Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014883.1 Corchorus capsularis cultivar CVL-1 contig14904, 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: 75416
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:348 original size:2 final size:2
Alignment explanation
Indices: 343--369 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
333 TATATTGACA
343 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 A
370 CTAGTTAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3172 original size:28 final size:28
Alignment explanation
Indices: 3132--3188 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
3122 TATTTACTTG
3132 TTAGACATGACACTATAGTCATCTCTTT
1 TTAGACATGACACTATAGTCATCTCTTT
3160 TTAGACATGACACTATAGTCATCTCTTT
1 TTAGACATGACACTATAGTCATCTCTTT
3188 T
1 T
3189 GGCTTGTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.40
Consensus pattern (28 bp):
TTAGACATGACACTATAGTCATCTCTTT
Found at i:3338 original size:2 final size:2
Alignment explanation
Indices: 3331--3360 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3321 TAGTATTGAA
*
3331 AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3361 TAATATTCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:7304 original size:896 final size:897
Alignment explanation
Indices: 5515--7310 Score: 3227
Period size: 896 Copynumber: 2.0 Consensus size: 897
5505 GATAAGGTTG
*
5515 TTCCAAGTTAAAAGTTGAAAGGGCTTGTGATTAAATTCCATAGGGGACAAAAATAATATATAACA
1 TTCCAAGTTAAAAGTTGAAAGGGCTTGTGAGTAAATTCCATAGGGGACAAAAATAATATATAACA
*
5580 AGTTATATTAGCCCGCGCTGGCGCTACGGGCATTCTTTATTTTAGAGTGGTGCTTGATTAACTGA
66 AGTTATATTAGCCCGCGCTGGCGCTACGGACATTCTTTATTTTAGAGTGGTGCTTGATTAACTGA
*
5645 TTGAATAAGGATATTAATATAATCAATTATATAAGGGCCAAGAACATTTTTTTATTCTAGAGTGG
131 TTGAATAAGGATATTAATATAATCAATTATATAAGGGCCAAGAACATTTTTTTATTCTAGAGCGG
*
5710 TGCTTGATTGATTAATTGATCGAATTATATAAGGTTGCAGTAAAAATGCAATTTAAATGGATTAG
196 TGCTTGATTGATTAATTAATCGAATTATATAAGGTTGCAGTAAAAATGCAATTTAAATGGATTAG
5775 TTTTAATTATGTCTCTAGCATAAATCTTTGTAAGCTAACTTTTTAGACATGAAAAATTAAGAAGG
261 TTTTAATTATGTCTCTAGCATAAATCTTTGTAAGCTAACTTTTTAGACATGAAAAATTAAGAAGG
* *
5840 TCAAGAACGTGTTTTTATTTGTAAGTAATAGGAAGTGCAAAGAGGTAATAAAATATGTTGTTAAT
326 TCAAGAACATGTTTTTATTTGTAAGTAATAGGAAGTGCAAAGAGATAATAAAATATGTTGTTAAT
*
5905 TGGATAATAATACTCACATTGAACAAAGGGTGGTGGCTTTAATTTAGAAGGGGAAAAATATTGAA
391 TGGATAATAATACTCACATTGAACAAAGGGTGGT-G-TTTAATTCAGAAGGGGAAAAATATTGAA
* * * *
5970 TGGTCCATATTGAAGGGATTGAGACAGAGAAGAAAGAGGAAAGAGATATGAAAGTGAAAACAGAG
454 CGGTCCATATTGAAGCGATGGAGACAGAGAAGAAAGAGGAAAGAGATATGAAAGTAAAAACAGAG
6035 GGGAGTGATGGAAAGGTTTGATTTTTGGCAAACCTGAAGATTGATCAGCACCGAGGAGTTGAAAG
519 GGGAGTGATGGAAAGGTTTGATTTTTGGCAAACCTGAAGATTGATCAGCACCGAGGAGTTGAAAG
6100 GAAGCAGCAACTGAGTTGGTGAGAGGAAAAAAGAAAACAACGAGAGAAACATTAATTAAAAGTAA
584 GAAGCAGCAACTGAGTTGGTGAGAGGAAAAAAGAAAACAACGAGAGAAACATTAATTAAAAGTAA
6165 TTAAGGGTTTAGGGTTTAGAAGCAATTAATTAAAAGCCTTAAACATTAATTAAAAACAATTAAGG
649 TTAAGGGTTTAGGGTTTAGAAGCAATTAATTAAAAGCCTTAAACATTAATTAAAAACAATTAAGG
* * *
6230 AAGGGAAATGTGTAATTGCAAAAAAGGGTAGAAGGAAAAGGAATGGAGGAAGCTCACAGAGGGGC
714 AAAGGAAATGTGTAATTACAAAAAAGGGTAGAAGGAAAAGGAATGGAGGAAACTCACAGAGGGGC
*
6295 TTTTTAGTCATCCGAAAAGTGAGAAAATACCAAAAATAGCCAAAATGTGGCACCACATTAATCCT
779 TTTTTAGTCATCCGAAAAGTGAGAAAAGACCAAAAATAGCCAAAATGTGGCACCACATTAATCCT
*
6360 CAATTTGGCCTTTTAGTAATTTCCATAGTAGTTAAAAATAATATATAGTATATA
844 CAATTTGACCTTTTAGTAATTTCCATAGTAGTTAAAAATAATATATAGTATATA
6414 TTCCAAGTTAAAAGTTGAAAGGGCTTGTGAGTAAATTCCATAGGGGACAAAAATAATATATAACA
1 TTCCAAGTTAAAAGTTGAAAGGGCTTGTGAGTAAATTCCATAGGGGACAAAAATAATATATAACA
*
6479 AGTTATATTAGCCCGCGCTGGCGCTACGGACGTTCTTTATTTTAGAGTGGTGCTTGATTAACTGA
66 AGTTATATTAGCCCGCGCTGGCGCTACGGACATTCTTTATTTTAGAGTGGTGCTTGATTAACTGA
*
6544 TTGAATAAGGATATTAATATAATCAATTATATAAGGGCCAAGAACATTTTTTTGTTCTAGAGCGG
131 TTGAATAAGGATATTAATATAATCAATTATATAAGGGCCAAGAACATTTTTTTATTCTAGAGCGG
*
6609 TGCTTGATTGATTAATTAATTGAATTATATAAGGTTGCAGTAAAAATGCAATTTAAATGGATTAG
196 TGCTTGATTGATTAATTAATCGAATTATATAAGGTTGCAGTAAAAATGCAATTTAAATGGATTAG
* * *
6674 TTTTAATTATGTCTCTGGCATAAATTTTTGTAAGCTAACTTTTTAGACATGCAAAATTAAGAAGG
261 TTTTAATTATGTCTCTAGCATAAATCTTTGTAAGCTAACTTTTTAGACATGAAAAATTAAGAAGG
*
6739 TCAAGAATATGTTTTTATTTGTAAGTAATAGGAAGTGCAAAGAGATAATAAAATATGTTGTTAAT
326 TCAAGAACATGTTTTTATTTGTAAGTAATAGGAAGTGCAAAGAGATAATAAAATATGTTGTTAAT
6804 TGGATAATAATACTCACATTGAACAAAGGGTGGT-TTTAATTCAGAAGGGGAAAAATATTGAACG
391 TGGATAATAATACTCACATTGAACAAAGGGTGGTGTTTAATTCAGAAGGGGAAAAATATTGAACG
* * * *
6868 GTCCATGTTGAAGCGATGGAGACGGAGAAGAAAGAGGAAAGAGATATGAAGGTAAAAACGGAGGG
456 GTCCATATTGAAGCGATGGAGACAGAGAAGAAAGAGGAAAGAGATATGAAAGTAAAAACAGAGGG
* *
6933 GGGTGATGGAAAGGTTTGATTTTTGGCAAACCTGAAGATTGATCAGTACCGAGGAGTTGAAAGGA
521 GAGTGATGGAAAGGTTTGATTTTTGGCAAACCTGAAGATTGATCAGCACCGAGGAGTTGAAAGGA
* * *
6998 AGTAGCAACTGAGTTGGTGAGAGGAAAAAAGAAAACAGCGAGAGAAACATTAATTAAGAGTAATT
586 AGCAGCAACTGAGTTGGTGAGAGGAAAAAAGAAAACAACGAGAGAAACATTAATTAAAAGTAATT
*
7063 AAGGGTTTAGGGTTTAGAAGCAATTAATTAAAAGTCTTAAACATTAATTAAAAACAATTAAGGAA
651 AAGGGTTTAGGGTTTAGAAGCAATTAATTAAAAGCCTTAAACATTAATTAAAAACAATTAAGGAA
*
7128 AGGAAATGTGTAATTACAAAAAAGGGTAGAAGGAAAAGGAATGG-GAGAAACTCATAGAGGGGCT
716 AGGAAATGTGTAATTACAAAAAAGGGTAGAAGGAAAAGGAATGGAG-GAAACTCACAGAGGGGCT
*
7192 TTTTAGTCATCTGAAAAGTGAGAAAAGACCAAAAATAGCCAAAATGTGGCACCACATTAATCCTC
780 TTTTAGTCATCCGAAAAGTGAGAAAAGACCAAAAATAGCCAAAATGTGGCACCACATTAATCCTC
*
7257 AATTTGACCTTTTAGTAATTTCCATGGTAGTTAAAAATAATATATAGTATATA
845 AATTTGACCTTTTAGTAATTTCCATAGTAGTTAAAAATAATATATAGTATATA
7310 T
1 T
7311 ATATATATAT
Statistics
Matches: 860, Mismatches: 36, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
895 1 0.00
896 448 0.52
899 411 0.48
ACGTcount: A:0.39, C:0.10, G:0.22, T:0.29
Consensus pattern (897 bp):
TTCCAAGTTAAAAGTTGAAAGGGCTTGTGAGTAAATTCCATAGGGGACAAAAATAATATATAACA
AGTTATATTAGCCCGCGCTGGCGCTACGGACATTCTTTATTTTAGAGTGGTGCTTGATTAACTGA
TTGAATAAGGATATTAATATAATCAATTATATAAGGGCCAAGAACATTTTTTTATTCTAGAGCGG
TGCTTGATTGATTAATTAATCGAATTATATAAGGTTGCAGTAAAAATGCAATTTAAATGGATTAG
TTTTAATTATGTCTCTAGCATAAATCTTTGTAAGCTAACTTTTTAGACATGAAAAATTAAGAAGG
TCAAGAACATGTTTTTATTTGTAAGTAATAGGAAGTGCAAAGAGATAATAAAATATGTTGTTAAT
TGGATAATAATACTCACATTGAACAAAGGGTGGTGTTTAATTCAGAAGGGGAAAAATATTGAACG
GTCCATATTGAAGCGATGGAGACAGAGAAGAAAGAGGAAAGAGATATGAAAGTAAAAACAGAGGG
GAGTGATGGAAAGGTTTGATTTTTGGCAAACCTGAAGATTGATCAGCACCGAGGAGTTGAAAGGA
AGCAGCAACTGAGTTGGTGAGAGGAAAAAAGAAAACAACGAGAGAAACATTAATTAAAAGTAATT
AAGGGTTTAGGGTTTAGAAGCAATTAATTAAAAGCCTTAAACATTAATTAAAAACAATTAAGGAA
AGGAAATGTGTAATTACAAAAAAGGGTAGAAGGAAAAGGAATGGAGGAAACTCACAGAGGGGCTT
TTTAGTCATCCGAAAAGTGAGAAAAGACCAAAAATAGCCAAAATGTGGCACCACATTAATCCTCA
ATTTGACCTTTTAGTAATTTCCATAGTAGTTAAAAATAATATATAGTATATA
Found at i:7309 original size:2 final size:2
Alignment explanation
Indices: 7296--7332 Score: 65
Period size: 2 Copynumber: 18.0 Consensus size: 2
7286 GTTAAAAATA
7296 AT AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7333 GTTGGAACTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:35613 original size:59 final size:58
Alignment explanation
Indices: 35495--35614 Score: 170
Period size: 60 Copynumber: 2.0 Consensus size: 58
35485 TTTAAACATC
* *
35495 ATTACAACTTTAGTTTACCCTTTTTTATAAGCTTGCCCTTCACATTTGATTTATAATAT
1 ATTACAACTTTAGTTTAACCTTTTTTATAAGCTTGCCCTTCACA-TTGATTCATAATAT
* *
35554 ATTACCACTTTAGTTTATACTTTTTTTATAAGCTTGCCCTTCACA-TGATTCATATATAT
1 ATTACAACTTTAGTTTA-ACCTTTTTTATAAGCTTGCCCTTCACATTGATTCATA-ATAT
35613 AT
1 AT
35615 AGATAGAAAC
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
58 8 0.15
59 22 0.40
60 25 0.45
ACGTcount: A:0.28, C:0.18, G:0.07, T:0.47
Consensus pattern (58 bp):
ATTACAACTTTAGTTTAACCTTTTTTATAAGCTTGCCCTTCACATTGATTCATAATAT
Found at i:38501 original size:51 final size:50
Alignment explanation
Indices: 38425--38522 Score: 160
Period size: 51 Copynumber: 1.9 Consensus size: 50
38415 TTTTTGGGGG
*
38425 TTTCAAACTTTTCATAACTTACCTCTTTAAGTTCTTTAAATTTGCATACAC
1 TTTCAAACTTTTCAAAACTTACCTC-TTAAGTTCTTTAAATTTGCATACAC
* *
38476 TTTCAAACTTTTCAAAATTTACCTCTTAGGTTCTTTAAATTTGCATA
1 TTTCAAACTTTTCAAAACTTACCTCTTAAGTTCTTTAAATTTGCATA
38523 TGCAAGACAC
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
50 21 0.48
51 23 0.52
ACGTcount: A:0.30, C:0.19, G:0.05, T:0.46
Consensus pattern (50 bp):
TTTCAAACTTTTCAAAACTTACCTCTTAAGTTCTTTAAATTTGCATACAC
Found at i:39328 original size:22 final size:22
Alignment explanation
Indices: 39303--39360 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
39293 GTGATTAAAA
*
39303 AAAAATACTTAAAAAATGTACC
1 AAAAATACTTAAAAAATATACC
*
39325 AAAAATACTT-AAATATATACC
1 AAAAATACTTAAAAAATATACC
*
39346 AAAGAATTCTTAAAA
1 AAA-AATACTTAAAA
39361 GATACTACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 12 0.39
22 16 0.52
23 3 0.10
ACGTcount: A:0.59, C:0.12, G:0.03, T:0.26
Consensus pattern (22 bp):
AAAAATACTTAAAAAATATACC
Found at i:68231 original size:71 final size:72
Alignment explanation
Indices: 68115--68256 Score: 250
Period size: 71 Copynumber: 2.0 Consensus size: 72
68105 ACATTGAGTT
* *
68115 CTATTAATCTTTCCGAATATTTTTATTTTCTCTATTCATGAGATTTCAACTGAAGTCTTTTTTTT
1 CTATTAATCTTTCCGAATATTATTATTTTCTCTATTCATAAGATTTCAACTGAAGTCTTTTTTTT
68180 T-TTTTG
66 TCTTTTG
*
68186 CTATTAATCTTTCCGAATATTATTATTTTCTTTATTCATAAGATTTCAACTGAAGTCTTTTTTTT
1 CTATTAATCTTTCCGAATATTATTATTTTCTCTATTCATAAGATTTCAACTGAAGTCTTTTTTTT
68251 TCTTTT
66 TCTTTT
68257 TGAGTGAGTA
Statistics
Matches: 67, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
71 63 0.94
72 4 0.06
ACGTcount: A:0.23, C:0.14, G:0.07, T:0.56
Consensus pattern (72 bp):
CTATTAATCTTTCCGAATATTATTATTTTCTCTATTCATAAGATTTCAACTGAAGTCTTTTTTTT
TCTTTTG
Found at i:70497 original size:20 final size:21
Alignment explanation
Indices: 70459--70504 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
70449 AAATATTATA
70459 TTTATCCTATAATGAGTAGTT
1 TTTATCCTATAATGAGTAGTT
* *
70480 TTTATCTTA-AATGGGTAGTT
1 TTTATCCTATAATGAGTAGTT
70500 TTTAT
1 TTTAT
70505 TTTATTTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.26, C:0.07, G:0.15, T:0.52
Consensus pattern (21 bp):
TTTATCCTATAATGAGTAGTT
Done.