Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005032.1 Corchorus capsularis cultivar CVL-1 contig05050, 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: 2625
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Found at i:151 original size:38 final size:37
Alignment explanation
Indices: 100--303 Score: 158
Period size: 38 Copynumber: 5.4 Consensus size: 37
90 ACCCCAATAA
* * *
100 AATTAAGAATCAAAACAATAATAATTAGTAAAATTGAT
1 AATTAAGAGTCAAAATAATAATAATCAGT-AAATTGAT
* * * * *
138 AATTAAGAGTCAAAGTAATAGTAATCAGTGAATTAAGC
1 AATTAAGAGTCAAAATAATAATAATCAGTAAATTGA-T
* * *
176 AATTAAGAATCAAAGTAATAATAATCAGGAAAATTGAT
1 AATTAAGAGTCAAAATAATAATAATCA-GTAAATTGAT
* * * *
214 AATTAAGAGTAAAAAAAATAGTAATCAGTAAATCGAT
1 AATTAAGAGTCAAAATAATAATAATCAGTAAATTGAT
* * * * *
251 CATTAAGAGTCAAGGTAAAAATAGTAATCAGT-AAGTCAGT
1 AATTAAGAGTCAA---AATAATAATAATCAGTAAATTGA-T
291 AATTAAGAGTCAA
1 AATTAAGAGTCAA
304 GGGATTAATC
Statistics
Matches: 133, Mismatches: 27, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
37 24 0.18
38 71 0.53
39 9 0.07
40 29 0.22
ACGTcount: A:0.52, C:0.07, G:0.15, T:0.26
Consensus pattern (37 bp):
AATTAAGAGTCAAAATAATAATAATCAGTAAATTGAT
Found at i:234 original size:76 final size:76
Alignment explanation
Indices: 100--242 Score: 223
Period size: 76 Copynumber: 1.9 Consensus size: 76
90 ACCCCAATAA
* * * **
100 AATTAAGAATCAAAACAATAATAATTAGTAAAATTGATAATTAAGAGTCAAAGTAATAGTAATCA
1 AATTAAGAATCAAAACAATAATAATCAGGAAAATTGATAATTAAGAGTAAAAAAAATAGTAATCA
165 GTGAATTAAGC
66 GTGAATTAAGC
**
176 AATTAAGAATCAAAGTAATAATAATCAGGAAAATTGATAATTAAGAGTAAAAAAAATAGTAATCA
1 AATTAAGAATCAAAACAATAATAATCAGGAAAATTGATAATTAAGAGTAAAAAAAATAGTAATCA
241 GT
66 GT
243 AAATCGATCA
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
76 60 1.00
ACGTcount: A:0.55, C:0.06, G:0.13, T:0.27
Consensus pattern (76 bp):
AATTAAGAATCAAAACAATAATAATCAGGAAAATTGATAATTAAGAGTAAAAAAAATAGTAATCA
GTGAATTAAGC
Found at i:275 original size:40 final size:40
Alignment explanation
Indices: 227--305 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 40
217 TAAGAGTAAA
*
227 AAAAATAGTAATCAGTAAATC-GATCATTAAGAGTCAAGGT
1 AAAAATAGTAATCAGTAAATCAG-TAATTAAGAGTCAAGGT
*
267 AAAAATAGTAATCAGTAAGTCAGTAATTAAGAGTCAAGG
1 AAAAATAGTAATCAGTAAATCAGTAATTAAGAGTCAAGG
306 GATTAATCAG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 35 0.97
41 1 0.03
ACGTcount: A:0.48, C:0.09, G:0.19, T:0.24
Consensus pattern (40 bp):
AAAAATAGTAATCAGTAAATCAGTAATTAAGAGTCAAGGT
Found at i:423 original size:21 final size:21
Alignment explanation
Indices: 398--437 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
388 TCAAGATAGT
*
398 AAAATAGTAATCAGTAAAGGA
1 AAAATAGTAAACAGTAAAGGA
* *
419 AAAATGGTAAAGAGTAAAG
1 AAAATAGTAAACAGTAAAG
438 AATAATCAGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.57, C:0.03, G:0.23, T:0.17
Consensus pattern (21 bp):
AAAATAGTAAACAGTAAAGGA
Found at i:468 original size:14 final size:14
Alignment explanation
Indices: 431--470 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
421 AATGGTAAAG
*
431 AGTAAAGAATAATC
1 AGTAAAGAGTAATC
* *
445 AGTAAGGAGTAATT
1 AGTAAAGAGTAATC
459 AGTAAAGAGTAA
1 AGTAAAGAGTAA
471 AATGATAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.53, C:0.03, G:0.23, T:0.23
Consensus pattern (14 bp):
AGTAAAGAGTAATC
Found at i:522 original size:50 final size:50
Alignment explanation
Indices: 403--499 Score: 142
Period size: 50 Copynumber: 2.0 Consensus size: 50
393 ATAGTAAAAT
* * * *
403 AGTAATCAGTAAAG-GAAAAATGGTAAAGAGTAAAGAATAATCAGTAAGG
1 AGTAATTAGTAAAGAGTAAAATGATAAAAAGTAAAGAATAATCAGTAAGG
*
452 AGTAATTAGTAAAGAGTAAAATGATAAAAAGTAAAGAGTAATCAGTAA
1 AGTAATTAGTAAAGAGTAAAATGATAAAAAGTAAAGAATAATCAGTAA
500 AGGAAGAATG
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
49 13 0.31
50 29 0.69
ACGTcount: A:0.55, C:0.03, G:0.22, T:0.21
Consensus pattern (50 bp):
AGTAATTAGTAAAGAGTAAAATGATAAAAAGTAAAGAATAATCAGTAAGG
Found at i:528 original size:35 final size:36
Alignment explanation
Indices: 445--535 Score: 98
Period size: 35 Copynumber: 2.6 Consensus size: 36
435 AAGAATAATC
* *
445 AGTAAGGAGTAATTAGTAAAGAGTAAAATGATAAAA
1 AGTAAAGAGTAATCAGTAAAGAGTAAAATGATAAAA
* *
481 AGTAAAGAGTAATCAGTAAAG-G-AAGAATGGTAAAT
1 AGTAAAGAGTAATCAGTAAAGAGTAA-AATGATAAAA
*
516 AGTAAA-AGGTAATCAATAAA
1 AGTAAAGA-GTAATCAGTAAA
536 AAAGTAATGA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
34 3 0.06
35 26 0.54
36 19 0.40
ACGTcount: A:0.55, C:0.02, G:0.22, T:0.21
Consensus pattern (36 bp):
AGTAAAGAGTAATCAGTAAAGAGTAAAATGATAAAA
Found at i:535 original size:21 final size:22
Alignment explanation
Indices: 510--681 Score: 151
Period size: 21 Copynumber: 8.0 Consensus size: 22
500 AGGAAGAATG
*
510 GTAAATAGTAAAA-GGTAATCA
1 GTAAAGAGTAAAATGGTAATCA
* * *
531 ATAAAAAAGT--AATGATAATCA
1 GT-AAAGAGTAAAATGGTAATCA
*
552 GTAAAG-GTAAAATAGTAATCA
1 GTAAAGAGTAAAATGGTAATCA
*
573 GT-AAGAGCAAAATGGTAATCA
1 GTAAAGAGTAAAATGGTAATCA
* * * *
594 AT-GAGAGCAAAATGATAATCA
1 GTAAAGAGTAAAATGGTAATCA
* *
615 GTAAAGAGTAAAATAGTAATTA
1 GTAAAGAGTAAAATGGTAATCA
*
637 GTAAAAAGTAAGAA-GGTAATCA
1 GTAAAGAGTAA-AATGGTAATCA
*
659 GTAAAGAGTAAAATAGTAATCA
1 GTAAAGAGTAAAATGGTAATCA
681 G
1 G
682 CAAATGGTAA
Statistics
Matches: 120, Mismatches: 23, Indels: 15
0.76 0.15 0.09
Matches are distributed among these distances:
19 2 0.02
20 8 0.07
21 54 0.45
22 54 0.45
23 2 0.02
ACGTcount: A:0.53, C:0.05, G:0.19, T:0.22
Consensus pattern (22 bp):
GTAAAGAGTAAAATGGTAATCA
Found at i:591 original size:63 final size:63
Alignment explanation
Indices: 519--658 Score: 169
Period size: 63 Copynumber: 2.2 Consensus size: 63
509 GGTAAATAGT
519 AAAAGGTAATCAAT-A-AAAAAGTAATGATAATCAGTAAAG-GTAAAATAGTAATCAGTAAGAGC
1 AAAAGGTAATCAATGAGAAAAA--AATGATAATCAGTAAAGAGTAAAATAGTAATCAGTAAGAGC
** * * *
581 AAAATGGTAATCAATGAGAGCAAAATGATAATCAGTAAAGAGTAAAATAGTAATTAGTAAAAAGT
1 AAAA-GGTAATCAATGAGAAAAAAATGATAATCAGTAAAGAGTAAAATAGTAATCAGT-AAGAGC
646 AAGAAGGTAATCA
1 AA-AAGGTAATCA
659 GTAAAGAGTA
Statistics
Matches: 67, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
62 4 0.06
63 27 0.40
64 17 0.25
65 17 0.25
66 2 0.03
ACGTcount: A:0.54, C:0.06, G:0.19, T:0.21
Consensus pattern (63 bp):
AAAAGGTAATCAATGAGAAAAAAATGATAATCAGTAAAGAGTAAAATAGTAATCAGTAAGAGC
Found at i:691 original size:22 final size:22
Alignment explanation
Indices: 546--756 Score: 150
Period size: 22 Copynumber: 9.5 Consensus size: 22
536 AAAGTAATGA
546 TAATCAGTAAAG-GTAAAATAG
1 TAATCAGTAAAGAGTAAAATAG
* *
567 TAATCAGT-AAGAGCAAAATGG
1 TAATCAGTAAAGAGTAAAATAG
* * *
588 TAATCAAT-GAGAGCAAAAT-G
1 TAATCAGTAAAGAGTAAAATAG
608 ATAATCAGTAAAGAGTAAAATAG
1 -TAATCAGTAAAGAGTAAAATAG
* * *
631 TAATTAGTAAAAAGTAAGAA-GG
1 TAATCAGTAAAGAGTAA-AATAG
653 TAATCAGTAAAGAGTAAAATAG
1 TAATCAGTAAAGAGTAAAATAG
* * *
675 TAATCAGCAAATG-GT-AATTAC
1 TAATCAGTAAA-GAGTAAAATAG
* *
696 TAA-GAGTAAAATAGTAATCAGTATAAGG
1 TAATCAGT-AAAGAGTAA--A--AT-A-G
*
724 TAATCAGTAAAGAGAAAAATAG
1 TAATCAGTAAAGAGTAAAATAG
746 TAATCAGTAAA
1 TAATCAGTAAA
757 AGGTAATCAG
Statistics
Matches: 149, Mismatches: 24, Indels: 33
0.72 0.12 0.16
Matches are distributed among these distances:
20 6 0.04
21 53 0.36
22 66 0.44
23 5 0.03
24 3 0.02
26 2 0.01
27 1 0.01
28 10 0.07
29 3 0.02
ACGTcount: A:0.52, C:0.06, G:0.19, T:0.23
Consensus pattern (22 bp):
TAATCAGTAAAGAGTAAAATAG
Found at i:691 original size:36 final size:34
Alignment explanation
Indices: 649--789 Score: 192
Period size: 35 Copynumber: 4.0 Consensus size: 34
639 AAAAAGTAAG
*
649 AAGGTAATCAGTAAAGAGTAAAATAGTAATCAGCA
1 AAGGTAATCAGT-AAGAGTAAAATAGTAATCAGTA
* *
684 AATGGTAATTACTAAGAGTAAAATAGTAATCAGTA
1 AA-GGTAATCAGTAAGAGTAAAATAGTAATCAGTA
*
719 TAAGGTAATCAGTAAAGAGAAAAATAGTAATCAGTAA
1 -AAGGTAATCAGT-AAGAGTAAAATAGTAATCAGT-A
*
756 AAGGTAATCAGTAAGAGTAAAACAGTAATCAGTA
1 AAGGTAATCAGTAAGAGTAAAATAGTAATCAGTA
790 GGAGCAAAGT
Statistics
Matches: 94, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
34 1 0.01
35 50 0.53
36 42 0.45
37 1 0.01
ACGTcount: A:0.51, C:0.07, G:0.19, T:0.23
Consensus pattern (34 bp):
AAGGTAATCAGTAAGAGTAAAATAGTAATCAGTA
Found at i:704 original size:71 final size:70
Alignment explanation
Indices: 629--776 Score: 197
Period size: 71 Copynumber: 2.1 Consensus size: 70
619 AGAGTAAAAT
* * * *
629 AGTAATTAGTAAAAAGTAAGAAGGTAATCAGTAAAGAGTAAAATAGTAATCAGCAAATGGTAATT
1 AGTAAATAGTAAAAAGT-AGAAGGTAATCAGTAAAGAGAAAAATAGTAATCAGCAAAAGGTAATC
694 ACTAAG
65 ACTAAG
** * *
700 AGTAAAATAGTAATCAGTATAAGGTAATCAGTAAAGAGAAAAATAGTAATCAGTAAAAGGTAATC
1 AGT-AAATAGTAAAAAGTAGAAGGTAATCAGTAAAGAGAAAAATAGTAATCAGCAAAAGGTAATC
*
765 AGTAAG
65 ACTAAG
771 AGTAAA
1 AGTAAA
777 ACAGTAATCA
Statistics
Matches: 67, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
70 3 0.04
71 53 0.79
72 11 0.16
ACGTcount: A:0.52, C:0.05, G:0.20, T:0.23
Consensus pattern (70 bp):
AGTAAATAGTAAAAAGTAGAAGGTAATCAGTAAAGAGAAAAATAGTAATCAGCAAAAGGTAATCA
CTAAG
Found at i:705 original size:35 final size:35
Alignment explanation
Indices: 651--829 Score: 180
Period size: 35 Copynumber: 4.9 Consensus size: 35
641 AAAGTAAGAA
651 GGTAATCAGTAAAGAGTAAAATAGTAATCAGCAAAT
1 GGTAATCAGT-AAGAGTAAAATAGTAATCAGCAAAT
* * *
687 GGTAATTACTAAGAGTAAAATAGTAATCAGTATAA-
1 GGTAATCAGTAAGAGTAAAATAGTAATCAGCA-AAT
* * *
722 GGTAATCAGTAAAGAGAAAAATAGTAATCAGTAAAA
1 GGTAATCAGT-AAGAGTAAAATAGTAATCAGCAAAT
*
758 GGTAATCAGTAAGAGTAAAACAGTAATCAGTAGGAGCAAAGT
1 GGTAATCAGTAAGAGTAAAATAGTAATC------AGCAAA-T
* *
800 GGTAATTAGTAAGGGTAAAATAGTAATCAG
1 GGTAATCAGTAAGAGTAAAATAGTAATCAG
830 TAATGAGTAA
Statistics
Matches: 120, Mismatches: 13, Indels: 20
0.78 0.08 0.13
Matches are distributed among these distances:
35 47 0.39
36 43 0.36
41 5 0.04
42 25 0.21
ACGTcount: A:0.49, C:0.07, G:0.22, T:0.23
Consensus pattern (35 bp):
GGTAATCAGTAAGAGTAAAATAGTAATCAGCAAAT
Found at i:777 original size:71 final size:71
Alignment explanation
Indices: 649--789 Score: 228
Period size: 71 Copynumber: 2.0 Consensus size: 71
639 AAAAAGTAAG
* * * *
649 AAGGTAATCAGTAAAGAGTAAAATAGTAATCAGCAAATGGTAATTACTAAGAGTAAAATAGTAAT
1 AAGGTAATCAGTAAAGAGAAAAATAGTAATCAGCAAAAGGTAATCACTAAGAGTAAAACAGTAAT
714 CAGTAT
66 CAGTAT
* *
720 AAGGTAATCAGTAAAGAGAAAAATAGTAATCAGTAAAAGGTAATCAGTAAGAGTAAAACAGTAAT
1 AAGGTAATCAGTAAAGAGAAAAATAGTAATCAGCAAAAGGTAATCACTAAGAGTAAAACAGTAAT
785 CAGTA
66 CAGTA
790 GGAGCAAAGT
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
71 64 1.00
ACGTcount: A:0.51, C:0.07, G:0.19, T:0.23
Consensus pattern (71 bp):
AAGGTAATCAGTAAAGAGAAAAATAGTAATCAGCAAAAGGTAATCACTAAGAGTAAAACAGTAAT
CAGTAT
Found at i:849 original size:21 final size:21
Alignment explanation
Indices: 708--854 Score: 96
Period size: 21 Copynumber: 7.3 Consensus size: 21
698 AGAGTAAAAT
* *
708 AGTAATCAGTATAAGGTAATC
1 AGTAATGAGTAAAAGGTAATC
*
729 AGTAAAGAG--AAA---AAT-
1 AGTAATGAGTAAAAGGTAATC
*
744 AGTAATCAGTAAAAGGTAATC
1 AGTAATGAGTAAAAGGTAATC
*
765 AGTAA-GAGTAAAACAGTAATC
1 AGTAATGAGTAAAA-GGTAATC
* * * *
786 AGT-AGGAGCAAAGTGGTAATT
1 AGTAATGAGTAAA-AGGTAATC
* *
807 AGTAA-GGGTAAAATAGTAATC
1 AGTAATGAGTAAAA-GGTAATC
*
828 AGTAATGAGTAAAAGGTGATC
1 AGTAATGAGTAAAAGGTAATC
849 AGTAAT
1 AGTAAT
855 TCCAAGAGTA
Statistics
Matches: 95, Mismatches: 19, Indels: 24
0.69 0.14 0.17
Matches are distributed among these distances:
15 7 0.07
16 3 0.03
17 3 0.03
19 2 0.02
20 11 0.12
21 61 0.64
22 8 0.08
ACGTcount: A:0.48, C:0.06, G:0.23, T:0.23
Consensus pattern (21 bp):
AGTAATGAGTAAAAGGTAATC
Found at i:853 original size:42 final size:42
Alignment explanation
Indices: 708--853 Score: 135
Period size: 42 Copynumber: 3.6 Consensus size: 42
698 AGAGTAAAAT
* * *
708 AGTAATCAGTATAAGGTAATCAGTAA-AG-AGAA-A--AAT-
1 AGTAATGAGTAAAAGGTAATCAGTAAGAGTAAAACAGTAATC
*
744 AGTAATCAGTAAAAGGTAATCAGTAAGAGTAAAACAGTAATC
1 AGTAATGAGTAAAAGGTAATCAGTAAGAGTAAAACAGTAATC
* * * * * *
786 AGT-AGGAGCAAAGTGGTAATTAGTAAGGGTAAAATAGTAATC
1 AGTAATGAGTAAA-AGGTAATCAGTAAGAGTAAAACAGTAATC
*
828 AGTAATGAGTAAAAGGTGATCAGTAA
1 AGTAATGAGTAAAAGGTAATCAGTAA
854 TTCCAAGAGT
Statistics
Matches: 88, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
36 25 0.28
37 2 0.02
38 3 0.03
39 1 0.01
41 9 0.10
42 41 0.47
43 7 0.08
ACGTcount: A:0.48, C:0.06, G:0.23, T:0.23
Consensus pattern (42 bp):
AGTAATGAGTAAAAGGTAATCAGTAAGAGTAAAACAGTAATC
Found at i:930 original size:13 final size:13
Alignment explanation
Indices: 914--960 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
904 GGTAATAAAT
914 AAAAGAGAGTAAG
1 AAAAGAGAGTAAG
* *
927 AAAAGAGTAATGAG
1 AAAAGAG-AGTAAG
941 TAAAA-AGAGTAAG
1 -AAAAGAGAGTAAG
954 AAAAGAG
1 AAAAGAG
961 TAAAAATGAC
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
12 4 0.15
13 13 0.48
14 6 0.22
15 4 0.15
ACGTcount: A:0.62, C:0.00, G:0.28, T:0.11
Consensus pattern (13 bp):
AAAAGAGAGTAAG
Done.