT-TTT-ACTC
** * * * *
11945 TTGTTGATTACCTTCTTACTTTTTAATGATTA-CCTTTTACTC
1 TTACTGATTACCTTTTTACTTCTTACTGATTAGCTTTTTACTC
* * *
11987 TTACTAACTACCATTTTAC
1 TTACTGATTACCTTTTTAC
12006 CCTTTCAGAT
Statistics
Matches: 154, Mismatches: 22, Indels: 29
0.75 0.11 0.14
Matches are distributed among these distances:
41 28 0.18
42 58 0.38
43 36 0.23
44 6 0.04
45 25 0.16
46 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.06, T:0.56
Consensus pattern (43 bp):
TTACTGATTACCTTTTTACTTCTTACTGATTAGCTTTTTACTC
Found at i:12003 original size:87 final size:84
Alignment explanation
Indices: 11774--12005 Score: 220
Period size: 87 Copynumber: 2.7 Consensus size: 84
11764 GCTCCCTTTT
* ** * *
11774 TTACTGATTACTCTTTTACTTTTTACTGATTGTCTTTTGCT-TTACTGATTACCTTTTTA-TTTT
1 TTACTGATTAC-CTTTTACTTTTTAATGATTACCTTTTACTCTTACTGATTACCATTTTACTTTT
*
11837 TTACTGATTAGCTTTTTACTC
65 TTACTGACTA-CTTTTTACTC
* * * * **
11858 TTACTGATTTCCTTTTACTTCTTACTTG-TTACTTTTTTACTCTTACTGATTAATATTTTACTTT
1 TTACTGATTACCTTTTACTTTTTA-ATGATTAC-CTTTTACTCTTACTGATTACCATTTTAC-TT
11922 TTTTACTGACTA-TTATTTCACTC
63 TTTTACTGACTACTT-TTT-ACTC
** * *
11945 TTGTTGATTACCTTCTTACTTTTTAATGATTACCTTTTACTCTTACTAACTACCATTTTAC
1 TTACTGATTACCTT-TTACTTTTTAATGATTACCTTTTACTCTTACTGATTACCATTTTAC
12006 CCTTTCAGAT
Statistics
Matches: 118, Mismatches: 21, Indels: 15
0.77 0.14 0.10
Matches are distributed among these distances:
83 14 0.12
84 18 0.15
85 17 0.14
86 3 0.03
87 53 0.45
88 13 0.11
ACGTcount: A:0.19, C:0.19, G:0.06, T:0.56
Consensus pattern (84 bp):
TTACTGATTACCTTTTACTTTTTAATGATTACCTTTTACTCTTACTGATTACCATTTTACTTTTT
TACTGACTACTTTTTACTC
Done.