Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009481.1 Corchorus capsularis cultivar CVL-1 contig09502, 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: 7009
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.31
Found at i:2747 original size:32 final size:32
Alignment explanation
Indices: 2723--2793 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
2713 GATTAATCAC
2723 AACAAAATTAAACATAATTGATGATCAAAACT
1 AACAAAATTAAACATAATTGATGATCAAAACT
** *
2755 AATTAAATTAAACATAATTGATCATCAAAACT
1 AACAAAATTAAACATAATTGATGATCAAAACT
2787 AATCAAA
1 AA-CAAA
2794 TAAAGTGAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
32 31 0.94
33 2 0.06
ACGTcount: A:0.56, C:0.13, G:0.04, T:0.27
Consensus pattern (32 bp):
AACAAAATTAAACATAATTGATGATCAAAACT
Found at i:3973 original size:434 final size:430
Alignment explanation
Indices: 3152--3959 Score: 1084
Period size: 434 Copynumber: 1.9 Consensus size: 430
3142 TGAATCATCC
* *
3152 ATGAAACTTACTAATCAAATTCAGCTTTCAAACCCTTAATGAAAGTCTTAGATCACAAAATAACC
1 ATGAAACTCACTAATCAAATTCAGCTTTCAAACCCTTAATGAAAGTCGTAGATCACAAAATAACC
* * * ** * * *
3217 CTTCAACCGACACTTAGAACAACTTCGGTCGGGCAAGTGGATAGAAAATTACACGATATTAAATA
66 CTTCAAACGACACCTAGAACAACCTCAATCGGACAAGTCGACAGAAAATTACACGATATTAAATA
* *
3282 GACCGACAATCGAAACCAAAAAATTTCAGAAGCATTTTAAAAAAAAAAATCAAATTGGATTCTGA
131 GACCGACAATCGAAACCAAAAAATTTCAGAAGCATTTTAAAAAAAAAAATAAAATTGGATTATGA
* * *
3347 GTTCTTCATGAAAGTTGTAGATCATGAAATTACCTCTCAATAAACACTTGAATCACTTTGATCGG
196 GTTCTTAATGAAAGTTGTAGATCATGAAATCACCTCTCAATAAACACTTGAATCACATTGATCGG
** * * * *
3412 ACAAATGGAAAAAAAATACAAAAATATGAGCCGAAGCGTTCAATCGTCCAACCATAATTGTAATG
261 ACAAATGGAAAAAAAATACAAAAATAAAAGCCGAAACATTAAATCGTCCAACCATAATTGTAAGG
* *
3477 ATTAAATAGCATAAAGTATAAAAGTATGAGGATTATTTATCAAATAATCCTAGAAAAAAAAATTG
326 ATTAAATAGCATAAAGTATAAAAGTATGAGGATCATTGATCAAATAATCC-AGAAAAAAAAATTG
3542 TTTATGAAGACTAAACATAAAAATTCCCTCTCGAACTCTTA
390 TTTATGAAGACTAAACATAAAAATTCCCTCTCGAACTCTTA
* ** * *
3583 ATGAAACTCATTAATCAAATTCAGCTTTCAGGCCCTTGATGAAAGTCGTAGATCACACAATAACC
1 ATGAAACTCACTAATCAAATTCAGCTTTCAAACCCTTAATGAAAGTCGTAGATCACAAAATAACC
* * * * * *
3648 TTTTAAACGACACCTA-AACAACCTCAATCGGACAATTCGACCGAATATTATACGATATTAAATA
66 CTTCAAACGACACCTAGAACAACCTCAATCGGACAAGTCGACAGAAAATTACACGATATTAAATA
* * * * * *
3712 GACCGGCAATCGAAACCACAAAATTTCGGAAGCATTTTTCAAAATCAAAACATTAAAATTGGCTT
131 GACCGACAATCGAAACCAAAAAATTTCAGAAGCA-TTTT-AAAA--AAAAAAATAAAATTGGATT
* * *
3777 ATGAGTTCTTAATGAAAGTTGTAGATCATGAAATCACCTTTTAATAGACACTTGAATCACATTGA
192 ATGAGTTCTTAATGAAAGTTGTAGATCATGAAATCACCTCTCAATAAACACTTGAATCACATTGA
* *
3842 TCGGACAAATAGGAAAAAAAATACAAAAA-AAAAGGC-AACACATTAAATCGTCTAACCCATAAT
257 TCGGACAAAT-GGAAAAAAAATACAAAAATAAAAGCCGAA-ACATTAAATCGTCCAA-CCATAAT
*
3905 TGTAAAGGATTAAATAGCATAAAGTATAAAAGTATGGGGATCATTCGAT-AAATAA
319 TGT-AAGGATTAAATAGCATAAAGTATAAAAGTATGAGGATCATT-GATCAAATAA
3960 CACGATAAAA
Statistics
Matches: 322, Mismatches: 46, Indels: 13
0.85 0.12 0.03
Matches are distributed among these distances:
430 69 0.21
431 74 0.23
432 4 0.01
433 2 0.01
434 99 0.31
435 28 0.09
436 44 0.14
437 2 0.01
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.26
Consensus pattern (430 bp):
ATGAAACTCACTAATCAAATTCAGCTTTCAAACCCTTAATGAAAGTCGTAGATCACAAAATAACC
CTTCAAACGACACCTAGAACAACCTCAATCGGACAAGTCGACAGAAAATTACACGATATTAAATA
GACCGACAATCGAAACCAAAAAATTTCAGAAGCATTTTAAAAAAAAAAATAAAATTGGATTATGA
GTTCTTAATGAAAGTTGTAGATCATGAAATCACCTCTCAATAAACACTTGAATCACATTGATCGG
ACAAATGGAAAAAAAATACAAAAATAAAAGCCGAAACATTAAATCGTCCAACCATAATTGTAAGG
ATTAAATAGCATAAAGTATAAAAGTATGAGGATCATTGATCAAATAATCCAGAAAAAAAAATTGT
TTATGAAGACTAAACATAAAAATTCCCTCTCGAACTCTTA
Found at i:4454 original size:22 final size:22
Alignment explanation
Indices: 4385--4467 Score: 80
Period size: 22 Copynumber: 3.8 Consensus size: 22
4375 TAAATTTTTT
*
4385 ATGAAATTTTGTTAACCTCCCTA
1 ATGAAATTTTGATAACCTCCC-A
* * *
4408 A-GGAATTTTGAAAACCT-CAA
1 ATGAAATTTTGATAACCTCCCA
*
4428 TATGAAATTTTGATAACTTCCCA
1 -ATGAAATTTTGATAACCTCCCA
*
4451 ATGAAATTGTGATAACC
1 ATGAAATTTTGATAACC
4468 AACACTATGG
Statistics
Matches: 47, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
20 1 0.02
21 2 0.04
22 41 0.87
23 3 0.06
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (22 bp):
ATGAAATTTTGATAACCTCCCA
Found at i:4613 original size:22 final size:23
Alignment explanation
Indices: 4563--4767 Score: 87
Period size: 22 Copynumber: 9.5 Consensus size: 23
4553 AATCACACTC
4563 TGAAATTTTGATAAACTTCCCTA
1 TGAAATTTTGATAAACTTCCCTA
* * * *
4586 TAAAATTTTGGT-AACTTTCTTA
1 TGAAATTTTGATAAACTTCCCTA
* *
4608 TGAAATCTTAAT-AA-----CTA
1 TGAAATTTTGATAAACTTCCCTA
*
4625 -CAAATTTTGATA-ACTTCCCTA
1 TGAAATTTTGATAAACTTCCCTA
** * **
4646 TGATTTTTTGAT-AACCTCGTTA
1 TGAAATTTTGATAAACTTCCCTA
* *
4668 TGAAATTTTGTTAATC-TCCCTA
1 TGAAATTTTGATAAACTTCCCTA
** * *
4690 TGAAATTTTGATCTACAT-ACTA
1 TGAAATTTTGATAAACTTCCCTA
* ***
4712 TAAAATTTTGA-AAACTAAACTA
1 TGAAATTTTGATAAACTTCCCTA
* *
4734 TGAAATTTTGATAACCTT-CATA
1 TGAAATTTTGATAAACTTCCCTA
*
4756 TGATATTTTGAT
1 TGAAATTTTGAT
4768 TTTCTCCCTG
Statistics
Matches: 130, Mismatches: 40, Indels: 25
0.67 0.21 0.13
Matches are distributed among these distances:
16 9 0.07
17 2 0.02
21 5 0.04
22 97 0.75
23 17 0.13
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (23 bp):
TGAAATTTTGATAAACTTCCCTA
Found at i:4785 original size:20 final size:20
Alignment explanation
Indices: 4760--4801 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
4750 TTCATATGAT
* *
4760 ATTTTGATTTTCTCCCTGAA
1 ATTTTGATATCCTCCCTGAA
*
4780 ATTTTGATATCCTCTCTGAA
1 ATTTTGATATCCTCCCTGAA
4800 AT
1 AT
4802 ATTTATTACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.24, C:0.19, G:0.10, T:0.48
Consensus pattern (20 bp):
ATTTTGATATCCTCCCTGAA
Found at i:4805 original size:22 final size:21
Alignment explanation
Indices: 4758--4805 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
4748 CCTTCATATG
* *
4758 ATATTTTGATTTTCTCCCTGA
1 ATATTTTGATATCCTCCCTGA
*
4779 A-ATTTTGATATCCTCTCTGAA
1 ATATTTTGATATCCTCCCTG-A
4800 ATATTT
1 ATATTT
4806 ATTACTCGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 15 0.68
21 3 0.14
22 4 0.18
ACGTcount: A:0.25, C:0.17, G:0.08, T:0.50
Consensus pattern (21 bp):
ATATTTTGATATCCTCCCTGA
Found at i:4961 original size:22 final size:22
Alignment explanation
Indices: 4911--5075 Score: 88
Period size: 22 Copynumber: 7.6 Consensus size: 22
4901 TCACATTTTG
4911 AAAA-TTTGATAACCTCTTTAT
1 AAAATTTTGATAACCTCTTTAT
* *
4932 GAAATTTTGATAAGCTCTTTAT
1 AAAATTTTGATAACCTCTTTAT
* * * *
4954 AAAATTTTGTTGACCCCTCTAT
1 AAAATTTTGATAACCTCTTTAT
* * * * * *
4976 GAAATTCTAATAATCACATTAT
1 AAAATTTTGATAACCTCTTTAT
* *
4998 ATAATTTTGATAACCTCGCTT-T
1 AAAATTTTGATAACCTC-TTTAT
* ** **
5020 GAAATTTTGATAACAACACTAT
1 AAAATTTTGATAACCTCTTTAT
*
5042 GAAATTTTGATAA--TCTTCGTAT
1 AAAATTTTGATAACCTCTT--TAT
5064 -AAATTTTGATAA
1 AAAATTTTGATAA
5076 TCTGATCTCT
Statistics
Matches: 106, Mismatches: 33, Indels: 10
0.71 0.22 0.07
Matches are distributed among these distances:
20 1 0.01
21 16 0.15
22 87 0.82
23 2 0.02
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.41
Consensus pattern (22 bp):
AAAATTTTGATAACCTCTTTAT
Found at i:4977 original size:44 final size:44
Alignment explanation
Indices: 4884--5075 Score: 133
Period size: 44 Copynumber: 4.4 Consensus size: 44
4874 AGAAATACCA
* * * *
4884 CTATGAAAATTTTG-TAATCACATTTTGAAAA-TTTGATAACCTCT
1 CTATG-AAATTTTGATAAGCACATTAT-AAAATTTTGATAACCCCG
* * * * * *
4928 TTATGAAATTTTGATAAGCTCTTTATAAAATTTTGTTGACCCCT
1 CTATGAAATTTTGATAAGCACATTATAAAATTTTGATAACCCCG
* * * * *
4972 CTATGAAATTCTAATAATCACATTATATAATTTTGATAACCTCG
1 CTATGAAATTTTGATAAGCACATTATAAAATTTTGATAACCCCG
* * * **
5016 CTTTGAAATTTTGATAA-CAACACTATGAAATTTTGATAATCTTCG
1 CTATGAAATTTTGATAAGC-ACATTATAAAATTTTGATAA-CCCCG
5061 -TAT-AAATTTTGATAA
1 CTATGAAATTTTGATAA
5076 TCTGATCTCT
Statistics
Matches: 117, Mismatches: 27, Indels: 9
0.76 0.18 0.06
Matches are distributed among these distances:
43 25 0.21
44 88 0.75
45 4 0.03
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (44 bp):
CTATGAAATTTTGATAAGCACATTATAAAATTTTGATAACCCCG
Found at i:5110 original size:22 final size:23
Alignment explanation
Indices: 5019--5121 Score: 92
Period size: 22 Copynumber: 4.6 Consensus size: 23
5009 AACCTCGCTT
*
5019 TGAAATTTTGATAA-CAACACTA
1 TGAAATTTTGATAATCAACTCTA
*
5041 TGAAATTTTGATAATC--TTCGTA
1 TGAAATTTTGATAATCAACTC-TA
*
5063 T-AAATTTTGATAATCTGATCTCTA
1 TGAAATTTTGATAATC--AACTCTA
*
5087 TGAAATTTGGATAATC-ACTCTA
1 TGAAATTTTGATAATCAACTCTA
*
5109 TGAGA-TTTGATAA
1 TGAAATTTTGATAA
5122 CCTTCTATCA
Statistics
Matches: 67, Mismatches: 7, Indels: 15
0.75 0.08 0.17
Matches are distributed among these distances:
21 22 0.33
22 26 0.39
23 1 0.01
24 3 0.04
25 15 0.22
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.40
Consensus pattern (23 bp):
TGAAATTTTGATAATCAACTCTA
Found at i:5226 original size:22 final size:22
Alignment explanation
Indices: 5196--5508 Score: 127
Period size: 22 Copynumber: 13.9 Consensus size: 22
5186 TATTACCATA
*
5196 CTATAAAATTTTGATAACCTCC
1 CTATGAAATTTTGATAACCTCC
* *
5218 CCATGAAATATT-AGTAACCT-C
1 CTATGAAATTTTGA-TAACCTCC
* * *
5239 CTAATGAAATTTTGTTAACCACA
1 CT-ATGAAATTTTGATAACCTCC
* *
5262 CTATGAAATTCTT-ATAATCTCG
1 CTATGAAATT-TTGATAACCTCC
* **
5284 CTATGACATTTTGATAACCTTT
1 CTATGAAATTTTGATAACCTCC
* *
5306 CTATAAAATTGTGATAATTAACCATACC
1 CTATGAAATT-T--TGA-TAACC-T-CC
* * **
5334 CTATGAAA-TTTCAGTAGCCAAC
1 CTATGAAATTTTGA-TAACCTCC
* * * *
5356 CTAAGAAATTTTAATAATCTGGCA
1 CTATGAAATTTTGATAACCT--CC
* *
5380 CTATGAAATTTT-AGTAACCACA
1 CTATGAAATTTTGA-TAACCTCC
* * *
5402 CTATGAAATTTTGATCACTTTC
1 CTATGAAATTTTGATAACCTCC
* * * *
5424 ATATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCTCC
*
5446 CTATGGAATTTTGATAACCT-C
1 CTATGAAATTTTGATAACCTCC
* * *
5467 CTCATGAAATTATAATAATCAT-C
1 CT-ATGAAATTTTGATAA-CCTCC
*
5490 TTATGAAATTTTGATAACC
1 CTATGAAATTTTGATAACC
5509 ACATAAAGAC
Statistics
Matches: 210, Mismatches: 62, Indels: 39
0.68 0.20 0.13
Matches are distributed among these distances:
21 8 0.04
22 149 0.71
23 15 0.07
24 21 0.10
25 2 0.01
26 6 0.03
27 2 0.01
28 7 0.03
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.36
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCTCC
Found at i:5474 original size:44 final size:44
Alignment explanation
Indices: 5335--5507 Score: 147
Period size: 44 Copynumber: 3.9 Consensus size: 44
5325 AACCATACCC
* * * *
5335 TATGAAATTTCAGTAGCCA-ACCTAAGAAATTTTAATAA-TCTGGCA
1 TATGAAATTTTAGTAACCACA-CTATGAAATTTTGATAACTCT--CA
* *
5380 CTATGAAATTTTAGTAACCACACTATGAAATTTTGATCACTTTCA
1 -TATGAAATTTTAGTAACCACACTATGAAATTTTGATAACTCTCA
* * *
5425 TATGAAATTTTGGTAACCACACTATGGAATTTTGATAAC-CTCC
1 TATGAAATTTTAGTAACCACACTATGAAATTTTGATAACTCTCA
* * * *
5468 TCATGAAATTATAATAATCATC-TTATGAAATTTTGATAAC
1 T-ATGAAATTTTAGTAACCA-CACTATGAAATTTTGATAAC
5508 CACATAAAGA
Statistics
Matches: 106, Mismatches: 17, Indels: 10
0.80 0.13 0.08
Matches are distributed among these distances:
43 3 0.03
44 66 0.62
45 3 0.03
46 31 0.29
47 3 0.03
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.36
Consensus pattern (44 bp):
TATGAAATTTTAGTAACCACACTATGAAATTTTGATAACTCTCA
Found at i:5707 original size:19 final size:20
Alignment explanation
Indices: 5675--5712 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
5665 TATTGACATT
5675 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
5694 TAAAATATTG-AATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
5713 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:5962 original size:122 final size:113
Alignment explanation
Indices: 5763--5997 Score: 308
Period size: 121 Copynumber: 2.0 Consensus size: 113
5753 CAATTTGGCA
* * *
5763 AACTTATAATTCGGTCTAAATTGAAATTTTTAATTAATTTTAAATAATAAATAATGGAAATTTAG
1 AACTTAAAATTCGATCTAAATTGAAATTTTTAATTAATTTTAAATAATAAATAATAGAAATTTAG
* * *
5828 AAATATATTTGAAAAAAAAGGTGCTATCGGAAAACATAAAGTTTCCCAT
66 AAATATAATTG-AAAAAAAGGTACAATCGGAAAACATAAAGTTTCCCAT
*
5877 AACTTAAAATTCGATCTAAATTGAAATTTTATAATTAATTTTTAAATAATAAATTTTAATAATAT
1 AACTTAAAATTCGATCTAAATTGAAATTTT-TAATTAA-TTTTAAATAATAAA---TAAT-AGA-
* *
5942 CAATTTAGAAATATAATTGAAAAAAGGGTACAATCGGAAAACATAAAGTTTTCCAT
59 -AATTTAGAAATATAATTGAAAAAAAGGTACAATCGGAAAACATAAAGTTTCCCAT
5998 TATTCATACT
Statistics
Matches: 104, Mismatches: 9, Indels: 9
0.85 0.07 0.07
Matches are distributed among these distances:
114 28 0.27
115 7 0.07
116 14 0.13
119 4 0.04
120 1 0.01
121 33 0.32
122 17 0.16
ACGTcount: A:0.47, C:0.08, G:0.10, T:0.36
Consensus pattern (113 bp):
AACTTAAAATTCGATCTAAATTGAAATTTTTAATTAATTTTAAATAATAAATAATAGAAATTTAG
AAATATAATTGAAAAAAAGGTACAATCGGAAAACATAAAGTTTCCCAT
Done.