Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006745.1 Corchorus capsularis cultivar CVL-1 contig06766, 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: 45442
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:283 original size:14 final size:14
Alignment explanation
Indices: 247--276 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
237 AAATTTTTAA
*
247 TAAAAAATAAAATT
1 TAAAAATTAAAATT
261 TAAAAATTAAAATT
1 TAAAAATTAAAATT
275 TA
1 TA
277 TATATTATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
TAAAAATTAAAATT
Found at i:2578 original size:29 final size:30
Alignment explanation
Indices: 2528--2585 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
2518 CCTAATAATG
* *
2528 TATACATATAAATCATTCAATTTTATTATC
1 TATAAATATAAATCATTCAATTATATTATC
*
2558 TATAAATAT-AATCATTTAATTATATTAT
1 TATAAATATAAATCATTCAATTATATTAT
2586 ATTATTTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (30 bp):
TATAAATATAAATCATTCAATTATATTATC
Found at i:3094 original size:2 final size:2
Alignment explanation
Indices: 3089--3129 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
3079 TATGTGTGTG
*
3089 TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3130 ATGGTTCGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5168 original size:13 final size:13
Alignment explanation
Indices: 5150--5175 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5140 CTTCATGGAA
5150 CTGATCTTGATTT
1 CTGATCTTGATTT
5163 CTGATCTTGATTT
1 CTGATCTTGATTT
5176 TTTATACATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.54
Consensus pattern (13 bp):
CTGATCTTGATTT
Found at i:13637 original size:31 final size:31
Alignment explanation
Indices: 13599--13661 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
13589 AAAAGGGCTA
13599 GAGCTCCGGTGTAAGCTCATCCAATGTAAAT
1 GAGCTCCGGTGTAAGCTCATCCAATGTAAAT
13630 GAGCTCCGGTGTAAGCTCATCCAATGTAAAT
1 GAGCTCCGGTGTAAGCTCATCCAATGTAAAT
13661 G
1 G
13662 CAAGTTACTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (31 bp):
GAGCTCCGGTGTAAGCTCATCCAATGTAAAT
Found at i:14609 original size:157 final size:157
Alignment explanation
Indices: 14313--14814 Score: 552
Period size: 157 Copynumber: 3.2 Consensus size: 157
14303 TGGCAAAAAC
* *** * * *
14313 TGACCCTTCGACCGAAAGGGTATTTTTGGAAAGTAAAATTAAA-TTGGAGATGCCAAAGTTGACC
1 TGACCATTCGACCGAAAGGGTATAACTCGAAAGTAGAATTAAACTT-GAGATGCAAAAGTTGACC
* * * * * *
14377 CCTCGATCGGAAGGGTAACTCGAAATGCAAAAACTGACCTTTCGA-TCGGAAGGGCATTACTAGA
65 CTTCGACCGGAAGGGTAACTCGAAATGCAAAAACTGACCCTTCGACT-AGAAGGGTATTACTGGA
*
14441 AAATGAGAATTGAACTTGAAATGCTAAGGT
129 AAGTGA-AATTGAACTTGAAATGCTAAGGT
*
14471 TGACCATTCGACCGAAAGGGTATAACTCGAAAGT-GAATTAAACTTGAGGTGCAAAAGTTGACCC
1 TGACCATTCGACCGAAAGGGTATAACTCGAAAGTAGAATTAAACTTGAGATGCAAAAGTTGACCC
* * * * * *
14535 TTCAACCGGAAGGGTAACTCGAAATGCAAAAACTTACCCTTCAACTAGAAGGGTATAATTGGGAA
66 TTCGACCGGAAGGGTAACTCGAAATGCAAAAACTGACCCTTCGACTAGAAGGGTATTACTGGAAA
**
14600 GTGAAAATTGAACTTGAAATGCTAAAAT
131 GTG-AAATTGAACTTGAAATGCTAAGGT
* * * * * * *
14628 TGACCATTCGACCGGAAGGGTATTACTAGAAAGTGAGAATTAAACTTCAAATGCTAAGGTTGACC
1 TGACCATTCGACCGAAAGGGTATAACTCGAAAGT-AGAATTAAACTTGAGATGCAAAAGTTGACC
*
14693 CTTGGACCGGAAGGGTAACTCGAAATG-AAAAATCTGACCCTTCGACTAGAAGGGTATTACTGGA
65 CTTCGACCGGAAGGGTAACTCGAAATGCAAAAA-CTGACCCTTCGACTAGAAGGGTATTACTGGA
* * *
14757 AAGTG-AATTAAACTTGAAGTGCAAAAGG-
129 AAGTGAAATTGAACTTGAAATGC-TAAGGT
** *
14785 TGACCCCTCGACCGGAAGGG--TAACTCGAAA
1 TGACCATTCGACCGAAAGGGTATAACTCGAAA
14815 TGCAAAAACT
Statistics
Matches: 290, Mismatches: 47, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
155 8 0.03
157 162 0.56
158 40 0.14
159 80 0.28
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.23
Consensus pattern (157 bp):
TGACCATTCGACCGAAAGGGTATAACTCGAAAGTAGAATTAAACTTGAGATGCAAAAGTTGACCC
TTCGACCGGAAGGGTAACTCGAAATGCAAAAACTGACCCTTCGACTAGAAGGGTATTACTGGAAA
GTGAAATTGAACTTGAAATGCTAAGGT
Found at i:14814 original size:97 final size:99
Alignment explanation
Indices: 14610--14948 Score: 409
Period size: 97 Copynumber: 3.4 Consensus size: 99
14600 GTGAAAATTG
* * * * *
14610 AACTTGAAATGCTAAAAT-TGACCATTCGACCGGAAGGGTATTACTAGAAAGTGAGAATTAAACT
1 AACTCGAAATGCAAAAATCTGACCCTTCGACTGGAAGGGTATTACTGGAAAGT-AGAATTAAACT
* * *
14674 TCAAATGC-TAAGGTTGACCCTTGGACCGGAAGGGT
65 TGAAATGCAAAAGG-TGACCCTTCGACCGGAAGGGT
*
14709 AACTCGAAATG-AAAAATCTGACCCTTCGACTAGAAGGGTATTACTGGAAAGT-GAATTAAACTT
1 AACTCGAAATGCAAAAATCTGACCCTTCGACTGGAAGGGTATTACTGGAAAGTAGAATTAAACTT
* *
14772 GAAGTGCAAAAGGTGACCCCTCGACCGGAAGGGT
66 GAAATGCAAAAGGTGACCCTTCGACCGGAAGGGT
14806 AACTCGAAATGCAAAAA-CTGACCCTTCGACTGGAAGGGTATTACTGGAAAGTGAGAATTAAACT
1 AACTCGAAATGCAAAAATCTGACCCTTCGACTGGAAGGGTATTACTGGAAAGT-AGAATTAAACT
* * * *
14870 TGAAATGCAAAAGCTCACCCTTCAACCGGAAGAGT
65 TGAAATGCAAAAGGTGACCCTTCGACCGGAAGGGT
** * * * * *
14905 ATTTTTGGAATGCAAAAAGCTGACCCTTTGACCGGAAGGGTATT
1 A-ACTCGAAATGCAAAAATCTGACCCTTCGACTGGAAGGGTATT
14949 TTTGGAACTT
Statistics
Matches: 209, Mismatches: 24, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
97 80 0.38
98 14 0.07
99 80 0.38
100 12 0.06
101 23 0.11
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.23
Consensus pattern (99 bp):
AACTCGAAATGCAAAAATCTGACCCTTCGACTGGAAGGGTATTACTGGAAAGTAGAATTAAACTT
GAAATGCAAAAGGTGACCCTTCGACCGGAAGGGT
Found at i:14835 original size:39 final size:39
Alignment explanation
Indices: 14767--14845 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 39
14757 AAGTGAATTA
* * **
14767 AACTTGAAGTGCAAAAGGTGACCCCTCGACCGGAAGGGT
1 AACTCGAAATGCAAAAACTGACCCCTCGACCGGAAGGGT
* *
14806 AACTCGAAATGCAAAAACTGACCCTTCGACTGGAAGGGT
1 AACTCGAAATGCAAAAACTGACCCCTCGACCGGAAGGGT
14845 A
1 A
14846 TTACTGGAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.34, C:0.23, G:0.27, T:0.16
Consensus pattern (39 bp):
AACTCGAAATGCAAAAACTGACCCCTCGACCGGAAGGGT
Found at i:14931 original size:41 final size:40
Alignment explanation
Indices: 14873--14955 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 40
14863 TTAAACTTGA
14873 AATGCAAAAGCTCACCCTTCAACCGGAAGAGTATTTTTGG
1 AATGCAAAAGCTCACCCTTCAACCGGAAGAGTATTTTTGG
* ** *
14913 AATGCAAAAAGCTGACCCTTTGACCGGAAGGGTATTTTTGG
1 AATGC-AAAAGCTCACCCTTCAACCGGAAGAGTATTTTTGG
14954 AA
1 AA
14956 CTTTAATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
40 5 0.13
41 33 0.87
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (40 bp):
AATGCAAAAGCTCACCCTTCAACCGGAAGAGTATTTTTGG
Found at i:16257 original size:18 final size:19
Alignment explanation
Indices: 16223--16258 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
16213 TCTAAAAAGA
*
16223 CCTAGAAACTGTTAAGAAC
1 CCTAAAAACTGTTAAGAAC
16242 CCTAAAAACT-TTAAGAA
1 CCTAAAAACTGTTAAGAA
16259 AATCCCAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.47, C:0.19, G:0.11, T:0.22
Consensus pattern (19 bp):
CCTAAAAACTGTTAAGAAC
Found at i:17722 original size:28 final size:27
Alignment explanation
Indices: 17673--17734 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 27
17663 AGGTCCAAAA
17673 ACCAAATAGTCCCAAGAAGCATACTCG
1 ACCAAATAGTCCCAAGAAGCATACTCG
* *
17700 AGCCAAATAGTCTCAA-AAGGCATATTCG
1 A-CCAAATAGTCCCAAGAA-GCATACTCG
17728 ACCAAAT
1 ACCAAAT
17735 GATAGGAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 9 0.29
28 22 0.71
ACGTcount: A:0.42, C:0.26, G:0.15, T:0.18
Consensus pattern (27 bp):
ACCAAATAGTCCCAAGAAGCATACTCG
Found at i:19348 original size:72 final size:72
Alignment explanation
Indices: 19227--19571 Score: 494
Period size: 72 Copynumber: 4.8 Consensus size: 72
19217 AGTAGTAGTG
* * *
19227 AGGATTGTGCAAAGGACTGCCAAATCTGGGAACTGCTTCGGCTACAATCGCAATG-AGAAAGATG
1 AGGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAAG-AAGATG
19291 ATCATGTA
65 ATCATGTA
* * * * *
19299 AGGATTGTGCGAAGGACTGTCAAATGTGGGAACTGCCTCGGCAATAATCGTAGTGAAGAAGATGA
1 AGGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAAGAAGATGA
*
19364 TTATGTA
66 TCATGTA
* * *
19371 AGGATTGTGCGAATGACTACCAAATGTGGGAACTGCCTCGGCTACAATCACAATGAAGAAGATGA
1 AGGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAAGAAGATGA
19436 TCATGTA
66 TCATGTA
* * * * *
19443 AGGGTTGTGTGAATGACTGCCAAATGTAGGAACTGCCTCGGCTACAATCGCAATGAAAAAGATGA
1 AGGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAAGAAGATGA
19508 TCATGTA
66 TCATGTA
* * *
19515 AGGATTGTGCGAAGGACTGCCAAATGTGGCAAATGCCTTGGCTACAATCGCAATGAA
1 AGGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAA
19572 TGTGGTTGCC
Statistics
Matches: 241, Mismatches: 31, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
72 239 0.99
73 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.27, T:0.23
Consensus pattern (72 bp):
AGGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAAGAAGATGA
TCATGTA
Found at i:26588 original size:30 final size:30
Alignment explanation
Indices: 26547--26629 Score: 93
Period size: 30 Copynumber: 2.8 Consensus size: 30
26537 ACAAACAAAC
* *
26547 ATTCTATCAATCAATTAACAA-ATATTTGCA
1 ATTCAATCAATCAATTAACAAGATA-TAGCA
26577 ATTCAATCAATCAA-TAACAAGATATAGCA
1 ATTCAATCAATCAATTAACAAGATATAGCA
*
26606 ATTCAAATCAA-CAATTGA-AAGATA
1 ATTC-AATCAATCAATTAACAAGATA
26630 GAATAAGCAA
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
29 23 0.49
30 24 0.51
ACGTcount: A:0.49, C:0.16, G:0.06, T:0.29
Consensus pattern (30 bp):
ATTCAATCAATCAATTAACAAGATATAGCA
Found at i:35739 original size:17 final size:18
Alignment explanation
Indices: 35700--35741 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
35690 ACGTTCTCTT
* *
35700 TTCTTTTCTGCCCTAATTT
1 TTCTTTTC-GCCCAAATTC
35719 TTCTTTTC-CCCAAATTC
1 TTCTTTTCGCCCAAATTC
35736 TTCTTT
1 TTCTTT
35742 GTCTTCCTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 13 0.62
19 8 0.38
ACGTcount: A:0.12, C:0.29, G:0.02, T:0.57
Consensus pattern (18 bp):
TTCTTTTCGCCCAAATTC
Found at i:41066 original size:21 final size:22
Alignment explanation
Indices: 41021--41067 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
41011 AAGCACAATT
41021 GAAATCGAAAATTACAAGCAAA
1 GAAATCGAAAATTACAAGCAAA
41043 GAAATCGAAAAATTA-AAG-AAA
1 GAAATCG-AAAATTACAAGCAAA
41064 GAAA
1 GAAA
41068 AAGGGAATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 7 0.29
22 10 0.42
23 7 0.29
ACGTcount: A:0.64, C:0.09, G:0.15, T:0.13
Consensus pattern (22 bp):
GAAATCGAAAATTACAAGCAAA
Done.