Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01000029.1 Corchorus capsularis cultivar CVL-1 contig00029, 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, 613
Length: 1022
ACGTcount: A:0.49, C:0.08, G:0.21, T:0.23
Found at i:77 original size:38 final size:37
Alignment explanation
Indices: 1--132 Score: 138
Period size: 38 Copynumber: 3.5 Consensus size: 37
* * * *
1 AAGAGTCAAAGTAATAGTAATCAGTGAATTAAGCAATT
1 AAGAGTCAAAGTAATAATAATCAGTAAATTGA-TAATT
*
39 AAGAATCAAAGTAATAATAATCAGTAAAATTGATAATT
1 AAGAGTCAAAGTAATAATAATCAGT-AAATTGATAATT
* * * * *
77 AAGAGTAAAAGAAATAGTAATCAGTAAATCGATCATT
1 AAGAGTCAAAGTAATAATAATCAGTAAATTGATAATT
* *
114 AAGAGTCAAGGTAAAAATA
1 AAGAGTCAAAGTAATAATA
133 GTAATCAGTA
Statistics
Matches: 77, Mismatches: 16, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
37 24 0.31
38 48 0.62
39 5 0.06
ACGTcount: A:0.52, C:0.07, G:0.16, T:0.25
Consensus pattern (37 bp):
AAGAGTCAAAGTAATAATAATCAGTAAATTGATAATT
Found at i:138 original size:40 final size:40
Alignment explanation
Indices: 51--164 Score: 130
Period size: 40 Copynumber: 2.9 Consensus size: 40
41 GAATCAAAGT
* *
51 AATAATAATCAGTAAAATTGATAATTAAGAGT-AA--AAGA
1 AATAGTAATCAGT-AAATCGATAATTAAGAGTCAAGGAAGA
*
89 AATAGTAATCAGTAAATCGATCATTAAGAGTCAAGGTAA-A
1 AATAGTAATCAGTAAATCGATAATTAAGAGTCAAGG-AAGA
*
129 AATAGTAATCAGTAAGTC-AGTAATTAAGAGTCAAGG
1 AATAGTAATCAGTAAATCGA-TAATTAAGAGTCAAGG
165 GATTAATCAT
Statistics
Matches: 66, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
37 16 0.24
38 14 0.21
39 1 0.02
40 33 0.50
41 2 0.03
ACGTcount: A:0.50, C:0.07, G:0.18, T:0.25
Consensus pattern (40 bp):
AATAGTAATCAGTAAATCGATAATTAAGAGTCAAGGAAGA
Found at i:357 original size:14 final size:14
Alignment explanation
Indices: 289--359 Score: 55
Period size: 14 Copynumber: 5.5 Consensus size: 14
279 AAATGGTAAG
* *
289 AGTAAAGAATAATC
1 AGTAAAGAGTAATA
* *
303 AGTAAGGAGTAATT
1 AGTAAAGAGTAATA
317 AGTAAAGAGTAA-A
1 AGTAAAGAGTAATA
*
330 A-T---GA-TAAAA
1 AGTAAAGAGTAATA
339 AGTAAAGAGTAATA
1 AGTAAAGAGTAATA
353 AGTAAAG
1 AGTAAAG
360 GAAGAATGGT
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
8 3 0.07
9 4 0.09
10 1 0.02
12 1 0.02
13 3 0.07
14 33 0.73
ACGTcount: A:0.56, C:0.01, G:0.21, T:0.21
Consensus pattern (14 bp):
AGTAAAGAGTAATA
Found at i:386 original size:35 final size:35
Alignment explanation
Indices: 311--420 Score: 95
Period size: 35 Copynumber: 3.1 Consensus size: 35
301 TCAGTAAGGA
* *
311 GTAATTAGTAAAGAGTAA-AATGATAAAAAGT-AAAG
1 GTAATAAGTAAAG-G-AAGAATGATAAATAGTAAAAG
*
346 AGTAATAAGTAAAGGAAGAATGGTAAATAGTAAAAG
1 -GTAATAAGTAAAGGAAGAATGATAAATAGTAAAAG
*
382 GTAATCAA-TAAA-AAAGTAATGAT-AATCAGTAAAAG
1 GTAAT-AAGTAAAGGAAG-AATGATAAAT-AGTAAAAG
417 GTAA
1 GTAA
421 AATAGTAATC
Statistics
Matches: 64, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
34 8 0.12
35 38 0.59
36 18 0.28
ACGTcount: A:0.56, C:0.02, G:0.20, T:0.22
Consensus pattern (35 bp):
GTAATAAGTAAAGGAAGAATGATAAATAGTAAAAG
Found at i:432 original size:22 final size:22
Alignment explanation
Indices: 404--550 Score: 106
Period size: 22 Copynumber: 6.8 Consensus size: 22
394 AAAGTAATGA
404 TAATCAGTAAAAGGTAAAATAG
1 TAATCAGTAAAAGGTAAAATAG
* * * *
426 TAATCAGTAAGA-GCAAACTGG
1 TAATCAGTAAAAGGTAAAATAG
* * * * *
447 TAATCAATGAGA-GCAAAATGG
1 TAATCAGTAAAAGGTAAAATAG
468 TAATCAGT-AAAGAGTAAAATAG
1 TAATCAGTAAAAG-GTAAAATAG
* * *
490 TAATTAGTAAAAAGTAAGAA-GG
1 TAATCAGTAAAAGGTAA-AATAG
*
512 TAATTAGT-AAAGAGTAAAATAG
1 TAATCAGTAAAAG-GTAAAATAG
*
534 TAATCAGCAAAAGGTAA
1 TAATCAGTAAAAGGTAA
551 TCAGTAAGAG
Statistics
Matches: 100, Mismatches: 18, Indels: 14
0.76 0.14 0.11
Matches are distributed among these distances:
20 2 0.02
21 36 0.36
22 53 0.53
23 9 0.09
ACGTcount: A:0.52, C:0.06, G:0.20, T:0.22
Consensus pattern (22 bp):
TAATCAGTAAAAGGTAAAATAG
Found at i:451 original size:21 final size:21
Alignment explanation
Indices: 399--712 Score: 125
Period size: 21 Copynumber: 15.7 Consensus size: 21
389 ATAAAAAAGT
* * *
399 AATGATAATCAGTAAAAGGTAA
1 AATGGTAATCAGTAAGA-GCAA
*
421 AATAGTAATCAGTAAGAGCAA
1 AATGGTAATCAGTAAGAGCAA
* * *
442 ACTGGTAATCAATGAGAGCAA
1 AATGGTAATCAGTAAGAGCAA
*
463 AATGGTAATCAGTAAAGAGTAA
1 AATGGTAATCAGT-AAGAGCAA
* * * *
485 AATAGTAATTAGTAAAAAGTAA
1 AATGGTAATCAGT-AAGAGCAA
* *
507 GAA-GGTAATTAGTAAAGAGTAA
1 -AATGGTAATCAGT-AAGAGCAA
*
529 AATAGTAATC------AGCAA
1 AATGGTAATCAGTAAGAGCAA
*
544 AA-GGTAATCAGTAAGAGTAA
1 AATGGTAATCAGTAAGAGCAA
* *
564 AATAGTAATCAGT------AT
1 AATGGTAATCAGTAAGAGCAA
*
579 AA-GGTAATCAGTAAAGAGAAA
1 AATGGTAATCAGT-AAGAGCAA
*
600 AATAGTAATCAGT------AA
1 AATGGTAATCAGTAAGAGCAA
*
615 AA-GGTAATCAGTAAGAGTAA
1 AATGGTAATCAGTAAGAGCAA
** *
635 AACAGTAATCAGTAGGAGCAA
1 AATGGTAATCAGTAAGAGCAA
* * * *
656 AGTGGTAATTAGTAAGGGTAA
1 AATGGTAATCAGTAAGAGCAA
* *
677 AATAGTAATCAGTAACGAGTAA
1 AATGGTAATCAGTAA-GAGCAA
*
699 AA-GGTGATCAGTAA
1 AATGGTAATCAGTAA
713 TTCCAAGATT
Statistics
Matches: 222, Mismatches: 44, Indels: 53
0.70 0.14 0.17
Matches are distributed among these distances:
14 24 0.11
15 13 0.06
20 10 0.05
21 96 0.43
22 77 0.35
23 2 0.01
ACGTcount: A:0.50, C:0.06, G:0.22, T:0.22
Consensus pattern (21 bp):
AATGGTAATCAGTAAGAGCAA
Found at i:498 original size:15 final size:15
Alignment explanation
Indices: 480--537 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
470 ATCAGTAAAG
*
480 AGTAAAATAGTAATT
1 AGTAAAATAGTAATA
*
495 AGTAAAA-AGTAAGA
1 AGTAAAATAGTAATA
*
509 AGGT-AATTAGTAA-A
1 A-GTAAAATAGTAATA
523 GAGTAAAATAGTAAT
1 -AGTAAAATAGTAAT
538 CAGCAAAAGG
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
14 11 0.32
15 23 0.68
ACGTcount: A:0.55, C:0.00, G:0.19, T:0.26
Consensus pattern (15 bp):
AGTAAAATAGTAATA
Found at i:548 original size:36 final size:35
Alignment explanation
Indices: 502--691 Score: 227
Period size: 35 Copynumber: 5.1 Consensus size: 35
492 ATTAGTAAAA
*
502 AGTAAGAAGGTAATTAGTAAAGAGTAAAATAGTAATC
1 AGTAA-AAGGTAATCAGT-AAGAGTAAAATAGTAATC
*
539 AGCAAAAGGTAATCAGTAAGAGTAAAATAGTAATC
1 AGTAAAAGGTAATCAGTAAGAGTAAAATAGTAATC
* *
574 AGTATAAGGTAATCAGTAAAGAGAAAAATAGTAATC
1 AGTAAAAGGTAATCAGT-AAGAGTAAAATAGTAATC
*
610 AGTAAAAGGTAATCAGTAAGAGTAAAACAGTAATC
1 AGTAAAAGGTAATCAGTAAGAGTAAAATAGTAATC
* *
645 AGTAGGAGCAAAGTGGTAATTAGTAAGGGTAAAATAGTAATC
1 AGT---A--AAA--GGTAATCAGTAAGAGTAAAATAGTAATC
687 AGTAA
1 AGTAA
692 CGAGTAAAAG
Statistics
Matches: 134, Mismatches: 11, Indels: 16
0.83 0.07 0.10
Matches are distributed among these distances:
35 52 0.39
36 44 0.33
37 5 0.04
38 1 0.01
39 1 0.01
40 3 0.02
42 28 0.21
ACGTcount: A:0.50, C:0.06, G:0.22, T:0.22
Consensus pattern (35 bp):
AGTAAAAGGTAATCAGTAAGAGTAAAATAGTAATC
Found at i:563 original size:71 final size:70
Alignment explanation
Indices: 488--635 Score: 215
Period size: 71 Copynumber: 2.1 Consensus size: 70
478 AGAGTAAAAT
* * *
488 AGTAATTAGTAAAAAGTAAGAAGGTAATTAGTAAAGAGTAAAATAGTAATCAGCAAAAGGTAATC
1 AGTAAATAGTAAAAAGT-AGAAGGTAATCAGTAAAGAGAAAAATAGTAATCAGCAAAAGGTAATC
553 AGTAAG
65 AGTAAG
** * *
559 AGTAAAATAGTAATCAGTATAAGGTAATCAGTAAAGAGAAAAATAGTAATCAGTAAAAGGTAATC
1 AGT-AAATAGTAAAAAGTAGAAGGTAATCAGTAAAGAGAAAAATAGTAATCAGCAAAAGGTAATC
624 AGTAAG
65 AGTAAG
630 AGTAAA
1 AGTAAA
636 ACAGTAATCA
Statistics
Matches: 69, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
70 3 0.04
71 55 0.80
72 11 0.16
ACGTcount: A:0.53, C:0.05, G:0.20, T:0.22
Consensus pattern (70 bp):
AGTAAATAGTAAAAAGTAGAAGGTAATCAGTAAAGAGAAAAATAGTAATCAGCAAAAGGTAATCA
GTAAG
Found at i:636 original size:71 final size:71
Alignment explanation
Indices: 508--648 Score: 246
Period size: 71 Copynumber: 2.0 Consensus size: 71
498 AAAAAGTAAG
* * *
508 AAGGTAATTAGTAAAGAGTAAAATAGTAATCAGCAAAAGGTAATCAGTAAGAGTAAAATAGTAAT
1 AAGGTAATCAGTAAAGAGAAAAATAGTAATCAGCAAAAGGTAATCAGTAAGAGTAAAACAGTAAT
573 CAGTAT
66 CAGTAT
*
579 AAGGTAATCAGTAAAGAGAAAAATAGTAATCAGTAAAAGGTAATCAGTAAGAGTAAAACAGTAAT
1 AAGGTAATCAGTAAAGAGAAAAATAGTAATCAGCAAAAGGTAATCAGTAAGAGTAAAACAGTAAT
644 CAGTA
66 CAGTA
649 GGAGCAAAGT
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 66 1.00
ACGTcount: A:0.52, C:0.06, G:0.20, T:0.22
Consensus pattern (71 bp):
AAGGTAATCAGTAAAGAGAAAAATAGTAATCAGCAAAAGGTAATCAGTAAGAGTAAAACAGTAAT
CAGTAT
Found at i:712 original size:42 final size:41
Alignment explanation
Indices: 425--712 Score: 166
Period size: 42 Copynumber: 7.3 Consensus size: 41
415 AGGTAAAATA
* * * *
425 GTAATCAGTAAGAG-CAAACTGGTAATCAATGA-GAGCAAAATG
1 GTAATCAGTAAGAGTAAAAC-AGTAATCAGT-ACGAGTAAAA-G
* * **
467 GTAATCAGTAAAGAGTAAAATAGTAATTAGTAAAAAGTAAGAAG
1 GTAATCAGT-AAGAGTAAAACAGTAATCAGT-ACGAGTAA-AAG
* *
511 GTAATTAGTAAAGAGTAAAATAGTAATCAG--C----AAAAG
1 GTAATCAGT-AAGAGTAAAACAGTAATCAGTACGAGTAAAAG
*
547 GTAATCAGTAAGAGTAAAATAGTAATCAGT---A-T--AAG
1 GTAATCAGTAAGAGTAAAACAGTAATCAGTACGAGTAAAAG
* *
582 GTAATCAGTAAAGAG-AAAA-A-TAGT-AAT-C-AGTAAAAG
1 GTAATCAGT-AAGAGTAAAACAGTAATCAGTACGAGTAAAAG
* * *
618 GTAATCAGTAAGAGTAAAACAGTAATCAGTAGGAGCAAAGTG
1 GTAATCAGTAAGAGTAAAACAGTAATCAGTACGAGTAAA-AG
* * *
660 GTAATTAGTAAGGGTAAAATAGTAATCAGTAACGAGTAAAAG
1 GTAATCAGTAAGAGTAAAACAGTAATCAGT-ACGAGTAAAAG
*
702 GTGATCAGTAA
1 GTAATCAGTAA
713 TTCCAAGATT
Statistics
Matches: 199, Mismatches: 27, Indels: 40
0.75 0.10 0.15
Matches are distributed among these distances:
32 2 0.01
33 4 0.02
34 2 0.01
35 41 0.21
36 32 0.16
37 3 0.02
38 3 0.02
39 2 0.01
41 5 0.03
42 47 0.24
43 20 0.10
44 36 0.18
45 2 0.01
ACGTcount: A:0.49, C:0.07, G:0.22, T:0.22
Consensus pattern (41 bp):
GTAATCAGTAAGAGTAAAACAGTAATCAGTACGAGTAAAAG
Found at i:790 original size:13 final size:13
Alignment explanation
Indices: 774--820 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
764 GGTAATAAAT
774 AAAAGAGAGTAAG
1 AAAAGAGAGTAAG
* *
787 AAAAGAGTAATGAG
1 AAAAGAG-AGTAAG
801 TAAAA-AGAGTAAG
1 -AAAAGAGAGTAAG
814 AAAAGAG
1 AAAAGAG
821 TAAAAAAGAC
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
Found at i:795 original size:11 final size:11
Alignment explanation
Indices: 779--829 Score: 50
Period size: 11 Copynumber: 4.3 Consensus size: 11
769 TAAATAAAAG
779 AGAGTAAGAAA
1 AGAGTAAGAAA
790 AGAGTAATGAGTAAAA
1 AGAGT-A--AG--AAA
806 AGAGTAAGAAA
1 AGAGTAAGAAA
817 AGAGTAA-AAA
1 AGAGTAAGAAA
827 AGA
1 AGA
830 CAAAAGTAGC
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
10 6 0.17
11 15 0.43
12 1 0.03
13 2 0.06
14 2 0.06
15 1 0.03
16 8 0.23
ACGTcount: A:0.63, C:0.00, G:0.25, T:0.12
Consensus pattern (11 bp):
AGAGTAAGAAA
Done.