Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01000506.1 Corchorus capsularis cultivar CVL-1 contig00506, 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, 616
Length: 1028
ACGTcount: A:0.50, C:0.06, G:0.22, T:0.22
Found at i:464 original size:34 final size:36
Alignment explanation
Indices: 425--505 Score: 96
Period size: 40 Copynumber: 2.2 Consensus size: 36
415 AGAGGAAGTG
425 ATCAGTA-G-AATTAAGAGTAAAAGTAAAAGGA-GTA
1 ATCAGTAGGTAATTAAGAGTAAAAGT-AAAGGAGGTA
459 ATCAGTAAAATGGTAATTAAGAGTAAAAGTAAAGGAGGTA
1 ATCAGT---A-GGTAATTAAGAGTAAAAGTAAAGGAGGTA
499 ATCAGTA
1 ATCAGTA
506 AATCGGTAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
34 6 0.15
37 2 0.05
39 7 0.17
40 25 0.62
ACGTcount: A:0.51, C:0.04, G:0.23, T:0.22
Consensus pattern (36 bp):
ATCAGTAGGTAATTAAGAGTAAAAGTAAAGGAGGTA
Found at i:591 original size:25 final size:26
Alignment explanation
Indices: 565--652 Score: 86
Period size: 32 Copynumber: 3.1 Consensus size: 26
555 GTAAAATAGT
565 AAAATGGTAATTAAATTCAAAGAGTAAA
1 AAAATGGTAATTAAATTCAAAGAGT--A
* *
593 ATGACAACTGGTGATTAAATTCAAAGAGTG
1 A--A-AA-TGGTAATTAAATTCAAAGAGTA
*
623 AAAATAGTAATTAAATTCAAGAGAGTA
1 AAAATGGTAATTAAATTCAA-AGAGTA
650 AAA
1 AAA
653 TGTAATCAGT
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
26 14 0.28
27 10 0.20
28 2 0.04
30 2 0.04
31 2 0.04
32 20 0.40
ACGTcount: A:0.52, C:0.06, G:0.17, T:0.25
Consensus pattern (26 bp):
AAAATGGTAATTAAATTCAAAGAGTA
Found at i:615 original size:32 final size:33
Alignment explanation
Indices: 550--632 Score: 116
Period size: 32 Copynumber: 2.5 Consensus size: 33
540 AGTAATCGGT
550 AAAGAGTAAAATAGTAAAATGGTAATTAAATTC
1 AAAGAGTAAAATAGTAAAATGGTAATTAAATTC
* *
583 AAAGAGTAAAAT-G-ACAACTGGTGATTAAATTC
1 AAAGAGTAAAATAGTA-AAATGGTAATTAAATTC
615 AAAGAGTGAAAATAGTAA
1 AAAGAGT-AAAATAGTAA
633 TTAAATTCAA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
31 1 0.02
32 23 0.52
33 17 0.39
34 2 0.05
35 1 0.02
ACGTcount: A:0.53, C:0.05, G:0.18, T:0.24
Consensus pattern (33 bp):
AAAGAGTAAAATAGTAAAATGGTAATTAAATTC
Found at i:657 original size:25 final size:26
Alignment explanation
Indices: 606--658 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
596 ACAACTGGTG
606 ATTAAATTCAAAGAGTGAAAATAGTA
1 ATTAAATTCAAAGAGTGAAAATAGTA
632 ATTAAATTCAAGAGAGT-AAAAT-GTA
1 ATTAAATTCAA-AGAGTGAAAATAGTA
657 AT
1 AT
659 CAGTAAAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
25 5 0.19
26 16 0.62
27 5 0.19
ACGTcount: A:0.53, C:0.04, G:0.15, T:0.28
Consensus pattern (26 bp):
ATTAAATTCAAAGAGTGAAAATAGTA
Found at i:663 original size:14 final size:14
Alignment explanation
Indices: 654--804 Score: 84
Period size: 14 Copynumber: 10.9 Consensus size: 14
644 AGAGTAAAAT
654 GTAATCAGTAAAGA
1 GTAATCAGTAAAGA
* **
668 GGAAAAAGTAAAGA
1 GTAATCAGTAAAGA
682 GTAATCAGTAAA-A
1 GTAATCAGTAAAGA
**
695 GTAAAAATGGTAAA-A
1 GTAATCA--GTAAAGA
710 GTAATCAGTAAAGA
1 GTAATCAGTAAAGA
*
724 GTAATCAGCGAAA-A
1 GTAATCAG-TAAAGA
** *
738 GTAAAAATGGCAAAGA
1 GTAATCA--GTAAAGA
*
754 GTAGT-A--AAAG-
1 GTAATCAGTAAAGA
* *
764 GTATTCAGGCAAA-A
1 GTAATCA-GTAAAGA
778 GTAATCAGTAAAGA
1 GTAATCAGTAAAGA
792 GTAATCAGTAAAG
1 GTAATCAGTAAAG
805 GAAGAATGAT
Statistics
Matches: 105, Mismatches: 19, Indels: 26
0.70 0.13 0.17
Matches are distributed among these distances:
10 4 0.04
11 5 0.05
13 15 0.14
14 58 0.55
15 18 0.17
16 5 0.05
ACGTcount: A:0.52, C:0.07, G:0.23, T:0.19
Consensus pattern (14 bp):
GTAATCAGTAAAGA
Found at i:677 original size:28 final size:27
Alignment explanation
Indices: 646--724 Score: 106
Period size: 28 Copynumber: 2.8 Consensus size: 27
636 AATTCAAGAG
646 AGTAAAATGTAATCAGTAAAGAGGAAAA
1 AGTAAAA-GTAATCAGTAAAGAGGAAAA
*
674 AGTAAAGAGTAATCAGTAAA-AGTAAAA
1 AGTAAA-AGTAATCAGTAAAGAGGAAAA
701 ATGGTAAAAGTAATCAGTAAAGAG
1 A--GTAAAAGTAATCAGTAAAGAG
725 TAATCAGCGA
Statistics
Matches: 46, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
27 7 0.15
28 31 0.67
29 8 0.17
ACGTcount: A:0.56, C:0.04, G:0.22, T:0.19
Consensus pattern (27 bp):
AGTAAAAGTAATCAGTAAAGAGGAAAA
Found at i:720 original size:42 final size:44
Alignment explanation
Indices: 674--756 Score: 134
Period size: 43 Copynumber: 1.9 Consensus size: 44
664 AAGAGGAAAA
* *
674 AGTAAAGAGTAATCAG-TAAAAGTAAAAATGGTAAA-AGTAATC
1 AGTAAAGAGTAATCAGCGAAAAGTAAAAATGGCAAAGAGTAATC
716 AGTAAAGAGTAATCAGCGAAAAGTAAAAATGGCAAAGAGTA
1 AGTAAAGAGTAATCAGCGAAAAGTAAAAATGGCAAAGAGTA
757 GTAAAAGGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
42 16 0.43
43 17 0.46
44 4 0.11
ACGTcount: A:0.54, C:0.06, G:0.22, T:0.18
Consensus pattern (44 bp):
AGTAAAGAGTAATCAGCGAAAAGTAAAAATGGCAAAGAGTAATC
Found at i:737 original size:28 final size:27
Alignment explanation
Indices: 649--741 Score: 98
Period size: 28 Copynumber: 3.3 Consensus size: 27
639 TCAAGAGAGT
* *
649 AAAATGTAATCAGTAAAGAGGAAAAAGT
1 AAAA-GTAATCAGTAAAGAGTAAAAAGG
677 AAAGAGTAATCAGTAAA-AGTAAAAATGG
1 AAA-AGTAATCAGTAAAGAGTAAAAA-GG
**
705 TAAAAGTAATCAGTAAAGAGTAATCAGCG
1 -AAAAGTAATCAGTAAAGAGTAAAAAG-G
734 AAAAGTAA
1 AAAAGTAA
742 AAATGGCAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
27 7 0.12
28 38 0.68
29 11 0.20
ACGTcount: A:0.56, C:0.05, G:0.20, T:0.18
Consensus pattern (27 bp):
AAAAGTAATCAGTAAAGAGTAAAAAGG
Found at i:974 original size:22 final size:22
Alignment explanation
Indices: 936--1004 Score: 86
Period size: 22 Copynumber: 3.2 Consensus size: 22
926 CGGTAAAATG
936 GTAAAAAGTAAAA-GGTAATCA
1 GTAAAAAGTAAAATGGTAATCA
** *
957 GTAAAGGGTAAAATGGTAATTA
1 GTAAAAAGTAAAATGGTAATCA
* *
979 GTAAAAAGTAAGATGGCAATCA
1 GTAAAAAGTAAAATGGTAATCA
1001 GTAA
1 GTAA
1005 GAAGAGGATA
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
21 11 0.28
22 28 0.72
ACGTcount: A:0.51, C:0.04, G:0.23, T:0.22
Consensus pattern (22 bp):
GTAAAAAGTAAAATGGTAATCA
Done.