Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007276.1 Corchorus capsularis cultivar CVL-1 contig07297, 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: 31481
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:683 original size:50 final size:50
Alignment explanation
Indices: 603--707 Score: 165
Period size: 50 Copynumber: 2.1 Consensus size: 50
593 AGTTTTTATG
* *
603 ATAAAGATGTAACCTTTGAGCAAAATATTGAACCTTTGAATAATTTGTAA
1 ATAAAGATGTAACCTTTGAGCAAAAGATTGAACCTTTGAATAACTTGTAA
* * *
653 ATAAAGATGTAGCCTTTGAGTAAAAGATTGAACTTTTGAATAACTTGTAA
1 ATAAAGATGTAACCTTTGAGCAAAAGATTGAACCTTTGAATAACTTGTAA
703 ATAAA
1 ATAAA
708 ATGAGATCTT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.33
Consensus pattern (50 bp):
ATAAAGATGTAACCTTTGAGCAAAAGATTGAACCTTTGAATAACTTGTAA
Found at i:900 original size:51 final size:51
Alignment explanation
Indices: 755--1005 Score: 230
Period size: 51 Copynumber: 4.9 Consensus size: 51
745 TTGATTTGTA
* * * * *
755 AATAGAAATGAAACCCTTGAACTAAAAGATGAAACTTCG-GATTAATTTGGTG
1 AATAAAAATGAAATCTTTGAACTAAATGATGGAACTT-GTGATTAA-TTGGTG
* *
807 -ATAAAGGA-GAAATCTTT-AAGCT-AATGATTGAACTTGTGATTAATTGGTG
1 AATAAA-AATGAAATCTTTGAA-CTAAATGATGGAACTTGTGATTAATTGGTG
* * *
856 AATAAAAATGAGATCTTTGAATTAAATGATGGAACTTGAGATTAATTGGTG
1 AATAAAAATGAAATCTTTGAACTAAATGATGGAACTTGTGATTAATTGGTG
* * *
907 AATAAAAATGAAATCTTT-AAGCT-AATGATTGAACTTGTGATTAATTTGTA
1 AATAAAAATGAAATCTTTGAA-CTAAATGATGGAACTTGTGATTAATTGGTG
* *
957 AACTAAAGTGATGAAATCTTTGAACCAAATGATGGAAC-TGTTGATTAAT
1 AA-TAAA--AATGAAATCTTTGAACTAAATGATGGAACTTG-TGATTAAT
1006 GAAACCTTTG
Statistics
Matches: 164, Mismatches: 21, Indels: 26
0.78 0.10 0.12
Matches are distributed among these distances:
49 8 0.05
50 59 0.36
51 62 0.38
52 1 0.01
53 14 0.09
54 20 0.12
ACGTcount: A:0.41, C:0.08, G:0.19, T:0.33
Consensus pattern (51 bp):
AATAAAAATGAAATCTTTGAACTAAATGATGGAACTTGTGATTAATTGGTG
Found at i:920 original size:101 final size:103
Alignment explanation
Indices: 761--995 Score: 300
Period size: 101 Copynumber: 2.3 Consensus size: 103
751 TGTAAATAGA
* * * * *
761 AATGAAACCCTTGAACTAAAAGATGAAACTTCGGATTAATTTGGTGATAAAGGAGAAATCTTTAA
1 AATGAAATCTTTGAACTAAATGATGGAACTTCGGATTAATTTGGTGATAAAGAAGAAATCTTTAA
*
826 GCTAATGATTGAACTTGTGATTAATTGGTGAA-TAAA-
66 GCTAATGATTGAACTTGTGATTAATTGGTAAACTAAAG
* *
862 AATGAGATCTTTGAATTAAATGATGGAACTT-GAGATTAA-TTGGTGAATAAA-AATGAAATCTT
1 AATGAAATCTTTGAACTAAATGATGGAACTTCG-GATTAATTTGGTG-ATAAAGAA-GAAATCTT
*
924 TAAGCTAATGATTGAACTTGTGATTAATTTGTAAACTAAAG
63 TAAGCTAATGATTGAACTTGTGATTAATTGGTAAACTAAAG
* *
965 TGATGAAATCTTTGAACCAAATGATGGAACT
1 -AATGAAATCTTTGAACTAAATGATGGAACT
996 GTTGATTAAT
Statistics
Matches: 115, Mismatches: 13, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
100 8 0.07
101 77 0.67
102 4 0.03
104 26 0.23
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.32
Consensus pattern (103 bp):
AATGAAATCTTTGAACTAAATGATGGAACTTCGGATTAATTTGGTGATAAAGAAGAAATCTTTAA
GCTAATGATTGAACTTGTGATTAATTGGTAAACTAAAG
Found at i:1949 original size:49 final size:49
Alignment explanation
Indices: 1889--2534 Score: 839
Period size: 49 Copynumber: 13.2 Consensus size: 49
1879 TTCCGTTTTT
*
1889 GCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCTATTTCCCAAAGC
1 GCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCTATTTCCCAAAAC
*
1938 GCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCTATTTCCCAAAGC
1 GCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCTATTTCCCAAAAC
* * * * *
1987 GCCCTTCCCAGACGGAAGCCATTCATCTTTAGTTGCTATCTCCCAAAAT
1 GCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCTATTTCCCAAAAC
* * *
2036 GCCCTT-CCAGACGTAAGCCATTTATTTTTGCTTGCTATCTCCCCAAAAC
1 GCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCTAT-TTCCCAAAAC
* * * *
2085 GCCCTTCCCGGACGGAAGCCGTTTATTTTTACTTGTTATTTCCCAAAGC
1 GCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCTATTTCCCAAAAC
* * *
2134 GCCCTTCCTAGATGGAAGCCATTTATTTTTGCTTGCTATTTCCCAAAAC
1 GCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCTATTTCCCAAAAC
* * * * * * *
2183 GCCCTTCCTAGATGAAAGCCATTCATCTTTAGTTGCTATCTCCCAAAAC
1 GCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCTATTTCCCAAAAC
* *
2232 ACGCC-TCCCAGACGGAAGCCATTTATTTTTGCTTGCTATTTCCCAAAAC
1 GC-CCTTCCCAGACGGAAGCCATTTATTTTTACTTGCTATTTCCCAAAAC
* * *
2281 GCCATTCCCAGACGGAAGCCATTCATCTTTACTTGCTATTTCCCAAAAC
1 GCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCTATTTCCCAAAAC
* * * * *
2330 GCCCTTCCCAGACGGAAGCCATTCATCTTTACTTGCTATCTCTCATAAC
1 GCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCTATTTCCCAAAAC
* * *
2379 ACCCTTCCCAGACGGAAGCCATTTAATTTTACTTGCTATTTCCCAAAGC
1 GCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCTATTTCCCAAAAC
* ** *
2428 GCCCTTCCCAGACGAAAGCCATTTATTTTCGCTTGCTATTTCCCAAAAT
1 GCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCTATTTCCCAAAAC
* * *
2477 GCCCTT-CCAGACGAAAGCCATTTATTTTTGCTTGCTATCTCCCCAAAAC
1 GCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCTAT-TTCCCAAAAC
*
2526 ACCCTTCCC
1 GCCCTTCCC
2535 GGACTTCAAT
Statistics
Matches: 520, Mismatches: 71, Indels: 11
0.86 0.12 0.02
Matches are distributed among these distances:
48 59 0.11
49 430 0.83
50 31 0.06
ACGTcount: A:0.24, C:0.32, G:0.13, T:0.32
Consensus pattern (49 bp):
GCCCTTCCCAGACGGAAGCCATTTATTTTTACTTGCTATTTCCCAAAAC
Found at i:3203 original size:21 final size:21
Alignment explanation
Indices: 3177--3223 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
3167 TGGCTAAATC
*
3177 ATGTCCAGGTGGCTAAAAAAG
1 ATGTCCAGGTAGCTAAAAAAG
* *
3198 ATGTCCAGGTATCTCAAAAAG
1 ATGTCCAGGTAGCTAAAAAAG
3219 ATGTC
1 ATGTC
3224 TCTCACGCGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.23
Consensus pattern (21 bp):
ATGTCCAGGTAGCTAAAAAAG
Found at i:9807 original size:30 final size:31
Alignment explanation
Indices: 9773--9837 Score: 89
Period size: 30 Copynumber: 2.1 Consensus size: 31
9763 AAAAGCGATT
*
9773 AATTTAGTCCATGTACTACA-AA-ATTGGGTC
1 AATTTAGTCCATGCACT-CATAAGATTGGGTC
*
9803 AATTTAGTCCCTGCACTCATAAGATTGGGTC
1 AATTTAGTCCATGCACTCATAAGATTGGGTC
9834 AATT
1 AATT
9838 GTGTTGAGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
29 2 0.06
30 17 0.55
31 12 0.39
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (31 bp):
AATTTAGTCCATGCACTCATAAGATTGGGTC
Found at i:10588 original size:6 final size:6
Alignment explanation
Indices: 10577--10613 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
10567 AACAAATACA
10577 TAGAAT TAGAAT TAGAAT TAGAAT TAGAAT TAGAAT T
1 TAGAAT TAGAAT TAGAAT TAGAAT TAGAAT TAGAAT T
10614 TTGCTTCAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.16, T:0.35
Consensus pattern (6 bp):
TAGAAT
Found at i:10976 original size:24 final size:23
Alignment explanation
Indices: 10948--10992 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
10938 ACCTCCAAAG
*
10948 AGAAAAATAGGGGAAAAGAAGAAA
1 AGAAAAA-AGAGGAAAAGAAGAAA
*
10972 AGAAAAAAGAGGCAAAGAAGA
1 AGAAAAAAGAGGAAAAGAAGA
10993 GGGATGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.67, C:0.02, G:0.29, T:0.02
Consensus pattern (23 bp):
AGAAAAAAGAGGAAAAGAAGAAA
Found at i:18132 original size:42 final size:43
Alignment explanation
Indices: 18080--18173 Score: 122
Period size: 45 Copynumber: 2.2 Consensus size: 43
18070 AGTGCTTTAC
18080 CTAA-ATTCTA-CTCCATCTCTACG-TAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCT-CGATAATTCATCAAAATAAAG
* *
18121 CTAATATTCTACTCCTCCATCTCTGGATAATTCATCAAAATAAAT
1 CTAATATTCTA--CCTCCATCTCTCGATAATTCATCAAAATAAAG
18166 CTAATATT
1 CTAATATT
18174 AATTGTTGCT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
44 1 0.02
45 35 0.76
ACGTcount: A:0.37, C:0.23, G:0.04, T:0.35
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTCGATAATTCATCAAAATAAAG
Found at i:21700 original size:15 final size:16
Alignment explanation
Indices: 21675--21709 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
21665 TAGGGCAAGG
*
21675 TATTCAATTTAATTAT
1 TATTCAATTTAATTAA
21691 TATT-AATTTAATTAA
1 TATTCAATTTAATTAA
21706 TATT
1 TATT
21710 GTACTATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (16 bp):
TATTCAATTTAATTAA
Found at i:24539 original size:2 final size:2
Alignment explanation
Indices: 24502--24526 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
24492 TTGTAGTGTG
24502 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 T
24527 TTGAGTGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27722 original size:141 final size:142
Alignment explanation
Indices: 27467--27743 Score: 484
Period size: 141 Copynumber: 2.0 Consensus size: 142
27457 TTGCTATAAA
* * *
27467 ATAAAGAAGAACAATAAGAACAAGAAATAAGAGAGAAAGCATAGATAATTTTTTTATTACTCAGA
1 ATAAAGAAAAACAATAAGAACAAGAAATAAGAGAGAAAGCAGAGAGAATTTTTTTATTACTCAGA
27532 GGAGAGAATTCAGAATTTGATGTGTGTGAAAAATAAATCTAGAACTCCTTTTATATAATGGAGGA
66 GGAGAGAATTCAGAATTTGATGTGTGTGAAAAATAAATCTAGAACTCCTTTTATATAATGGAGGA
27597 AATCCCTTGTAC
131 AATCCCTTGTAC
*
27609 ATAAAGAAAAACAATAAGAACAAGAAATAAGAGAGAAAGTAGAGAGAA-TTTTTTATTACTCAGA
1 ATAAAGAAAAACAATAAGAACAAGAAATAAGAGAGAAAGCAGAGAGAATTTTTTTATTACTCAGA
** *
27673 GGAGAGAATTCAGAATTTGATGTGTGTGAAAAATAGTTCTAGGACTCCTTTTATATAATGGAGGA
66 GGAGAGAATTCAGAATTTGATGTGTGTGAAAAATAAATCTAGAACTCCTTTTATATAATGGAGGA
27738 AATCCC
131 AATCCC
27744 CTAAACATTA
Statistics
Matches: 128, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
141 84 0.66
142 44 0.34
ACGTcount: A:0.44, C:0.09, G:0.19, T:0.27
Consensus pattern (142 bp):
ATAAAGAAAAACAATAAGAACAAGAAATAAGAGAGAAAGCAGAGAGAATTTTTTTATTACTCAGA
GGAGAGAATTCAGAATTTGATGTGTGTGAAAAATAAATCTAGAACTCCTTTTATATAATGGAGGA
AATCCCTTGTAC
Found at i:27973 original size:19 final size:19
Alignment explanation
Indices: 27949--27987 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
27939 CTTTAAGTTT
27949 ATTCTAATTATCTTTTGTC
1 ATTCTAATTATCTTTTGTC
27968 ATTCTAATTATCTTTTGTC
1 ATTCTAATTATCTTTTGTC
27987 A
1 A
27988 AAACATAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.23, C:0.15, G:0.05, T:0.56
Consensus pattern (19 bp):
ATTCTAATTATCTTTTGTC
Found at i:29016 original size:11 final size:11
Alignment explanation
Indices: 29002--29039 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
28992 ATTCATAACA
29002 AATTTATAATT
1 AATTTATAATT
29013 AATTTATAATT
1 AATTTATAATT
29024 -ATTTGATAATT
1 AATTT-ATAATT
*
29035 TATTT
1 AATTT
29040 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Done.