Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011851.1 Corchorus capsularis cultivar CVL-1 contig11872, 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: 13268
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Found at i:150 original size:38 final size:38
Alignment explanation
Indices: 108--293 Score: 169
Period size: 38 Copynumber: 4.8 Consensus size: 38
98 ACCCCAATAA
* *
108 AATTAAGAATCAAAACAATAGTAATCAGTAAAATTGAT
1 AATTAAGAGTCAAAAAAATAGTAATCAGTAAAATTGAT
** * * *
146 AATTAAGAGTCAAAGTAATAGTAATCAGT-GAATTAAGC
1 AATTAAGAGTCAAAAAAATAGTAATCAGTAAAATTGA-T
* ** *
184 AATTAAGAATCAAAGTAATAATAATCAGTAAAATTGAT
1 AATTAAGAGTCAAAAAAATAGTAATCAGTAAAATTGAT
* * *
222 AATTAAGAGTAAGAAAAAATATTTAATCAGT-AAATCGAT
1 AATTAAGAGTCA-AAAAAATA-GTAATCAGTAAAATTGAT
*
261 CATTAAGAGTCAAGGTAAAAATAGTAATCAGTA
1 AATTAAGAGTCAA---AAAAATAGTAATCAGTA
294 GGTCAGTAAT
Statistics
Matches: 120, Mismatches: 20, Indels: 13
0.78 0.13 0.08
Matches are distributed among these distances:
37 5 0.04
38 64 0.53
39 28 0.23
40 16 0.13
41 7 0.06
ACGTcount: A:0.52, C:0.07, G:0.14, T:0.27
Consensus pattern (38 bp):
AATTAAGAGTCAAAAAAATAGTAATCAGTAAAATTGAT
Found at i:432 original size:21 final size:21
Alignment explanation
Indices: 408--466 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
398 TCAAGAGAGT
**
408 AAAATAGTAATTAGTAAAGGA
1 AAAATAGTAAAGAGTAAAGGA
*
429 AAAATGGTAAAGAGTAAA-GA
1 AAAATAGTAAAGAGTAAAGGA
* *
449 ATAATCAGTAAGGAGTAA
1 AAAAT-AGTAAAGAGTAA
467 TTAGTAAAGA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
20 6 0.19
21 25 0.81
ACGTcount: A:0.56, C:0.02, G:0.22, T:0.20
Consensus pattern (21 bp):
AAAATAGTAAAGAGTAAAGGA
Found at i:478 original size:14 final size:14
Alignment explanation
Indices: 441--480 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
431 AATGGTAAAG
*
441 AGTAAAGAATAATC
1 AGTAAAGAGTAATC
* *
455 AGTAAGGAGTAATT
1 AGTAAAGAGTAATC
469 AGTAAAGAGTAA
1 AGTAAAGAGTAA
481 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:532 original size:50 final size:50
Alignment explanation
Indices: 413--509 Score: 151
Period size: 50 Copynumber: 2.0 Consensus size: 50
403 AGAGTAAAAT
* * *
413 AGTAATTAGTAAAG-GAAAAATGGTAAAGAGTAAAGAATAATCAGTAAGG
1 AGTAATTAGTAAAGAGTAAAATGATAAAAAGTAAAGAATAATCAGTAAGG
*
462 AGTAATTAGTAAAGAGTAAAATGATAAAAAGTAAAGAGTAATCAGTAA
1 AGTAATTAGTAAAGAGTAAAATGATAAAAAGTAAAGAATAATCAGTAA
510 AGGAAGAATG
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
49 14 0.33
50 29 0.67
ACGTcount: A:0.55, C:0.02, G:0.22, T:0.22
Consensus pattern (50 bp):
AGTAATTAGTAAAGAGTAAAATGATAAAAAGTAAAGAATAATCAGTAAGG
Found at i:538 original size:35 final size:35
Alignment explanation
Indices: 463--572 Score: 102
Period size: 35 Copynumber: 3.1 Consensus size: 35
453 TCAGTAAGGA
* *
463 GTAATTAGTAAAGAGTAA-AATGATAAAAAGT-AAAG
1 GTAATCAGTAAAG-G-AAGAATGATAAATAGTAAAAG
*
498 AGTAATCAGTAAAGGAAGAATGGTAAATAGTAAAAG
1 -GTAATCAGTAAAGGAAGAATGATAAATAGTAAAAG
* *
534 GTAATCAATAAA-AAAGTAATGAT-AATCAGTAAAAG
1 GTAATCAGTAAAGGAAG-AATGATAAAT-AGTAAAAG
569 GTAA
1 GTAA
573 AATAGTAATC
Statistics
Matches: 64, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
34 8 0.12
35 40 0.62
36 16 0.25
ACGTcount: A:0.55, C:0.03, G:0.20, T:0.22
Consensus pattern (35 bp):
GTAATCAGTAAAGGAAGAATGATAAATAGTAAAAG
Found at i:538 original size:71 final size:71
Alignment explanation
Indices: 450--907 Score: 315
Period size: 71 Copynumber: 6.1 Consensus size: 71
440 GAGTAAAGAA
* *
450 TAATCAGT-AAGGAGTAATTAGTAAAGAGTAAAAT-GATAAAAAGTAAAGA-GTAATCAGTAAAG
1 TAATCAGTAAAAG-GTAATCAGTAAAGAGTAAAATAG-TAAAAAGTAAAGAGGTAATCAGTAAAG
*
512 GAAGAATGG
64 GAA-AATAG
* * * *
521 TAAAT-AGTAAAAGGTAATCAATAAAAAAGTAATGATAATCAGTAAAAGGTAAA-ATAGTAATCA
1 T-AATCAGTAAAAGGTAATCAGT-AAAGAGT-A--A-AAT-AGTAAAAAGTAAAGA-GGTAATCA
* *
584 GTAAGAGCAAAATGG
58 GTAA-AGGAAAATAG
*
599 TAATCAATGAGAACAAAATGGTAATCAGTAAAGAGTAAAATAGTAATTAGTAAAAAGT-AAGAAG
1 TAATC----AG--TAAAA-GGTAATCAGTAAAGAGT---A-A--AA-TAGTAAAAAGTAAAG-AG
663 GTAATCAGTAAAGAGTAAAATAG
51 GTAATCAGTAAAG-G-AAAATAG
** ** *
686 TAATCAACAAAAGGTAATCAGT-AAGAGTAAAATAGTAATCAGTATA-AGGTAATCAGTAAAGAG
1 TAATCAGTAAAAGGTAATCAGTAAAGAGTAAAATAGTAAAAAGTAAAGAGGTAATCAGTAAAG-G
749 AAAAATAG
65 -AAAATAG
* ** * *
757 TAATCAGTAGAAGGTAATCAGTAAAGAGTAAAATAGTAATCAGCAAA-AGGTAATCAGTAAGAGT
1 TAATCAGTAAAAGGTAATCAGTAAAGAGTAAAATAGTAAAAAGTAAAGAGGTAATCAGTAA-AGG
821 AAAATAG
65 AAAATAG
* * ** *
828 TAATCAGTATAAGGTAATCAGTAAAGAGAAAAATAGTAATCAGTAAA-AGGTAATCAGTAAGAGT
1 TAATCAGTAAAAGGTAATCAGTAAAGAGTAAAATAGTAAAAAGTAAAGAGGTAATCAGTAA-AGG
*
892 AAAACAG
65 AAAATAG
899 TAATCAGTA
1 TAATCAGTA
908 GGAGCAAAGT
Statistics
Matches: 327, Mismatches: 29, Indels: 62
0.78 0.07 0.15
Matches are distributed among these distances:
71 137 0.42
72 56 0.17
73 6 0.02
75 2 0.01
76 5 0.02
77 13 0.04
78 18 0.06
79 10 0.03
80 10 0.03
81 5 0.02
82 2 0.01
83 1 0.00
84 10 0.03
85 14 0.04
86 25 0.08
87 13 0.04
ACGTcount: A:0.53, C:0.06, G:0.20, T:0.22
Consensus pattern (71 bp):
TAATCAGTAAAAGGTAATCAGTAAAGAGTAAAATAGTAAAAAGTAAAGAGGTAATCAGTAAAGGA
AAATAG
Found at i:565 original size:85 final size:85
Alignment explanation
Indices: 413--580 Score: 189
Period size: 85 Copynumber: 2.0 Consensus size: 85
403 AGAGTAAAAT
* * ** * *
413 AGTAATTAGTAAAGGAAAAATGGTAAAGAGTAAAGAATAATCAGTAAGGAGTAATTAGTAAAGAG
1 AGTAATCAGTAAAGGAAAAATGGTAAAGAGTAAAGAATAATCAATAAAAAGTAATGAGTAAACAG
478 TAAAATGATAAAA-AGTAAAG
66 TAAAA-GATAAAATAGTAAAG
* * * *
498 AGTAATCAGTAAAGGAAGAATGGTAAATAGTAAA-AGGTAATCAATAAAAAAGTAATGA-TAATC
1 AGTAATCAGTAAAGGAAAAATGGTAAAGAGTAAAGA-ATAATCAAT-AAAAAGTAATGAGTAAAC
*
561 AGTAAAAGGTAAAATAGTAA
64 AGTAAAAGATAAAATAGTAA
581 TCAGTAAGAG
Statistics
Matches: 69, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
84 7 0.10
85 53 0.77
86 9 0.13
ACGTcount: A:0.55, C:0.02, G:0.21, T:0.21
Consensus pattern (85 bp):
AGTAATCAGTAAAGGAAAAATGGTAAAGAGTAAAGAATAATCAATAAAAAGTAATGAGTAAACAG
TAAAAGATAAAATAGTAAAG
Found at i:584 original size:22 final size:22
Alignment explanation
Indices: 556--702 Score: 108
Period size: 22 Copynumber: 6.8 Consensus size: 22
546 AAAGTAATGA
556 TAATCAGTAAAAGGTAAAATAG
1 TAATCAGTAAAAGGTAAAATAG
* * *
578 TAATCAGTAAGA-GCAAAATGG
1 TAATCAGTAAAAGGTAAAATAG
* * * *
599 TAATCAATGAGAA--CAAAATGG
1 TAATCAGT-AAAAGGTAAAATAG
620 TAATCAGT-AAAGAGTAAAATAG
1 TAATCAGTAAAAG-GTAAAATAG
* * *
642 TAATTAGTAAAAAGTAAGAA-GG
1 TAATCAGTAAAAGGTAA-AATAG
664 TAATCAGT-AAAGAGTAAAATAG
1 TAATCAGTAAAAG-GTAAAATAG
**
686 TAATCAACAAAAGGTAA
1 TAATCAGTAAAAGGTAA
703 TCAGTAAGAG
Statistics
Matches: 98, Mismatches: 18, Indels: 18
0.73 0.13 0.13
Matches are distributed among these distances:
19 2 0.02
21 34 0.35
22 53 0.54
23 9 0.09
ACGTcount: A:0.54, C:0.06, G:0.19, T:0.21
Consensus pattern (22 bp):
TAATCAGTAAAAGGTAAAATAG
Found at i:602 original size:64 final size:63
Alignment explanation
Indices: 529--669 Score: 162
Period size: 64 Copynumber: 2.2 Consensus size: 63
519 GGTAAATAGT
529 AAAAGGTAATCAAT-A-AAAAAGTAATGATAATCAGTAAA-AGGTAAAATAGTAATCAGTAAGAG
1 AAAAGGTAATCAATGAGAAAAA--AATGATAATCAGTAAAGA-GTAAAATAGTAATCAGTAAGAG
591 C
63 C
* * * * *
592 AAAATGGTAATCAATGAGAACAAAATGGTAATCAGTAAAGAGTAAAATAGTAATTAGTAAAAAGT
1 AAAA-GGTAATCAATGAGAAAAAAATGATAATCAGTAAAGAGTAAAATAGTAATCAGT-AAGAGC
657 AAGAAGGTAATCA
1 AA-AAGGTAATCA
670 GTAAAGAGTA
Statistics
Matches: 67, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
63 4 0.06
64 41 0.61
65 16 0.24
66 6 0.09
ACGTcount: A:0.55, C:0.06, G:0.18, T:0.21
Consensus pattern (63 bp):
AAAAGGTAATCAATGAGAAAAAAATGATAATCAGTAAAGAGTAAAATAGTAATCAGTAAGAGC
Found at i:700 original size:36 final size:36
Alignment explanation
Indices: 654--907 Score: 397
Period size: 36 Copynumber: 7.1 Consensus size: 36
644 ATTAGTAAAA
654 AGTAAGAAGGTAATCAGTAAAGAGTAAAATAGTAATC
1 AGTAA-AAGGTAATCAGTAAAGAGTAAAATAGTAATC
**
691 AACAAAAGGTAATCAGT-AAGAGTAAAATAGTAATC
1 AGTAAAAGGTAATCAGTAAAGAGTAAAATAGTAATC
* *
726 AGTATAAGGTAATCAGTAAAGAGAAAAATAGTAATC
1 AGTAAAAGGTAATCAGTAAAGAGTAAAATAGTAATC
*
762 AGTAGAAGGTAATCAGTAAAGAGTAAAATAGTAATC
1 AGTAAAAGGTAATCAGTAAAGAGTAAAATAGTAATC
*
798 AGCAAAAGGTAATCAGT-AAGAGTAAAATAGTAATC
1 AGTAAAAGGTAATCAGTAAAGAGTAAAATAGTAATC
* *
833 AGTATAAGGTAATCAGTAAAGAGAAAAATAGTAATC
1 AGTAAAAGGTAATCAGTAAAGAGTAAAATAGTAATC
*
869 AGTAAAAGGTAATCAGT-AAGAGTAAAACAGTAATC
1 AGTAAAAGGTAATCAGTAAAGAGTAAAATAGTAATC
904 AGTA
1 AGTA
908 GGAGCAAAGT
Statistics
Matches: 199, Mismatches: 16, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
35 85 0.43
36 111 0.56
37 3 0.02
ACGTcount: A:0.52, C:0.07, G:0.20, T:0.21
Consensus pattern (36 bp):
AGTAAAAGGTAATCAGTAAAGAGTAAAATAGTAATC
Found at i:787 original size:14 final size:14
Alignment explanation
Indices: 719--787 Score: 55
Period size: 14 Copynumber: 5.4 Consensus size: 14
709 AGAGTAAAAT
719 AGTAATCAGTATAAG
1 AGTAATCAGTA-AAG
734 -GTAATCAGTAAAG
1 AGTAATCAGTAAAG
*
747 AG--A--A--AAAT
1 AGTAATCAGTAAAG
755 AGTAATCAGTAGAAG
1 AGTAATCAGTA-AAG
770 -GTAATCAGTAAAG
1 AGTAATCAGTAAAG
783 AGTAA
1 AGTAA
788 AATAGTAATC
Statistics
Matches: 43, Mismatches: 2, Indels: 19
0.67 0.03 0.30
Matches are distributed among these distances:
8 5 0.12
10 2 0.05
12 2 0.05
13 6 0.14
14 26 0.60
15 2 0.05
ACGTcount: A:0.51, C:0.06, G:0.22, T:0.22
Consensus pattern (14 bp):
AGTAATCAGTAAAG
Found at i:792 original size:107 final size:107
Alignment explanation
Indices: 658--949 Score: 460
Period size: 107 Copynumber: 2.7 Consensus size: 107
648 GTAAAAAGTA
658 AGAAGGTAATCAGTAAAGAGTAAAATAGTAATCAACAAAAGGTAATCAGTAAGAGTAAAATAGTA
1 AGAAGGTAATCAGTAAAGAGTAAAATAGTAATCAACAAAAGGTAATCAGTAAGAGTAAAATAGTA
723 ATCAGTATAAGGTAATCAGTAAAGAGAAAAATAGTAATCAGT
66 ATCAGTATAAGGTAATCAGTAAAGAGAAAAATAGTAATCAGT
*
765 AGAAGGTAATCAGTAAAGAGTAAAATAGTAATCAGCAAAAGGTAATCAGTAAGAGTAAAATAGTA
1 AGAAGGTAATCAGTAAAGAGTAAAATAGTAATCAACAAAAGGTAATCAGTAAGAGTAAAATAGTA
830 ATCAGTATAAGGTAATCAGTAAAGAGAAAAATAGTAATCAGT
66 ATCAGTATAAGGTAATCAGTAAAGAGAAAAATAGTAATCAGT
* * * * *
872 AAAAGGTAATCAGT-AAGAGTAAAACAGTAATCAGTAGGAGCAAAGTGGTAATTAGTAAGGGTAA
1 AGAAGGTAATCAGTAAAGAGTAAAATAGTAATC---A--A-CAAA-AGGTAATCAGTAAGAGTAA
936 AATAGTAATCAGTA
59 AATAGTAATCAGTA
950 ACGACTAAAA
Statistics
Matches: 171, Mismatches: 7, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
106 17 0.10
107 119 0.70
109 1 0.01
112 4 0.02
113 30 0.18
ACGTcount: A:0.51, C:0.07, G:0.21, T:0.22
Consensus pattern (107 bp):
AGAAGGTAATCAGTAAAGAGTAAAATAGTAATCAACAAAAGGTAATCAGTAAGAGTAAAATAGTA
ATCAGTATAAGGTAATCAGTAAAGAGAAAAATAGTAATCAGT
Found at i:901 original size:21 final size:21
Alignment explanation
Indices: 888--959 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
878 TAATCAGTAA
* *
888 GAGTAAAACAGTAATCAGTAG
1 GAGTAAAATAGTAATCAGTAA
* * * *
909 GAGCAAAGTGGTAATTAGTAA
1 GAGTAAAATAGTAATCAGTAA
*
930 GGGTAAAATAGTAATCAGTAA
1 GAGTAAAATAGTAATCAGTAA
*
951 CGACTAAAA
1 -GAGTAAAA
960 GGTGATCAGT
Statistics
Matches: 37, Mismatches: 13, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
21 31 0.84
22 6 0.16
ACGTcount: A:0.47, C:0.08, G:0.24, T:0.21
Consensus pattern (21 bp):
GAGTAAAATAGTAATCAGTAA
Found at i:971 original size:42 final size:42
Alignment explanation
Indices: 871--971 Score: 116
Period size: 42 Copynumber: 2.4 Consensus size: 42
861 TAGTAATCAG
*
871 TAAAAGGTAATCAGTAAGAGTAAAACAGTAATCAGTAGGAGC
1 TAAAAGGTAATCAGTAAGAGTAAAACAGTAATCAGTACGAGC
* * * *
913 -AAAGTGGTAATTAGTAAGGGTAAAATAGTAATCAGTAACGA-C
1 TAAA-AGGTAATCAGTAAGAGTAAAACAGTAATCAGT-ACGAGC
*
955 TAAAAGGTGATCAGTAA
1 TAAAAGGTAATCAGTAA
972 TTCCAAGAGT
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
41 3 0.06
42 39 0.81
43 6 0.12
ACGTcount: A:0.47, C:0.08, G:0.24, T:0.22
Consensus pattern (42 bp):
TAAAAGGTAATCAGTAAGAGTAAAACAGTAATCAGTACGAGC
Found at i:2054 original size:33 final size:33
Alignment explanation
Indices: 1973--2096 Score: 112
Period size: 33 Copynumber: 3.7 Consensus size: 33
1963 CCGCGCAACA
1973 CCGGCCACAAGACCGGCCACGCGACATGGACATAT-
1 CCGGCCAC-A-ACCGGCCACGCGACATGGACAT-TG
* *
2008 CCTGCCATC-ACCGGCCATGCGACATGGACATTG
1 CCGGCCA-CAACCGGCCACGCGACATGGACATTG
* ** *
2041 CCGGCTACAACCGGCCAAACGAC-TCGGCCA-TG
1 CCGGCCACAACCGGCCACGCGACAT-GGACATTG
2073 CCCGGCCACAACCGGCCACGCGAC
1 -CCGGCCACAACCGGCCACGCGAC
2097 CCTTTGTCTA
Statistics
Matches: 74, Mismatches: 10, Indels: 12
0.77 0.10 0.12
Matches are distributed among these distances:
32 5 0.07
33 62 0.84
35 6 0.08
36 1 0.01
ACGTcount: A:0.24, C:0.41, G:0.25, T:0.10
Consensus pattern (33 bp):
CCGGCCACAACCGGCCACGCGACATGGACATTG
Found at i:3016 original size:8 final size:8
Alignment explanation
Indices: 3003--3036 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
2993 CCTTCTTGAA
3003 AAAAATTC
1 AAAAATTC
3011 AAAAATTC
1 AAAAATTC
*
3019 AGAAACTTC
1 A-AAAATTC
3028 AAAAATTC
1 AAAAATTC
3036 A
1 A
3037 TACCCGATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.59, C:0.15, G:0.03, T:0.24
Consensus pattern (8 bp):
AAAAATTC
Found at i:8545 original size:33 final size:33
Alignment explanation
Indices: 8495--8618 Score: 144
Period size: 33 Copynumber: 3.7 Consensus size: 33
8485 CCGCGCAACA
*
8495 CCGGCCACAAGACCGGCCACGCGACATGGACATGT
1 CCGGCCAC-A-ACCGGCCACGCGACATGGACATGC
*
8530 CCGGCCATC-ACCGGCCACGCGACATGGACATGG
1 CCGGCCA-CAACCGGCCACGCGACATGGACATGC
* ** *
8563 CCGGCTACAACCGGCCAAACGAC-TCGGCCATGC
1 CCGGCCACAACCGGCCACGCGACAT-GGACATGC
8596 CCGGCCACAACCGGCCACGCGAC
1 CCGGCCACAACCGGCCACGCGAC
8619 CCTTTGTCTA
Statistics
Matches: 77, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
32 2 0.03
33 67 0.87
35 7 0.09
36 1 0.01
ACGTcount: A:0.23, C:0.42, G:0.27, T:0.07
Consensus pattern (33 bp):
CCGGCCACAACCGGCCACGCGACATGGACATGC
Done.