Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009515.1 Corchorus capsularis cultivar CVL-1 contig09536, 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: 26735
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Found at i:4563 original size:38 final size:39
Alignment explanation
Indices: 4521--4616 Score: 104
Period size: 38 Copynumber: 2.5 Consensus size: 39
4511 AGTGAAAAGA
* * * *
4521 AAAAGAAGTAATTAGTCAATTGGTAATTAAGAG-GAAGT
1 AAAAGAAGTAATCAGTAAATTGATAACTAAGAGAGAAGT
* *
4559 AAAAGGATTAATCAGTAAATTGATAACTAAGAGAAGAAGT
1 AAAAGAAGTAATCAGTAAATTGATAACTAAGAG-AGAAGT
* *
4599 AAAAGTAGCAATCAGTAA
1 AAAAGAAGTAATCAGTAA
4617 GTAAGGGTCA
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
38 27 0.57
40 20 0.43
ACGTcount: A:0.51, C:0.05, G:0.21, T:0.23
Consensus pattern (39 bp):
AAAAGAAGTAATCAGTAAATTGATAACTAAGAGAGAAGT
Found at i:4612 original size:40 final size:38
Alignment explanation
Indices: 4538--4616 Score: 95
Period size: 40 Copynumber: 2.0 Consensus size: 38
4528 GTAATTAGTC
* * **
4538 AATTGGTAATTAAGAGGAAGTAAAAGGATTAATCAGTA
1 AATTGATAACTAAGAGGAAGTAAAAGGAGCAATCAGTA
*
4576 AATTGATAACTAAGAGAAGAAGTAAAAGTAGCAATCAGTA
1 AATTGATAACTAAGAG--GAAGTAAAAGGAGCAATCAGTA
4616 A
1 A
4617 GTAAGGGTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
38 14 0.41
40 20 0.59
ACGTcount: A:0.51, C:0.05, G:0.22, T:0.23
Consensus pattern (38 bp):
AATTGATAACTAAGAGGAAGTAAAAGGAGCAATCAGTA
Found at i:4727 original size:37 final size:37
Alignment explanation
Indices: 4637--4801 Score: 119
Period size: 37 Copynumber: 4.5 Consensus size: 37
4627 AAGTAAAAGG
* * *
4637 GTAAGTCAGTAATTAAGAGTCAAGGTAGAAAAATTAATCA
1 GTAAATCAGTAATTAAGAGTCAAGGT---AATAGTAATCA
*
4677 GTAAAT-TGATAATTAAGAGTCAAGGTAATAGTAATCA
1 GTAAATCAG-TAATTAAGAGTCAAGGTAATAGTAATCA
*
4714 GTAAATCAGTAATT-A-AGTAAAAGG-AGAT--TAATCA
1 GTAAATCAGTAATTAAGAGT-CAAGGTA-ATAGTAATCA
* * * * *
4748 GTAAAT-TGATAATTCAGAGTCAAAGTGACAGTAATCA
1 GTAAATCAG-TAATTAAGAGTCAAGGTAATAGTAATCA
*
4785 GTAAACCAGTAATTAAG
1 GTAAATCAGTAATTAAG
4802 TAAAAGGAAA
Statistics
Matches: 100, Mismatches: 14, Indels: 25
0.72 0.10 0.18
Matches are distributed among these distances:
33 1 0.01
34 17 0.17
35 9 0.09
36 10 0.10
37 38 0.38
38 2 0.02
39 1 0.01
40 22 0.22
ACGTcount: A:0.47, C:0.08, G:0.19, T:0.27
Consensus pattern (37 bp):
GTAAATCAGTAATTAAGAGTCAAGGTAATAGTAATCA
Found at i:4751 original size:34 final size:34
Alignment explanation
Indices: 4708--4819 Score: 127
Period size: 34 Copynumber: 3.2 Consensus size: 34
4698 AAGGTAATAG
*
4708 TAATCAGTAAATCAGTAATTAAGTAAAAGGAGAT
1 TAATCAGTAAATCAGTAATTAAGTAAAAGGAAAT
* * * *
4742 TAATCAGTAAAT-TGATAATTCAGAGTCAAAGTGACAG
1 TAATCAGTAAATCAG-TAATT-A-AGTAAAAG-GAAAT
*
4779 TAATCAGTAAACCAGTAATTAAGTAAAAGGAAAT
1 TAATCAGTAAATCAGTAATTAAGTAAAAGGAAAT
4813 TAATCAG
1 TAATCAG
4820 AGTTAAGGTA
Statistics
Matches: 64, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
33 1 0.02
34 27 0.42
35 8 0.12
36 8 0.12
37 19 0.30
38 1 0.02
ACGTcount: A:0.48, C:0.09, G:0.17, T:0.26
Consensus pattern (34 bp):
TAATCAGTAAATCAGTAATTAAGTAAAAGGAAAT
Found at i:4751 original size:71 final size:71
Alignment explanation
Indices: 4667--4819 Score: 252
Period size: 71 Copynumber: 2.2 Consensus size: 71
4657 CAAGGTAGAA
* * *
4667 AAATTAATCAGTAAATTGATAATTAAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATTAAGT
1 AAATTAATCAGTAAATTGATAATTAAGAGTCAAAGTAACAGTAATCAGTAAACCAGTAATTAAGT
4732 AAAAGG
66 AAAAGG
* * *
4738 AGATTAATCAGTAAATTGATAATTCAGAGTCAAAGTGACAGTAATCAGTAAACCAGTAATTAAGT
1 AAATTAATCAGTAAATTGATAATTAAGAGTCAAAGTAACAGTAATCAGTAAACCAGTAATTAAGT
4803 AAAAGG
66 AAAAGG
4809 AAATTAATCAG
1 AAATTAATCAG
4820 AGTTAAGGTA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
71 75 1.00
ACGTcount: A:0.48, C:0.08, G:0.17, T:0.27
Consensus pattern (71 bp):
AAATTAATCAGTAAATTGATAATTAAGAGTCAAAGTAACAGTAATCAGTAAACCAGTAATTAAGT
AAAAGG
Found at i:10047 original size:127 final size:128
Alignment explanation
Indices: 9818--10134 Score: 467
Period size: 127 Copynumber: 2.5 Consensus size: 128
9808 ATACCTCACC
*
9818 AACGCCCCAAAAAGAGGGCTCAACGCCAGCGGGCGGGGCGATCGACACGATATGACCCCGACTCA
1 AACGCCCCAAAAGGAGGGCTCAACGCCAGCGGGCGGGGCGATCGACACGATATGACCCCGACTCA
* *
9883 GCATGGCCCCCCACTTGCAGGAGATGAGTACAAAACCATCCCTAGACAAGTATG-GAACGAAG
66 GCATGGCCCCCAACTTGCAGGAGATGAGTACAAAACCATCCCTAGACAAGTATGAGAACCAAG
* *
9945 AATGCCCCAAAAGGAGGGCTCAACGCCAGCGGGCGGGGCGATTGACACGATATGACCCCGACTCA
1 AACGCCCCAAAAGGAGGGCTCAACGCCAGCGGGCGGGGCGATCGACACGATATGACCCCGACTCA
* * * *
10010 GCATGGCCCTCAACTTGTAGGTGATGAGTACAAAACCATCCCTAGACAAGTATGAGAACCATG
66 GCATGGCCCCCAACTTGCAGGAGATGAGTACAAAACCATCCCTAGACAAGTATGAGAACCAAG
* * * * * * *
10073 AACGACCCAAAAGGAGGGCTCAACCCCAGCAGGCGAGGCGGTCGAGAAGACT-TGACCCCGAC
1 AACGCCCCAAAAGGAGGGCTCAACGCCAGCGGGCGGGGCGATCGACACGA-TATGACCCCGAC
10135 CTAACACGGC
Statistics
Matches: 170, Mismatches: 18, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
127 112 0.66
128 57 0.34
129 1 0.01
ACGTcount: A:0.31, C:0.30, G:0.27, T:0.12
Consensus pattern (128 bp):
AACGCCCCAAAAGGAGGGCTCAACGCCAGCGGGCGGGGCGATCGACACGATATGACCCCGACTCA
GCATGGCCCCCAACTTGCAGGAGATGAGTACAAAACCATCCCTAGACAAGTATGAGAACCAAG
Found at i:10174 original size:128 final size:127
Alignment explanation
Indices: 9818--10171 Score: 349
Period size: 127 Copynumber: 2.8 Consensus size: 127
9808 ATACCTCACC
* * * * * *
9818 AACGCCCCAAAAAGAGGGCTCAACGCCAGCGGGCGGGGCGATCGACACGATATGACCCCGACTCA
1 AACGACCCAAAAGGAGGGCTCAACCCCAGCAGGCGAGGCGATCGACAAGATATGACCCCGACTCA
* * * * * ** * *
9883 GCATGGCCCCCCACTTGCAGGAGATGAGTACAAAACCATCCCTAGACAAGTATGGAACGAAG
66 ACACGGCCCTCAACTTGTAAAAGACGAGTACAAAACCATCCCTAGACAAGTATGGAACCAAG
* * * * * * *
9945 AATGCCCCAAAAGGAGGGCTCAACGCCAGCGGGCGGGGCGATTGACACGATATGACCCCGACTCA
1 AACGACCCAAAAGGAGGGCTCAACCCCAGCAGGCGAGGCGATCGACAAGATATGACCCCGACTCA
* * *** * *
10010 GCATGGCCCTCAACTTGTAGGTGATGAGTACAAAACCATCCCTAGACAAGTATGAGAACCATG
66 ACACGGCCCTCAACTTGTAAAAGACGAGTACAAAACCATCCCTAGACAAGTATG-GAACCAAG
* *
10073 AACGACCCAAAAGGAGGGCTCAACCCCAGCAGGCGAGGCGGTCGAGAAGACT-TGACCCCGAC-C
1 AACGACCCAAAAGGAGGGCTCAACCCCAGCAGGCGAGGCGATCGACAAGA-TATGACCCCGACTC
10136 TAACACGG-CCTCCAACTTGTCAAAAG-CGAGT-CAAAA
65 -AACACGGCCCT-CAACTTGT-AAAAGACGAGTACAAAA
10172 ACCGCCCCGA
Statistics
Matches: 198, Mismatches: 24, Indels: 10
0.85 0.10 0.04
Matches are distributed among these distances:
127 121 0.61
128 74 0.37
129 3 0.02
ACGTcount: A:0.32, C:0.30, G:0.26, T:0.12
Consensus pattern (127 bp):
AACGACCCAAAAGGAGGGCTCAACCCCAGCAGGCGAGGCGATCGACAAGATATGACCCCGACTCA
ACACGGCCCTCAACTTGTAAAAGACGAGTACAAAACCATCCCTAGACAAGTATGGAACCAAG
Found at i:16815 original size:234 final size:234
Alignment explanation
Indices: 16406--16872 Score: 925
Period size: 234 Copynumber: 2.0 Consensus size: 234
16396 ACAAGCATAA
16406 GGTAATCAAGAGTCGACCACAACGTAACGGATGACAATGCAAAGGAACAAGAGAAGGAAAACGAC
1 GGTAATCAAGAGTCGACCACAACGTAACGGATGACAATGCAAAGGAACAAGAGAAGGAAAACGAC
*
16471 AAACCGGAAACAAAAGAGGGCAAAAAGGATTGGCAGAGCACAAAAAAATCCACAAACAACAATTG
66 AAACCAGAAACAAAAGAGGGCAAAAAGGATTGGCAGAGCACAAAAAAATCCACAAACAACAATTG
16536 GAGGAGAAACACAAACACATGCGGATCGAAGGGGGACAAACCAAGAGAAGCAGCAAGACGCAAGA
131 GAGGAGAAACACAAACACATGCGGATCGAAGGGGGACAAACCAAGAGAAGCAGCAAGACGCAAGA
16601 CGCAAAAATCGAGGCAGCAAACCCTCCTTTTCGATAAAT
196 CGCAAAAATCGAGGCAGCAAACCCTCCTTTTCGATAAAT
16640 GGTAATCAAGAGTCGACCACAACGTAACGGATGACAATGCAAAGGAACAAGAGAAGGAAAACGAC
1 GGTAATCAAGAGTCGACCACAACGTAACGGATGACAATGCAAAGGAACAAGAGAAGGAAAACGAC
16705 AAACCAGAAACAAAAGAGGGCAAAAAGGATTGGCAGAGCACAAAAAAATCCACAAACAACAATTG
66 AAACCAGAAACAAAAGAGGGCAAAAAGGATTGGCAGAGCACAAAAAAATCCACAAACAACAATTG
16770 GAGGAGAAACACAAACACATGCGGATCGAAGGGGGACAAACCAAGAGAAGCAGCAAGACGCAAGA
131 GAGGAGAAACACAAACACATGCGGATCGAAGGGGGACAAACCAAGAGAAGCAGCAAGACGCAAGA
16835 CGCAAAAATCGAGGCAGCAAACCCTCCTTTTCGATAAA
196 CGCAAAAATCGAGGCAGCAAACCCTCCTTTTCGATAAA
16873 AGAGGTGAGC
Statistics
Matches: 232, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
234 232 1.00
ACGTcount: A:0.47, C:0.21, G:0.24, T:0.09
Consensus pattern (234 bp):
GGTAATCAAGAGTCGACCACAACGTAACGGATGACAATGCAAAGGAACAAGAGAAGGAAAACGAC
AAACCAGAAACAAAAGAGGGCAAAAAGGATTGGCAGAGCACAAAAAAATCCACAAACAACAATTG
GAGGAGAAACACAAACACATGCGGATCGAAGGGGGACAAACCAAGAGAAGCAGCAAGACGCAAGA
CGCAAAAATCGAGGCAGCAAACCCTCCTTTTCGATAAAT
Found at i:17692 original size:50 final size:50
Alignment explanation
Indices: 17602--17743 Score: 180
Period size: 50 Copynumber: 2.8 Consensus size: 50
17592 CAAACATGGG
* *
17602 ATGGGCGCTCGACCCACCATCTTCATGTGTGGGT-GAGCGCCAACCCCATAT
1 ATGGGCGCTCGACCCACCATCTTCA-GAGT-GGTCGAGCGCCAACCCCATAC
* *
17653 TTGGGCACTCGACCCA-CATCTTCACGAGTGGTCGAGCGCCAACCCCATAC
1 ATGGGCGCTCGACCCACCATCTTCA-GAGTGGTCGAGCGCCAACCCCATAC
* *
17703 ATGGGCGCTCGACCCACCATCTCCATATGTGGTCGAGCGCC
1 ATGGGCGCTCGACCCACCATCTTCAGA-GTGGTCGAGCGCC
17744 CACGCTCGAC
Statistics
Matches: 79, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
49 3 0.04
50 42 0.53
51 34 0.43
ACGTcount: A:0.20, C:0.36, G:0.25, T:0.20
Consensus pattern (50 bp):
ATGGGCGCTCGACCCACCATCTTCAGAGTGGTCGAGCGCCAACCCCATAC
Found at i:18130 original size:26 final size:26
Alignment explanation
Indices: 18094--18211 Score: 100
Period size: 26 Copynumber: 4.5 Consensus size: 26
18084 GCCAAATGGC
* *
18094 ACTCCACACGTGACCTCCAACGTACG
1 ACTCCAAACGTGACCTCCAACGTACA
*
18120 AC-CCTAAACGTGATCCTCGAA-GTACA
1 ACTCC-AAACGTGA-CCTCCAACGTACA
*
18146 ACTCCACACGTGACCTCCAACAG-ACA
1 ACTCCAAACGTGACCTCCAAC-GTACA
* *
18172 CCTTCAACACGTGACCTCCGAA-GTACA
1 ACTCCAA-ACGTGACCTCC-AACGTACA
*
18199 ACTCCACACGTGA
1 ACTCCAAACGTGA
18212 TCTCGCGCGT
Statistics
Matches: 73, Mismatches: 11, Indels: 16
0.73 0.11 0.16
Matches are distributed among these distances:
25 8 0.11
26 36 0.49
27 27 0.37
28 2 0.03
ACGTcount: A:0.31, C:0.38, G:0.14, T:0.16
Consensus pattern (26 bp):
ACTCCAAACGTGACCTCCAACGTACA
Found at i:18152 original size:52 final size:53
Alignment explanation
Indices: 18094--18211 Score: 172
Period size: 53 Copynumber: 2.2 Consensus size: 53
18084 GCCAAATGGC
18094 ACTCCACACGTGACCTCCAAC-GTACGACCCT-AA-ACGTGATCCT-CGAAGTACA
1 ACTCCACACGTGACCTCCAACAG-AC-ACCCTCAACACGTGA-CCTCCGAAGTACA
*
18146 ACTCCACACGTGACCTCCAACAGACACCTTCAACACGTGACCTCCGAAGTACA
1 ACTCCACACGTGACCTCCAACAGACACCCTCAACACGTGACCTCCGAAGTACA
18199 ACTCCACACGTGA
1 ACTCCACACGTGA
18212 TCTCGCGCGT
Statistics
Matches: 61, Mismatches: 1, Indels: 7
0.88 0.01 0.10
Matches are distributed among these distances:
51 4 0.07
52 28 0.46
53 29 0.48
ACGTcount: A:0.31, C:0.38, G:0.14, T:0.16
Consensus pattern (53 bp):
ACTCCACACGTGACCTCCAACAGACACCCTCAACACGTGACCTCCGAAGTACA
Done.