Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013449.1 Corchorus capsularis cultivar CVL-1 contig13470, 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: 91941
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:8225 original size:1 final size:1
Alignment explanation
Indices: 8219--8245 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
8209 AATTAGCTTC
8219 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
8246 AAAAGAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:12534 original size:12 final size:12
Alignment explanation
Indices: 12495--12542 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
12485 AATATCCACC
12495 GTGTGAAGGTGT
1 GTGTGAAGGTGT
* *
12507 GTGGGAAGGAGT
1 GTGTGAAGGTGT
12519 GTGTGAAGGTGT
1 GTGTGAAGGTGT
*
12531 GTGTGATGGTGT
1 GTGTGAAGGTGT
12543 TGATGGAGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.17, C:0.00, G:0.52, T:0.31
Consensus pattern (12 bp):
GTGTGAAGGTGT
Found at i:16326 original size:31 final size:31
Alignment explanation
Indices: 16291--16351 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
16281 TTTGAAACAT
*
16291 GTGGCATGCCACGTGTCACTTTTTGGTACAC
1 GTGGCATGACACGTGTCACTTTTTGGTACAC
* *
16322 GTGGCGTGACATGTGTCACTTTTTGGTACA
1 GTGGCATGACACGTGTCACTTTTTGGTACA
16352 TGTGACACGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.16, C:0.21, G:0.28, T:0.34
Consensus pattern (31 bp):
GTGGCATGACACGTGTCACTTTTTGGTACAC
Found at i:22809 original size:14 final size:14
Alignment explanation
Indices: 22790--22830 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
22780 GTTATGACTG
22790 AATGTGTTAAAATA
1 AATGTGTTAAAATA
22804 AATGTGTT---ATA
1 AATGTGTTAAAATA
22815 AATGTGTTAAAATA
1 AATGTGTTAAAATA
22829 AA
1 AA
22831 GAAATCTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
11 11 0.46
14 13 0.54
ACGTcount: A:0.49, C:0.00, G:0.15, T:0.37
Consensus pattern (14 bp):
AATGTGTTAAAATA
Found at i:24930 original size:6 final size:6
Alignment explanation
Indices: 24919--24945 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
24909 GTTTTTCATT
24919 GAAATG GAAATG GAAATG GAAATG GAA
1 GAAATG GAAATG GAAATG GAAATG GAA
24946 GAAGCTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.33, T:0.15
Consensus pattern (6 bp):
GAAATG
Found at i:28847 original size:25 final size:24
Alignment explanation
Indices: 28810--28866 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 24
28800 CTTCATGCAA
* *
28810 CAAAATCAGGAACAAGCACAAGCAG
1 CAAAATCAAGAACAAGAACAAGC-G
28835 CAAAATCAAGAACAAGAACAAGCG
1 CAAAATCAAGAACAAGAACAAGCG
28859 C-AAATCAA
1 CAAAATCAA
28867 ATAAACTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 7 0.23
24 2 0.07
25 21 0.70
ACGTcount: A:0.56, C:0.23, G:0.16, T:0.05
Consensus pattern (24 bp):
CAAAATCAAGAACAAGAACAAGCG
Found at i:29379 original size:44 final size:44
Alignment explanation
Indices: 29316--29401 Score: 154
Period size: 44 Copynumber: 2.0 Consensus size: 44
29306 TAATGTCAAT
*
29316 TGGAACCATTCTCATCAAAAGTTCCGTAAGCTCTAATTTTCACC
1 TGGAACCATTCTCATCAAAAGTTCCGTAAGCTCTAACTTTCACC
*
29360 TGGAACCATTCTCATCAAAAGTTCCGTGAGCTCTAACTTTCA
1 TGGAACCATTCTCATCAAAAGTTCCGTAAGCTCTAACTTTCA
29402 TAGGAATTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (44 bp):
TGGAACCATTCTCATCAAAAGTTCCGTAAGCTCTAACTTTCACC
Found at i:29590 original size:2 final size:2
Alignment explanation
Indices: 29583--29610 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29573 AAGGTTAATA
29583 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29611 CTTTATCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29847 original size:49 final size:49
Alignment explanation
Indices: 29785--29953 Score: 133
Period size: 49 Copynumber: 3.3 Consensus size: 49
29775 TCTTTCCCCC
29785 AAATTTTCATCAATCTCACCCTACGTCTATTTTATTTGTTTTTTTGCCT
1 AAATTTTCATCAATCTCACCCTACGTCTATTTTATTTGTTTTTTTGCCT
* *** * * * ** * ** *
29834 AAATTTTCTTCAATCTCTTAAAATAC-CCTTACCTTAACAATCTCTTTTTCCCCC
1 AAATTTTCATCAATCTC--ACCCTACGTC-TA-TTTTA-TTTGT-TTTTTTGCCT
* *
29888 ACATTTTCATCATTCTCACCCTACGTCTATTTTATTTGTTTTTTTGCCT
1 AAATTTTCATCAATCTCACCCTACGTCTATTTTATTTGTTTTTTTGCCT
*
29937 AAATTTTCTTCAATCTC
1 AAATTTTCATCAATCTC
29954 TTAAAATACC
Statistics
Matches: 82, Mismatches: 31, Indels: 14
0.65 0.24 0.11
Matches are distributed among these distances:
49 37 0.45
50 3 0.04
51 9 0.11
52 9 0.11
53 3 0.04
54 21 0.26
ACGTcount: A:0.22, C:0.26, G:0.04, T:0.48
Consensus pattern (49 bp):
AAATTTTCATCAATCTCACCCTACGTCTATTTTATTTGTTTTTTTGCCT
Found at i:29895 original size:103 final size:105
Alignment explanation
Indices: 29757--29965 Score: 377
Period size: 103 Copynumber: 2.0 Consensus size: 105
29747 ATTAATTGAA
*
29757 TTACCTTAACAATCTTTTTCTTTCCCCCAAATTTTCATCAATCTCACCCTACGTCTATTTTATTT
1 TTACCTTAACAATCTTCTTCTTTCCCCCAAATTTTCATCAATCTCACCCTACGTCTATTTTATTT
29822 GTTTTTTTGCCTAAATTTTCTTCAATCTCTTAAAATACCC
66 GTTTTTTTGCCTAAATTTTCTTCAATCTCTTAAAATACCC
* *
29862 TTACCTTAACAATC-TCTT-TTTCCCCCACATTTTCATCATTCTCACCCTACGTCTATTTTATTT
1 TTACCTTAACAATCTTCTTCTTTCCCCCAAATTTTCATCAATCTCACCCTACGTCTATTTTATTT
29925 GTTTTTTTGCCTAAATTTTCTTCAATCTCTTAAAATACCC
66 GTTTTTTTGCCTAAATTTTCTTCAATCTCTTAAAATACCC
29965 T
1 T
29966 AATCCTTCTA
Statistics
Matches: 101, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
103 84 0.83
104 3 0.03
105 14 0.14
ACGTcount: A:0.23, C:0.27, G:0.03, T:0.47
Consensus pattern (105 bp):
TTACCTTAACAATCTTCTTCTTTCCCCCAAATTTTCATCAATCTCACCCTACGTCTATTTTATTT
GTTTTTTTGCCTAAATTTTCTTCAATCTCTTAAAATACCC
Found at i:31599 original size:17 final size:17
Alignment explanation
Indices: 31542--31593 Score: 95
Period size: 17 Copynumber: 3.1 Consensus size: 17
31532 CTCCCTCTCA
*
31542 TACTAGGTAGTATGATG
1 TACTAGGTAGTATGAGG
31559 TACTAGGTAGTATGAGG
1 TACTAGGTAGTATGAGG
31576 TACTAGGTAGTATGAGG
1 TACTAGGTAGTATGAGG
31593 T
1 T
31594 GATAGGCTGC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 34 1.00
ACGTcount: A:0.29, C:0.06, G:0.33, T:0.33
Consensus pattern (17 bp):
TACTAGGTAGTATGAGG
Found at i:38810 original size:15 final size:15
Alignment explanation
Indices: 38790--38818 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
38780 ACCAATAACA
38790 ATGGTAATATGATTT
1 ATGGTAATATGATTT
38805 ATGGTAATATGATT
1 ATGGTAATATGATT
38819 CTTGGATGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.00, G:0.21, T:0.45
Consensus pattern (15 bp):
ATGGTAATATGATTT
Found at i:44748 original size:15 final size:14
Alignment explanation
Indices: 44728--44757 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
44718 TACAAAGATG
44728 AAGAAGAAAGAAGAA
1 AAGAAGAAAG-AGAA
44743 AAGAAGAAAGAGAA
1 AAGAAGAAAGAGAA
44757 A
1 A
44758 GAGTAAAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (14 bp):
AAGAAGAAAGAGAA
Found at i:58606 original size:16 final size:16
Alignment explanation
Indices: 58585--58616 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
58575 CTGAAGCAGT
*
58585 ATATGGACATTTGAGG
1 ATATGGACACTTGAGG
58601 ATATGGACACTTGAGG
1 ATATGGACACTTGAGG
58617 CATCAGTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.28
Consensus pattern (16 bp):
ATATGGACACTTGAGG
Found at i:58685 original size:70 final size:70
Alignment explanation
Indices: 58601--58778 Score: 347
Period size: 70 Copynumber: 2.5 Consensus size: 70
58591 ACATTTGAGG
*
58601 ATATGGACACTTGAGGCATCAGTATACTCTTGTATTGACTGAAGCGGTATAAATGGCAAACCAAA
1 ATATGGACATTTGAGGCATCAGTATACTCTTGTATTGACTGAAGCGGTATAAATGGCAAACCAAA
58666 GGAGT
66 GGAGT
58671 ATATGGACATTTGAGGCATCAGTATACTCTTGTATTGACTGAAGCGGTATAAATGGCAAACCAAA
1 ATATGGACATTTGAGGCATCAGTATACTCTTGTATTGACTGAAGCGGTATAAATGGCAAACCAAA
58736 GGAGT
66 GGAGT
58741 ATATGGACATTTGAGGCATCAGTATACTCTTGTATTGA
1 ATATGGACATTTGAGGCATCAGTATACTCTTGTATTGA
58779 TATGGTTGAG
Statistics
Matches: 107, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 107 1.00
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.29
Consensus pattern (70 bp):
ATATGGACATTTGAGGCATCAGTATACTCTTGTATTGACTGAAGCGGTATAAATGGCAAACCAAA
GGAGT
Found at i:60381 original size:12 final size:12
Alignment explanation
Indices: 60364--60418 Score: 74
Period size: 12 Copynumber: 4.5 Consensus size: 12
60354 CATCGATACC
*
60364 TCGATATATCCA
1 TCGATATATCCG
60376 TCGATATATCCG
1 TCGATATATCCG
* *
60388 TTGATATATCTG
1 TCGATATATCCG
60400 TTCGATATATCCG
1 -TCGATATATCCG
60413 TCGATA
1 TCGATA
60419 CCTGTATTTG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
12 27 0.73
13 10 0.27
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (12 bp):
TCGATATATCCG
Found at i:60423 original size:23 final size:24
Alignment explanation
Indices: 60376--60423 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
60366 GATATATCCA
* *
60376 TCGATATATCCGTTGATATATCTGT
1 TCGATATATCCGTCGA-ATACCTGT
60401 TCGATATATCCGTCG-ATACCTGT
1 TCGATATATCCGTCGAATACCTGT
60424 ATTTGTTGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 7 0.33
25 14 0.67
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.40
Consensus pattern (24 bp):
TCGATATATCCGTCGAATACCTGT
Found at i:71215 original size:30 final size:30
Alignment explanation
Indices: 71179--71256 Score: 90
Period size: 29 Copynumber: 2.6 Consensus size: 30
71169 CATCAGAAAA
71179 GGGCTTATTTGGCCTTTTTAA-AGAGTTCAG
1 GGGCTTATTTGGCC-TTTTAATAGAGTTCAG
**
71209 GGGCTTATTTGG-C-TGCAATTAGAGTTCAG
1 GGGCTTATTTGGCCTTTTAA-TAGAGTTCAG
71238 GGGCTTATTTGGCCGTTTT
1 GGGCTTATTTGGCC-TTTT
71257 GTGTAAATTC
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
27 3 0.08
29 22 0.56
30 13 0.33
32 1 0.03
ACGTcount: A:0.17, C:0.14, G:0.29, T:0.40
Consensus pattern (30 bp):
GGGCTTATTTGGCCTTTTAATAGAGTTCAG
Found at i:72816 original size:13 final size:13
Alignment explanation
Indices: 72798--72828 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
72788 AAACATGTAA
*
72798 TTCAGAAGTACTT
1 TTCAGAAGCACTT
72811 TTCAGAAGCACTT
1 TTCAGAAGCACTT
72824 TTCAG
1 TTCAG
72829 TTGTTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.35
Consensus pattern (13 bp):
TTCAGAAGCACTT
Found at i:81425 original size:6 final size:6
Alignment explanation
Indices: 81414--81440 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
81404 TATATAATAA
81414 ATAGAT ATAGAT ATAGAT ATAGAT ATA
1 ATAGAT ATAGAT ATAGAT ATAGAT ATA
81441 TATAATCACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.15, T:0.33
Consensus pattern (6 bp):
ATAGAT
Found at i:90964 original size:32 final size:32
Alignment explanation
Indices: 90922--90995 Score: 103
Period size: 32 Copynumber: 2.3 Consensus size: 32
90912 AAAATAGCCG
* * *
90922 AGCCGTCCCACCGGCGCGACCTGCCGTGGCGA
1 AGCCGCCCCACCGGCGCGACCTGCCCTGGCAA
* *
90954 AGCCGCCCCACCGGGGCGGCCTGCCCTGGCAA
1 AGCCGCCCCACCGGCGCGACCTGCCCTGGCAA
90986 AGCCGCCCCA
1 AGCCGCCCCA
90996 GTGGGGCGGC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.14, C:0.47, G:0.32, T:0.07
Consensus pattern (32 bp):
AGCCGCCCCACCGGCGCGACCTGCCCTGGCAA
Found at i:91058 original size:34 final size:33
Alignment explanation
Indices: 90952--91104 Score: 166
Period size: 32 Copynumber: 4.7 Consensus size: 33
90942 CTGCCGTGGC
* ** *
90952 GAAGCCGCCCCACCGGGGCGGCCTGCCC-TGGC
1 GAAGCCGCCCTAGTGGGGCGGCCTGCCCATGGT
* * *** *
90984 AAAGCCGCCCCAGTGGGGCGGCCTATTCATAGT
1 GAAGCCGCCCTAGTGGGGCGGCCTGCCCATGGT
91017 GAAGCCGCCCTAGTGGGGCGGCCTGCCCAATGGT
1 GAAGCCGCCCTAGTGGGGCGGCCTGCCC-ATGGT
91051 GAAGCCGCCCTAGTGGGGCGGCCTGCCCATGGT
1 GAAGCCGCCCTAGTGGGGCGGCCTGCCCATGGT
* **
91084 -AAGCCGCACTCTTGGGGCGGC
1 GAAGCCGCCCTAGTGGGGCGGC
91105 ACAGGTCATC
Statistics
Matches: 102, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
32 40 0.39
33 30 0.29
34 32 0.31
ACGTcount: A:0.14, C:0.35, G:0.37, T:0.14
Consensus pattern (33 bp):
GAAGCCGCCCTAGTGGGGCGGCCTGCCCATGGT
Found at i:91100 original size:32 final size:34
Alignment explanation
Indices: 90966--91104 Score: 135
Period size: 34 Copynumber: 4.2 Consensus size: 34
90956 CCGCCCCACC
** * *
90966 GGGGCGGCCTGCCC--TGGCAAAGCCGCCCCAGT
1 GGGGCGGCCTGCCCAATGGTGAAGCCGCACTAGT
*** * *
90998 GGGGCGGCCTATTC-ATAGTGAAGCCGCCCTAGT
1 GGGGCGGCCTGCCCAATGGTGAAGCCGCACTAGT
*
91031 GGGGCGGCCTGCCCAATGGTGAAGCCGCCCTAGT
1 GGGGCGGCCTGCCCAATGGTGAAGCCGCACTAGT
**
91065 GGGGCGGCCTGCCC-ATGGT-AAGCCGCACTCTT
1 GGGGCGGCCTGCCCAATGGTGAAGCCGCACTAGT
91097 GGGGCGGC
1 GGGGCGGC
91105 ACAGGTCATC
Statistics
Matches: 91, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
32 29 0.32
33 30 0.33
34 32 0.35
ACGTcount: A:0.14, C:0.33, G:0.38, T:0.15
Consensus pattern (34 bp):
GGGGCGGCCTGCCCAATGGTGAAGCCGCACTAGT
Done.