Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007499.1 Corchorus capsularis cultivar CVL-1 contig07520, 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: 47314
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:355 original size:16 final size:15
Alignment explanation
Indices: 334--380 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
324 AGGAATAGGC
334 AATCAATCAAAGCAA
1 AATCAATCAAAGCAA
*
349 TAATCAATCGAAGCAA
1 -AATCAATCAAAGCAA
365 AA-CAATGCAAAG-AA
1 AATCAAT-CAAAGCAA
379 AA
1 AA
381 AGTAAATGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 8 0.29
15 6 0.21
16 14 0.50
ACGTcount: A:0.60, C:0.17, G:0.11, T:0.13
Consensus pattern (15 bp):
AATCAATCAAAGCAA
Found at i:1806 original size:20 final size:20
Alignment explanation
Indices: 1777--1822 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1767 CCAGTTAATT
* *
1777 GCTGATGTGGAATTTTTGTG
1 GCTGACGTGGAATTTCTGTG
1797 GCTGACGTGGAATTTCTGTG
1 GCTGACGTGGAATTTCTGTG
*
1817 ACTGAC
1 GCTGAC
1823 ATGTAGGGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.17, C:0.13, G:0.33, T:0.37
Consensus pattern (20 bp):
GCTGACGTGGAATTTCTGTG
Found at i:2538 original size:92 final size:92
Alignment explanation
Indices: 2377--2752 Score: 673
Period size: 92 Copynumber: 4.1 Consensus size: 92
2367 TTTTTTCATA
* * *
2377 TTTT-AGTTGATGAGTTCTTGGTAATTCTGAGTTTTGATTTGTAATTATGGGTTGGCTTTGATTT
1 TTTTCAGTTGATGAGTTCTTGGTAATTATGGGTTTGGATTTGTAATTATGGGTTGGCTTTGATTT
2441 TCATTATCATTGTTCATCATCAATTCG
66 TCATTATCATTGTTCATCATCAATTCG
2468 TTTTCAGTTGATGAGTTCTTGGTAATTATGGGTTTGGATTTGTAATTATGGGTTGGCTTTGATTT
1 TTTTCAGTTGATGAGTTCTTGGTAATTATGGGTTTGGATTTGTAATTATGGGTTGGCTTTGATTT
2533 TCATTATCATTGTTCATCATCAATTCG
66 TCATTATCATTGTTCATCATCAATTCG
2560 TTTTCAGTTGATGAGTTCTTGGTAATTATGGGTTTGGATTTGTAATTATGGGTTGGCTTTGATTT
1 TTTTCAGTTGATGAGTTCTTGGTAATTATGGGTTTGGATTTGTAATTATGGGTTGGCTTTGATTT
2625 TCATTATCATTGTTCATCATCAATTCG
66 TCATTATCATTGTTCATCATCAATTCG
* * *
2652 TTTTCAGTTGATGAGTTCTTGGTAATTTTGGGTTTTGATTTATAATTATGGGTTGGCTTTGATTT
1 TTTTCAGTTGATGAGTTCTTGGTAATTATGGGTTTGGATTTGTAATTATGGGTTGGCTTTGATTT
* *
2717 TCATTATCATTGTTCATTATCAATTCA
66 TCATTATCATTGTTCATCATCAATTCG
2744 TTTTCAGTT
1 TTTTCAGTT
2753 CATTATCAAA
Statistics
Matches: 276, Mismatches: 8, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
91 4 0.01
92 272 0.99
ACGTcount: A:0.20, C:0.10, G:0.20, T:0.51
Consensus pattern (92 bp):
TTTTCAGTTGATGAGTTCTTGGTAATTATGGGTTTGGATTTGTAATTATGGGTTGGCTTTGATTT
TCATTATCATTGTTCATCATCAATTCG
Found at i:10100 original size:2 final size:2
Alignment explanation
Indices: 10093--10119 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
10083 ATAGATGCAA
10093 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
10120 GTAAGAATTA
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:19803 original size:31 final size:32
Alignment explanation
Indices: 19744--19805 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
19734 CATGCTGACG
19744 TGGCAATGCCACGTTGGATCAAAAATGCCACA
1 TGGCAATGCCACGTTGGATCAAAAATGCCACA
* *
19776 TGGCAATGCCATGTTGGA-CCAAAATGCCAC
1 TGGCAATGCCACGTTGGATCAAAAATGCCAC
19806 GCGGTAAGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 11 0.39
32 17 0.61
ACGTcount: A:0.32, C:0.26, G:0.23, T:0.19
Consensus pattern (32 bp):
TGGCAATGCCACGTTGGATCAAAAATGCCACA
Found at i:23985 original size:335 final size:335
Alignment explanation
Indices: 23375--24019 Score: 1094
Period size: 335 Copynumber: 1.9 Consensus size: 335
23365 TTACTTTTTG
23375 TTCTATTTGTCCGATCAATGTGATTCAAGTGTCTATTGAAAGATAATTTAATGACTTGCAACTTT
1 TTCTATTTGTCCGATCAATGTGATTCAAGTGTCTATTGAAAGATAATTTAATGACTTGCAACTTT
* * *
23440 CATTAAGGACTCAAAAGCTAATTTTGAGATTTCAGTTCTCAAAAATGTTTCTGAAATTTGGTGGT
66 CATTAAGGACTCAAAAGCCAATTTTGAGATTTCAATTCTCAAAAATGTTTCCGAAATTTGGTGGT
* * * * * * *
23505 CTCGCTTGACGGTCTATCTAATTTTGATTCACGTGTTCGATTGAAGTTGTTTAACATTTAGTTAA
131 CTCGCTTAACGGTCTATCTAATTTTAATCCACGTATTCGATTGAAGTTGTTCAACAGTCAGTTAA
* *
23570 AAGGTTTTTGCTTGATCTACGACTTTCATGAAGGTGAAGGAATTGAAAACCAATTTTTATATTTC
196 AAGGTTTTTGCTTAATCTACGACTTTCATAAAGGTGAAGGAATTGAAAACCAATTTTTATATTTC
23635 AATTCTAAAAAGTGCTTCCGAAA-TTTAGTCATTTCATAACTAACTGTTCCGAAATTTAGTGCTT
261 AATTCTAAAAAGTGCTTCC-AAATTTTAGTCATTTCATAACTAACTGTTCCGAAATTTAGTGCTT
23699 CCAAAATTCAA
325 CCAAAATTCAA
*
23710 TTCTATTTGTCCGATCAATGTGATTCAAGTGTTTATTGAAAGATAATTTAATGACTTGCAACTTT
1 TTCTATTTGTCCGATCAATGTGATTCAAGTGTCTATTGAAAGATAATTTAATGACTTGCAACTTT
* *
23775 CATTAAGGACTCAAAAGCCAATTTTGAGGTTTCAATTCTCAAAAATGTTTCCGAAATTTTGTGGT
66 CATTAAGGACTCAAAAGCCAATTTTGAGATTTCAATTCTCAAAAATGTTTCCGAAATTTGGTGGT
*
23840 CTCGCTTAACGGTCTATCTAATTTTAATCCACGTATTCGATTGAAGTTGTTCAACAGTCGGTTAA
131 CTCGCTTAACGGTCTATCTAATTTTAATCCACGTATTCGATTGAAGTTGTTCAACAGTCAGTTAA
* *
23905 AATGTTTTTGCTTAATCTACGACTTTCATAAAGGTGAAGGAATTGAAAACTAATTTTTATATTTC
196 AAGGTTTTTGCTTAATCTACGACTTTCATAAAGGTGAAGGAATTGAAAACCAATTTTTATATTTC
* *
23970 AATTCTAAAAAGTGCTTCCAAATTTTAGTCATTTCATAATTAATTGTTCC
261 AATTCTAAAAAGTGCTTCCAAATTTTAGTCATTTCATAACTAACTGTTCC
24020 CTCCCTTTAC
Statistics
Matches: 289, Mismatches: 20, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
334 3 0.01
335 286 0.99
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (335 bp):
TTCTATTTGTCCGATCAATGTGATTCAAGTGTCTATTGAAAGATAATTTAATGACTTGCAACTTT
CATTAAGGACTCAAAAGCCAATTTTGAGATTTCAATTCTCAAAAATGTTTCCGAAATTTGGTGGT
CTCGCTTAACGGTCTATCTAATTTTAATCCACGTATTCGATTGAAGTTGTTCAACAGTCAGTTAA
AAGGTTTTTGCTTAATCTACGACTTTCATAAAGGTGAAGGAATTGAAAACCAATTTTTATATTTC
AATTCTAAAAAGTGCTTCCAAATTTTAGTCATTTCATAACTAACTGTTCCGAAATTTAGTGCTTC
CAAAATTCAA
Found at i:33618 original size:12 final size:12
Alignment explanation
Indices: 33601--33630 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
33591 TATCTAGAAA
33601 ATTGAGTAGGTG
1 ATTGAGTAGGTG
*
33613 ATTGAGTATGTG
1 ATTGAGTAGGTG
33625 ATTGAG
1 ATTGAG
33631 GACGAAGTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.27, C:0.00, G:0.37, T:0.37
Consensus pattern (12 bp):
ATTGAGTAGGTG
Found at i:40969 original size:21 final size:21
Alignment explanation
Indices: 40943--41002 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 21
40933 GGGGAAGAAG
*
40943 GAGAAGAGAAAAAGAAGAAAA
1 GAGAAGAGAAAAAGAAAAAAA
*
40964 GAGAAGAGAAGAAGCAAAAAAAA
1 GAGAAGAGAAAAAG--AAAAAAA
*
40987 AAGAAGAAGAAAAAGA
1 GAGAAG-AGAAAAAGA
41003 GCGGAAAGGG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
21 13 0.41
22 1 0.03
23 11 0.34
24 7 0.22
ACGTcount: A:0.72, C:0.02, G:0.27, T:0.00
Consensus pattern (21 bp):
GAGAAGAGAAAAAGAAAAAAA
Found at i:40994 original size:26 final size:27
Alignment explanation
Indices: 40936--40996 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 27
40926 AAGGGTCGGG
40936 GAAGAAGGAGAAGAGAAAAAGAAGAAAA
1 GAAGAA-GAGAAGAGAAAAAGAAGAAAA
*
40964 G-AGAAGAGAAGAAGCAAAA-AA-AAAA
1 GAAGAAGAGAAG-AGAAAAAGAAGAAAA
40989 GAAGAAGA
1 GAAGAAGA
40997 AAAAGAGCGG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
25 5 0.17
26 14 0.47
27 10 0.33
28 1 0.03
ACGTcount: A:0.69, C:0.02, G:0.30, T:0.00
Consensus pattern (27 bp):
GAAGAAGAGAAGAGAAAAAGAAGAAAA
Found at i:41000 original size:18 final size:18
Alignment explanation
Indices: 40954--41000 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
40944 AGAAGAGAAA
* * *
40954 AAGAAGAAAAGAGAAGAG
1 AAGAAGAAAAAAAAAAAG
*
40972 AAGAAGCAAAAAAAAAAG
1 AAGAAGAAAAAAAAAAAG
40990 AAGAAGAAAAA
1 AAGAAGAAAAA
41001 GAGCGGAAAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.74, C:0.02, G:0.23, T:0.00
Consensus pattern (18 bp):
AAGAAGAAAAAAAAAAAG
Found at i:41274 original size:23 final size:23
Alignment explanation
Indices: 41221--41276 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
41211 TAATTCGAAG
* * **
41221 TTAATTTGAAATAACTTTTTTTT
1 TTAATTTTAAATAACTTTATTAA
41244 TTAATTTTAAATAACTTTATTAA
1 TTAATTTTAAATAACTTTATTAA
*
41267 TTAGTTTTAA
1 TTAATTTTAA
41277 TTAATTTTCC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.57
Consensus pattern (23 bp):
TTAATTTTAAATAACTTTATTAA
Found at i:41903 original size:2 final size:2
Alignment explanation
Indices: 41896--41927 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
41886 AACACTGAAT
*
41896 TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41928 ATCTAGTAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:42519 original size:23 final size:23
Alignment explanation
Indices: 42493--42536 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
42483 TATTTTCGGA
42493 TTTCTAAAAGTGATGTAATTTTT
1 TTTCTAAAAGTGATGTAATTTTT
*
42516 TTTCTAGAAGTGATGTAATTT
1 TTTCTAAAAGTGATGTAATTT
42537 CGAATTTCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.05, G:0.16, T:0.50
Consensus pattern (23 bp):
TTTCTAAAAGTGATGTAATTTTT
Found at i:42984 original size:83 final size:82
Alignment explanation
Indices: 42886--43051 Score: 264
Period size: 83 Copynumber: 2.0 Consensus size: 82
42876 GGTTTTCACT
* *
42886 AACGTTTCAAAAAATGTCTCTA-TTACTTGTCTCAACAACTGTCTCTACCTAGAAACATAATCTG
1 AACGTTTCAAAAAATGTCTCTACTTACCTGTCTCAACAACTGTCTCTA-CTAGAAACAAAATCTG
*
42950 AGACGTAT-TATTGGCGGG
65 AGACGT-TCCATTGGCGGG
42968 AACGTTTTCAAAAAATGTCTCTACTTACCTGTCTCAACAACTGTCTCTACTAGAAACAAAATCTG
1 AACG-TTTCAAAAAATGTCTCTACTTACCTGTCTCAACAACTGTCTCTACTAGAAACAAAATCTG
43033 AGACGTTCCATTGGCGGG
65 AGACGTTCCATTGGCGGG
43051 A
1 A
43052 GAAGCGCACC
Statistics
Matches: 78, Mismatches: 3, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
82 5 0.06
83 49 0.63
84 24 0.31
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (82 bp):
AACGTTTCAAAAAATGTCTCTACTTACCTGTCTCAACAACTGTCTCTACTAGAAACAAAATCTGA
GACGTTCCATTGGCGGG
Found at i:46740 original size:34 final size:36
Alignment explanation
Indices: 46688--46757 Score: 126
Period size: 34 Copynumber: 2.0 Consensus size: 36
46678 TGAGAATTAC
46688 ACTCATTTATATATATGTCAATAATAGGAAAGGATA
1 ACTCATTTATATATATGTCAATAATAGGAAAGGATA
46724 ACTCA-TT-TATATATGTCAATAATAGGAAAGGATA
1 ACTCATTTATATATATGTCAATAATAGGAAAGGATA
46758 TCAAGTCCAC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
34 27 0.79
35 2 0.06
36 5 0.15
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (36 bp):
ACTCATTTATATATATGTCAATAATAGGAAAGGATA
Found at i:47283 original size:2 final size:2
Alignment explanation
Indices: 47271--47306 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
47261 TACCACTTTA
47271 AT AT A- 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 AT AT A
47307 CACTATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Done.