Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008849.1 Corchorus capsularis cultivar CVL-1 contig08870, 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: 51303
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:543 original size:88 final size:87
Alignment explanation
Indices: 438--758 Score: 470
Period size: 87 Copynumber: 3.7 Consensus size: 87
428 AAATTAACAA
*
438 AATAATTAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGGTTTAGGAGATATTTTAAGA
1 AATAA-TAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGGAGATATTTTAAGA
*
503 AAATAAATAAATTATAAAAATAG
65 AAACAAATAAATTATAAAAATAG
*
526 AATTAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGGTTTAGGAGATATTTTAAGA
1 AA-TAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGGAGATATTTTAAGA
591 AAACAAATAAATTAT--AAA-AG
65 AAACAAATAAATTATAAAAATAG
* *
611 AATAATAAAGTTGAGAATATTTTTTAAATCTTGCCAAATTGTGGAAGATTTAGGAGGTATTTTAA
1 AATAAT-AA--TGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGGAGATATTTTAA
* *
676 G-AAACAAATAAATAATAAAAATTG
63 GAAAACAAATAAATTATAAAAATAG
* * *
700 AATAGTAATGAGAATATTTCTCTAAATCTTGCCAGATTGTGGGAGATTTAGGAGATATT
1 AATAATAATGAGAATATTT-TCTAAATCTTGCCAAATTGTGGAAGATTTAGGAGATATT
759 AAATAATAAT
Statistics
Matches: 214, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
84 4 0.02
85 6 0.03
86 28 0.13
87 87 0.41
88 80 0.37
89 9 0.04
ACGTcount: A:0.44, C:0.06, G:0.17, T:0.34
Consensus pattern (87 bp):
AATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTAGGAGATATTTTAAGAA
AACAAATAAATTATAAAAATAG
Found at i:775 original size:174 final size:172
Alignment explanation
Indices: 415--775 Score: 498
Period size: 174 Copynumber: 2.1 Consensus size: 172
405 GTTCATATAA
* * *
415 AAATAATAATTAA-AAATTAACAAAATAATTAATGAGAATATTTTCTAAATCTTGCCAAATTGTG
1 AAATAATAATAAATAAATTAAAAAAATAATAAATGAGAATATTTTCTAAATCTTGCCAAATTGTG
* * *
479 GAAGGTTTAGGAGATATTTTAAGAAAATAAATAAATTATAAAAATAGAATTAATAATGAGAATAT
66 GAAGATTTAGGAGATATTTTAAGAAAACAAATAAATAATAAAAATAGAATTAATAATGAGAATAT
*
544 TTTCTAAATCTTGCCAAATTGTGGAAGGTTTAGGAGATATTT
131 TTTCTAAATCTTGCCAAATTGTGGAAGATTTAGGAGATATTT
* * * *
586 TAAGAA-AACAAATAAATTATAAAAGAATAATAAAGTTGAGAATATTTTTTAAATCTTGCCAAAT
1 AAATAATAATAAATAAATTA-AAAA-AATAATAAA--TGAGAATATTTTCTAAATCTTGCCAAAT
* * *
650 TGTGGAAGATTTAGGAGGTATTTTAAG-AAACAAATAAATAATAAAAATTGAA-TAGTAATGAGA
62 TGTGGAAGATTTAGGAGATATTTTAAGAAAACAAATAAATAATAAAAATAGAATTAATAATGAGA
* *
713 ATATTTCTCTAAATCTTGCCAGATTGTGGGAGATTTAGGAGATA-TT
127 ATATTT-TCTAAATCTTGCCAAATTGTGGAAGATTTAGGAGATATTT
759 AAATAATAATAAATAAA
1 AAATAATAATAAATAAA
776 AAGTTAAGAT
Statistics
Matches: 164, Mismatches: 19, Indels: 11
0.85 0.10 0.06
Matches are distributed among these distances:
170 4 0.02
171 10 0.06
172 3 0.02
173 30 0.18
174 65 0.40
175 52 0.32
ACGTcount: A:0.47, C:0.05, G:0.15, T:0.33
Consensus pattern (172 bp):
AAATAATAATAAATAAATTAAAAAAATAATAAATGAGAATATTTTCTAAATCTTGCCAAATTGTG
GAAGATTTAGGAGATATTTTAAGAAAACAAATAAATAATAAAAATAGAATTAATAATGAGAATAT
TTTCTAAATCTTGCCAAATTGTGGAAGATTTAGGAGATATTT
Found at i:8584 original size:2 final size:2
Alignment explanation
Indices: 8577--8603 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
8567 TCACAAATTG
8577 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
8604 GGTAAATGAG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8631 original size:18 final size:19
Alignment explanation
Indices: 8605--8691 Score: 106
Period size: 19 Copynumber: 4.6 Consensus size: 19
8595 TATATATATG
*
8605 GTAAATGAGTATGGCC-TT
1 GTAAGTGAGTATGGCCTTT
* *
8623 GTAAGTGAGCATAGCCTTT
1 GTAAGTGAGTATGGCCTTT
*
8642 GTATGTGAGTAT-GCCTTTT
1 GTAAGTGAGTATGGCC-TTT
*
8661 GTACGTGAGTATGGCCTTT
1 GTAAGTGAGTATGGCCTTT
8680 GTAAGTGAGTAT
1 GTAAGTGAGTAT
8692 TGTATTGGGT
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
18 16 0.27
19 40 0.68
20 3 0.05
ACGTcount: A:0.23, C:0.11, G:0.29, T:0.37
Consensus pattern (19 bp):
GTAAGTGAGTATGGCCTTT
Found at i:8705 original size:16 final size:16
Alignment explanation
Indices: 8684--8729 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
8674 GCCTTTGTAA
8684 GTGAGTATTGTATTGG
1 GTGAGTATTGTATTGG
* * *
8700 GTGAGTGTTATACTGG
1 GTGAGTATTGTATTGG
*
8716 GTCAGTATTGTATT
1 GTGAGTATTGTATT
8730 CGATTAGTAG
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.20, C:0.04, G:0.33, T:0.43
Consensus pattern (16 bp):
GTGAGTATTGTATTGG
Found at i:9672 original size:25 final size:25
Alignment explanation
Indices: 9629--9681 Score: 65
Period size: 23 Copynumber: 2.1 Consensus size: 25
9619 CTCTCTATTT
9629 TTTTTTCAAATAACGAAT-AT-ATA
1 TTTTTTCAAATAACGAATAATAATA
*
9652 TTTTTTCAAAGTAATGAAATAATAATA
1 TTTTTTCAAA-TAACG-AATAATAATA
9679 TTT
1 TTT
9682 GATATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 10 0.40
24 4 0.16
25 3 0.12
26 2 0.08
27 6 0.24
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (25 bp):
TTTTTTCAAATAACGAATAATAATA
Found at i:9790 original size:25 final size:25
Alignment explanation
Indices: 9735--9790 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
9725 CGTATGCTGG
*
9735 GGGAGTCTCCCCTAGCGCGCAGCAA
1 GGGAGTCTCCCATAGCGCGCAGCAA
** * *
9760 ATGAGTCTCCCATGGCGCGCAGTAA
1 GGGAGTCTCCCATAGCGCGCAGCAA
9785 GGGAGT
1 GGGAGT
9791 AGCTCCCTCT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.21, C:0.29, G:0.34, T:0.16
Consensus pattern (25 bp):
GGGAGTCTCCCATAGCGCGCAGCAA
Found at i:12364 original size:27 final size:27
Alignment explanation
Indices: 12333--12395 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
12323 CAGCAGTGCG
*
12333 TCCACCATTGTTCACCTCTGACACGAC
1 TCCACCATTGCTCACCTCTGACACGAC
*
12360 TCCACCATTGCTCACCTCTGACACGTC
1 TCCACCATTGCTCACCTCTGACACGAC
12387 TCCACCATT
1 TCCACCATT
12396 AGCAGTGGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.21, C:0.43, G:0.10, T:0.27
Consensus pattern (27 bp):
TCCACCATTGCTCACCTCTGACACGAC
Found at i:13062 original size:19 final size:19
Alignment explanation
Indices: 13038--13087 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
13028 TGTATATATG
* *
13038 GTAAGTGAGTATGGTCTTT
1 GTAAGTGAGTATAGCCTTT
13057 GTAAGTGAGTATAGCCTTT
1 GTAAGTGAGTATAGCCTTT
13076 GTAAGTGAGTAT
1 GTAAGTGAGTAT
13088 TGTATTGGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.26, C:0.06, G:0.30, T:0.38
Consensus pattern (19 bp):
GTAAGTGAGTATAGCCTTT
Found at i:13108 original size:16 final size:16
Alignment explanation
Indices: 13080--13135 Score: 85
Period size: 16 Copynumber: 3.5 Consensus size: 16
13070 GCCTTTGTAA
13080 GTGAGTATTGTATTGG
1 GTGAGTATTGTATTGG
* *
13096 GTTAGTGTTGTATTGG
1 GTGAGTATTGTATTGG
13112 GTGAGTATTGTATTGG
1 GTGAGTATTGTATTGG
*
13128 ATGAGTAT
1 GTGAGTAT
13136 GTTGGAAACA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.20, C:0.00, G:0.36, T:0.45
Consensus pattern (16 bp):
GTGAGTATTGTATTGG
Found at i:14379 original size:31 final size:31
Alignment explanation
Indices: 14295--14381 Score: 126
Period size: 31 Copynumber: 2.9 Consensus size: 31
14285 GTTTTATGCT
*
14295 TAAAAAT--AATTCAAGG-TATAAGCTTTGCC
1 TAAAAATGCAATTC-AGGATATAAGGTTTGCC
14324 TAAAAATGCAATTCAGGATATAAGGTTTGCC
1 TAAAAATGCAATTCAGGATATAAGGTTTGCC
*
14355 TGAAAATGCAATTCAGGATATAAGGTT
1 TAAAAATGCAATTCAGGATATAAGGTT
14382 ACAAAAAGTT
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
29 7 0.13
30 3 0.06
31 43 0.81
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.30
Consensus pattern (31 bp):
TAAAAATGCAATTCAGGATATAAGGTTTGCC
Found at i:14464 original size:11 final size:12
Alignment explanation
Indices: 14439--14467 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
14429 ATTAAAATAC
14439 ACGTGGCATCCT
1 ACGTGGCATCCT
14451 ACGTGGCA-CCT
1 ACGTGGCATCCT
14462 ACGTGG
1 ACGTGG
14468 ATCAGTTAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.17, C:0.31, G:0.31, T:0.21
Consensus pattern (12 bp):
ACGTGGCATCCT
Found at i:14552 original size:24 final size:24
Alignment explanation
Indices: 14520--14568 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
14510 AAATTTATCC
14520 TTAATTGTAACCTTTTCATAACGT
1 TTAATTGTAACCTTTTCATAACGT
14544 TTAATTGTAACCTTTTCATAACGT
1 TTAATTGTAACCTTTTCATAACGT
14568 T
1 T
14569 ATATCCTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.16, G:0.08, T:0.47
Consensus pattern (24 bp):
TTAATTGTAACCTTTTCATAACGT
Found at i:17807 original size:52 final size:52
Alignment explanation
Indices: 17720--17833 Score: 210
Period size: 52 Copynumber: 2.2 Consensus size: 52
17710 AGTCGAGCTG
*
17720 CAATTTTCCTCATCTCCTTTGCTTTCTCCTTCATCTCCTCCAATTTTTGCTA
1 CAATTTTCTTCATCTCCTTTGCTTTCTCCTTCATCTCCTCCAATTTTTGCTA
*
17772 CAATCTTCTTCATCTCCTTTGCTTTCTCCTTCATCTCCTCCAATTTTTGCTA
1 CAATTTTCTTCATCTCCTTTGCTTTCTCCTTCATCTCCTCCAATTTTTGCTA
17824 CAATTTTCTT
1 CAATTTTCTT
17834 TAGTTTTGCT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 59 1.00
ACGTcount: A:0.14, C:0.33, G:0.04, T:0.49
Consensus pattern (52 bp):
CAATTTTCTTCATCTCCTTTGCTTTCTCCTTCATCTCCTCCAATTTTTGCTA
Found at i:18089 original size:21 final size:21
Alignment explanation
Indices: 18064--18108 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
18054 TTGGGAATTC
18064 TTGATTTAGTCATCAAAAGAA
1 TTGATTTAGTCATCAAAAGAA
** *
18085 TTGATTTAGTTTTCAAGAGAA
1 TTGATTTAGTCATCAAAAGAA
18106 TTG
1 TTG
18109 GGAATTTTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.36, C:0.07, G:0.18, T:0.40
Consensus pattern (21 bp):
TTGATTTAGTCATCAAAAGAA
Found at i:22477 original size:11 final size:11
Alignment explanation
Indices: 22461--22485 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
22451 AACTCAATAA
22461 CTTATTTTCAT
1 CTTATTTTCAT
22472 CTTATTTTCAT
1 CTTATTTTCAT
22483 CTT
1 CTT
22486 CCAATTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.20, G:0.00, T:0.64
Consensus pattern (11 bp):
CTTATTTTCAT
Found at i:31334 original size:30 final size:31
Alignment explanation
Indices: 31298--31360 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 31
31288 CACCTAGAAC
*
31298 CACAACCAATAGCTGTAAA-CCCCAAATCAT
1 CACAACCAACAGCTGTAAACCCCCAAATCAT
31328 CACAACCAACAGCTGTAAACCCCCAAATCAT
1 CACAACCAACAGCTGTAAACCCCCAAATCAT
31359 CA
1 CA
31361 TTTGAATTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 18 0.58
31 13 0.42
ACGTcount: A:0.43, C:0.37, G:0.06, T:0.14
Consensus pattern (31 bp):
CACAACCAACAGCTGTAAACCCCCAAATCAT
Found at i:34222 original size:45 final size:45
Alignment explanation
Indices: 34171--34260 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 45
34161 TAATAGAGTA
34171 GTGGAATTACTAAAAAATCCCTACCCC-GAATTAATGATAAGCTGG
1 GTGGAATTACTAAAAAATCCCTACCCCAG-ATTAATGATAAGCTGG
* *
34216 GTGGAATTACTAAAAGATCCCTACCCCAGATTAATGATGAGCTGG
1 GTGGAATTACTAAAAAATCCCTACCCCAGATTAATGATAAGCTGG
34261 AGAAGTAATC
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
45 41 0.98
46 1 0.02
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (45 bp):
GTGGAATTACTAAAAAATCCCTACCCCAGATTAATGATAAGCTGG
Found at i:34422 original size:72 final size:72
Alignment explanation
Indices: 34341--34486 Score: 283
Period size: 72 Copynumber: 2.0 Consensus size: 72
34331 GTACTTAAAT
34341 GTCCTAACTTTTGATTCTTGAGGGGATTAAATAAATAATCTTTTTGGTCATTTCTAAATGGACTT
1 GTCCTAACTTTTGATTCTTGAGGGGATTAAATAAATAATCTTTTTGGTCATTTCTAAATGGACTT
34406 GAATAGA
66 GAATAGA
*
34413 GTCCTAACTTTTGATTCTTGAGGGGATTAAATAAATAATCTTTTTGGTCATTTCTAAATGGATTT
1 GTCCTAACTTTTGATTCTTGAGGGGATTAAATAAATAATCTTTTTGGTCATTTCTAAATGGACTT
34478 GAATAGA
66 GAATAGA
34485 GT
1 GT
34487 GGTGGAATTA
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.30, C:0.10, G:0.18, T:0.41
Consensus pattern (72 bp):
GTCCTAACTTTTGATTCTTGAGGGGATTAAATAAATAATCTTTTTGGTCATTTCTAAATGGACTT
GAATAGA
Found at i:35188 original size:3 final size:3
Alignment explanation
Indices: 35180--35209 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
35170 ATATTAAGAA
*
35180 AAT AAT AAT AAT AAT AAT CAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
35210 GTACTAGTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:37559 original size:10 final size:10
Alignment explanation
Indices: 37544--37569 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
37534 AATTTAATAT
37544 GGATATTTAC
1 GGATATTTAC
37554 GGATATTTAC
1 GGATATTTAC
37564 GGATAT
1 GGATAT
37570 ATCGAGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (10 bp):
GGATATTTAC
Found at i:38962 original size:5 final size:5
Alignment explanation
Indices: 38952--38993 Score: 61
Period size: 5 Copynumber: 8.8 Consensus size: 5
38942 TCAAGTTTTT
*
38952 AAAGG AAAGG AAAGG --GGG AAAGG AAAGG AAAGG AAAGG AAAG
1 AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AAAG
38994 TTTTTTGAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 2 0.06
5 31 0.94
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (5 bp):
AAAGG
Found at i:39822 original size:6 final size:6
Alignment explanation
Indices: 39811--39841 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
39801 ATATATGTAG
*
39811 TATAGA TATAGA TATAGA TATAAA TATAGA T
1 TATAGA TATAGA TATAGA TATAGA TATAGA T
39842 TAATGAAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.13, T:0.35
Consensus pattern (6 bp):
TATAGA
Found at i:40551 original size:17 final size:17
Alignment explanation
Indices: 40529--40562 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
40519 CATTTACAAG
40529 GATTTAAGCTTGTTGCT
1 GATTTAAGCTTGTTGCT
40546 GATTTAAGCTTGTTGCT
1 GATTTAAGCTTGTTGCT
40563 AAAAATTCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.12, G:0.24, T:0.47
Consensus pattern (17 bp):
GATTTAAGCTTGTTGCT
Found at i:47989 original size:7 final size:7
Alignment explanation
Indices: 47977--48001 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
47967 GCCTCTGCTT
47977 ACTCTCA
1 ACTCTCA
47984 ACTCTCA
1 ACTCTCA
47991 ACTCTCA
1 ACTCTCA
47998 ACTC
1 ACTC
48002 CAAGCCTCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.44, G:0.00, T:0.28
Consensus pattern (7 bp):
ACTCTCA
Done.