Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010024.1 Corchorus capsularis cultivar CVL-1 contig10045, 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: 55523
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1009 original size:2 final size:2
Alignment explanation
Indices: 1002--1029 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
992 AATTTTCTGA
1002 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
1030 TTAAAAAATG
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:9553 original size:18 final size:18
Alignment explanation
Indices: 9538--9590 Score: 70
Period size: 20 Copynumber: 2.8 Consensus size: 18
9528 ACACGATTAC
9538 GACACGAAATACGATTCG
1 GACACGAAATACGATTCG
*
9556 GACACGATTACTACGATTCG
1 GACACGA--AATACGATTCG
*
9576 GACACGAGATACGAT
1 GACACGAAATACGAT
9591 AAGTCAAACA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 13 0.43
20 17 0.57
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.19
Consensus pattern (18 bp):
GACACGAAATACGATTCG
Found at i:13266 original size:22 final size:22
Alignment explanation
Indices: 13238--13283 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
13228 TCTTATCGCT
13238 CTTCTTTCAAGCACTCAAATCA
1 CTTCTTTCAAGCACTCAAATCA
13260 CTTCTTTCAAGCACTCAAATCA
1 CTTCTTTCAAGCACTCAAATCA
13282 CT
1 CT
13284 CCATCGATCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.30, C:0.33, G:0.04, T:0.33
Consensus pattern (22 bp):
CTTCTTTCAAGCACTCAAATCA
Found at i:20472 original size:14 final size:14
Alignment explanation
Indices: 20448--20481 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
20438 TTTTGGCGGA
20448 AAAAGAAAATAAAAT
1 AAAA-AAAATAAAAT
*
20463 AAAAAAAATAAAGT
1 AAAAAAAATAAAAT
20477 AAAAA
1 AAAAA
20482 CCCTTTAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (14 bp):
AAAAAAAATAAAAT
Found at i:21664 original size:12 final size:12
Alignment explanation
Indices: 21647--21693 Score: 85
Period size: 12 Copynumber: 3.9 Consensus size: 12
21637 CAGATCCAAT
*
21647 TGAAGAAAGGGC
1 TGAAGAAAGAGC
21659 TGAAGAAAGAGC
1 TGAAGAAAGAGC
21671 TGAAGAAAGAGC
1 TGAAGAAAGAGC
21683 TGAAGAAAGAG
1 TGAAGAAAGAG
21694 ATGGTGAAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.49, C:0.06, G:0.36, T:0.09
Consensus pattern (12 bp):
TGAAGAAAGAGC
Found at i:22032 original size:21 final size:21
Alignment explanation
Indices: 22007--22048 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
21997 GTTTGGGCAT
22007 GTTGTTGAAGAAGAAGATGAA
1 GTTGTTGAAGAAGAAGATGAA
*
22028 GTTGTTGAAGAAGTAGATGAA
1 GTTGTTGAAGAAGAAGATGAA
22049 ATGATTGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.33, T:0.26
Consensus pattern (21 bp):
GTTGTTGAAGAAGAAGATGAA
Found at i:22056 original size:21 final size:21
Alignment explanation
Indices: 22009--22056 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
21999 TTGGGCATGT
*
22009 TGTTGAAGAAGAAGATGAAGT
1 TGTTGAAGAAGAAGATGAAGA
*
22030 TGTTGAAGAAGTAGATGAA-A
1 TGTTGAAGAAGAAGATGAAGA
22050 TGATTGA
1 TG-TTGA
22057 TGACAACTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.42, C:0.00, G:0.31, T:0.27
Consensus pattern (21 bp):
TGTTGAAGAAGAAGATGAAGA
Found at i:25859 original size:3 final size:3
Alignment explanation
Indices: 25851--25887 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
25841 CCTTTCCTGG
*
25851 AGA AGA AGA AGA AGA AGA AGA AGG AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
25888 AAAAAACCCC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:26564 original size:68 final size:69
Alignment explanation
Indices: 26450--26579 Score: 226
Period size: 68 Copynumber: 1.9 Consensus size: 69
26440 CCGTCTTAGC
*
26450 TAGGTTTTGTGCAGAGTGAATAAATAAGTTTATCTTCCTCAACCGTTCTTCGTTGTTTAAGCTCC
1 TAGGTTTTGTGCAGAGTGAATAAATAAGTTTATCTTCCTCAACCGTTCTTCATTGTTTAAGCTCC
26515 GTCT
66 GTCT
**
26519 TAGGTTTTGTGCAGAGTGAAT-AATAAGTTTATCTTCCTCCTCCGTTCTTCATTGTTTAAGC
1 TAGGTTTTGTGCAGAGTGAATAAATAAGTTTATCTTCCTCAACCGTTCTTCATTGTTTAAGC
26580 ATGGCAAGGA
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
68 37 0.64
69 21 0.36
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.42
Consensus pattern (69 bp):
TAGGTTTTGTGCAGAGTGAATAAATAAGTTTATCTTCCTCAACCGTTCTTCATTGTTTAAGCTCC
GTCT
Found at i:34127 original size:21 final size:20
Alignment explanation
Indices: 34101--34149 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
34091 GTACTGGAGT
* *
34101 ACATGGGTCGCGAGGCAAACC
1 ACATGGGT-GCCAAGCAAACC
34122 ACATGGGGTGCCAAGCAAACC
1 ACAT-GGGTGCCAAGCAAACC
34143 ACATGGG
1 ACATGGG
34150 CGCCCAGTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 3 0.12
21 18 0.72
22 4 0.16
ACGTcount: A:0.31, C:0.27, G:0.33, T:0.10
Consensus pattern (20 bp):
ACATGGGTGCCAAGCAAACC
Found at i:38715 original size:35 final size:36
Alignment explanation
Indices: 38661--38739 Score: 106
Period size: 35 Copynumber: 2.2 Consensus size: 36
38651 AAAAAAAAGT
* *
38661 AATTATAAGTAAAATAAAATAATTACA-GTTAGGGA
1 AATTATAAGTAAAAGAAAATAATTACACGTTAGGAA
* *
38696 AATTATAAGTCAAAGAAAATAATTGCACGTTAGGAA
1 AATTATAAGTAAAAGAAAATAATTACACGTTAGGAA
*
38732 AATAATAA
1 AATTATAA
38740 ATCTTAATCA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
35 24 0.63
36 14 0.37
ACGTcount: A:0.54, C:0.05, G:0.14, T:0.27
Consensus pattern (36 bp):
AATTATAAGTAAAAGAAAATAATTACACGTTAGGAA
Found at i:44381 original size:27 final size:26
Alignment explanation
Indices: 44348--44412 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 26
44338 AAATGTTAAA
*
44348 TATAAATATATAAA-TTATTATAAAACAT
1 TATAAAT-TAAAAACTTA-TATAAAA-AT
44376 TA-AAATTAAAAACTTATATAAAAAT
1 TATAAATTAAAAACTTATATAAAAAT
44401 TATAAATTAAAA
1 TATAAATTAAAA
44413 CTAAAATTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
25 4 0.12
26 21 0.62
27 7 0.21
28 2 0.06
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (26 bp):
TATAAATTAAAAACTTATATAAAAAT
Found at i:44616 original size:14 final size:14
Alignment explanation
Indices: 44597--44625 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
44587 CGGTGTAATA
44597 TCGGTTTCGGTCGG
1 TCGGTTTCGGTCGG
44611 TCGGTTTCGGTCGG
1 TCGGTTTCGGTCGG
44625 T
1 T
44626 TTTAGTCGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.21, G:0.41, T:0.38
Consensus pattern (14 bp):
TCGGTTTCGGTCGG
Found at i:46537 original size:15 final size:16
Alignment explanation
Indices: 46512--46541 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
46502 AATAATTATT
46512 TTTAGATTATAATATA
1 TTTAGATTATAATATA
46528 TTTA-ATTATAATAT
1 TTTAGATTATAATAT
46542 TATTATTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGATTATAATATA
Found at i:47420 original size:13 final size:14
Alignment explanation
Indices: 47398--47433 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
47388 TATTTTAGAA
*
47398 AAAATTTCA-TGAG
1 AAAATATCATTGAG
47411 AAAATATCATTGAG
1 AAAATATCATTGAG
47425 AAAATATCA
1 AAAATATCA
47434 AAATTTCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.53, C:0.08, G:0.11, T:0.28
Consensus pattern (14 bp):
AAAATATCATTGAG
Found at i:47482 original size:22 final size:21
Alignment explanation
Indices: 47429--47509 Score: 72
Period size: 22 Copynumber: 3.7 Consensus size: 21
47419 ATTGAGAAAA
* *
47429 TATCAAAATTTCATAAGATAGT
1 TATCAAAATTTCATAGGA-GGT
* *
47451 TATTATAATTTCATGAGGAGGT
1 TATCAAAATTTCAT-AGGAGGT
* *
47473 TATCAAAATTCCATAGTGTGGT
1 TATCAAAATTTCATAG-GAGGT
*
47495 TACCAAAATTTCATA
1 TATCAAAATTTCATA
47510 TGGAAATTAT
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
21 2 0.04
22 42 0.89
23 3 0.06
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (21 bp):
TATCAAAATTTCATAGGAGGT
Found at i:47544 original size:22 final size:22
Alignment explanation
Indices: 47457--47568 Score: 100
Period size: 22 Copynumber: 5.5 Consensus size: 22
47447 TAGTTATTAT
* *
47457 AATTTCATGAG-GAGGTTATCAA
1 AATTTCAT-AGTGTGGTTACCAA
*
47479 AATTCCATAGTGTGGTTACCAA
1 AATTTCATAGTGTGGTTACCAA
47501 AATTTCATA---TGG--A--AA
1 AATTTCATAGTGTGGTTACCAA
*
47516 TTATTTCATAGTGTGGTTACCAA
1 -AATTTCATAGTGTGGTTACCAA
47539 AATTTC--AGTGTGGTTACCAA
1 AATTTCATAGTGTGGTTACCAA
47559 AATTTCATAG
1 AATTTCATAG
47569 GATCAGGTTA
Statistics
Matches: 73, Mismatches: 6, Indels: 22
0.72 0.06 0.22
Matches are distributed among these distances:
15 2 0.03
16 8 0.11
17 1 0.01
19 6 0.08
20 20 0.27
21 3 0.04
22 31 0.42
23 2 0.03
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (22 bp):
AATTTCATAGTGTGGTTACCAA
Found at i:47550 original size:20 final size:20
Alignment explanation
Indices: 47525--47565 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
47515 ATTATTTCAT
47525 AGTGTGGTTACCAAAATTTC
1 AGTGTGGTTACCAAAATTTC
47545 AGTGTGGTTACCAAAATTTC
1 AGTGTGGTTACCAAAATTTC
47565 A
1 A
47566 TAGGATCAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.34
Consensus pattern (20 bp):
AGTGTGGTTACCAAAATTTC
Found at i:47802 original size:22 final size:23
Alignment explanation
Indices: 47728--47859 Score: 121
Period size: 22 Copynumber: 5.9 Consensus size: 23
47718 TATCAAAATT
* *
47728 TGATTATCGAAATTTCATAGAGA
1 TGATTATCAAAATTTCATAGTGA
47751 TCAGATTATCAAAATTT-ATAG-GA
1 T--GATTATCAAAATTTCATAGTGA
* *
47774 AGATTATCAAAATTTCATAGTGT
1 TGATTATCAAAATTTCATAGTGA
* *
47797 TG-TTATCAAAATTTCAAAGCGA
1 TGATTATCAAAATTTCATAGTGA
* * *
47819 -GGTTATCAAAATTACATAATG-
1 TGATTATCAAAATTTCATAGTGA
*
47840 TGATTATCAGAATTTCATAG
1 TGATTATCAAAATTTCATAG
47860 AAGGGTCAAC
Statistics
Matches: 88, Mismatches: 15, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
21 15 0.17
22 51 0.58
23 5 0.06
24 4 0.05
25 13 0.15
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (23 bp):
TGATTATCAAAATTTCATAGTGA
Found at i:47922 original size:22 final size:21
Alignment explanation
Indices: 47798--47919 Score: 95
Period size: 22 Copynumber: 5.6 Consensus size: 21
47788 TCATAGTGTT
*
47798 GTTATCAAAATTTCA-AAGCGAG
1 GTTATC-AAATTTCATAA-AGAG
* * *
47820 GTTATCAAAATTACATAATGTG
1 GTTATC-AAATTTCATAAAGAG
*
47842 ATTATCAGAATTTCATAGAAG-G
1 GTTATCA-AATTTCATA-AAGAG
* * *
47864 GTCAACGAAATTTTATAAAGAG
1 GTTATC-AAATTTCATAAAGAG
47886 GTTATCGAAATTTCATAAAGAG
1 GTTATC-AAATTTCATAAAGAG
47908 GTTATCAAATTT
1 GTTATCAAATTT
47920 TCAAAATGTG
Statistics
Matches: 82, Mismatches: 13, Indels: 11
0.77 0.12 0.10
Matches are distributed among these distances:
21 10 0.12
22 67 0.82
23 5 0.06
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (21 bp):
GTTATCAAATTTCATAAAGAG
Found at i:48096 original size:22 final size:22
Alignment explanation
Indices: 48071--48300 Score: 71
Period size: 22 Copynumber: 10.6 Consensus size: 22
48061 AGTTTCGTTT
48071 TCAAAATTTCATAAGAGGGTTA
1 TCAAAATTTCATAAGAGGGTTA
* *
48093 TCAAAATTTCAT-AGTA-TGTAGA
1 TCAAAATTTCATAAG-AGGGT-TA
48115 TCAAAATTTCAT-AG-GGAGATTA
1 TCAAAATTTCATAAGAGG-G-TTA
* * *
48137 ACAAAATCTCA-AAAATGAGGTTA
1 TCAAAATTTCATAAGA-G-GGTTA
* *
48160 TCAAAAAATT-AT-AGGGAGGTTA
1 TC-AAAATTTCATAAGAG-GGTTA
48182 TCAAAA--TC-T--GTA--GTTA
1 TCAAAATTTCATAAG-AGGGTTA
* **
48198 TCAAGATTTCATAAGAAAGTTA
1 TCAAAATTTCATAAGAGGGTTA
48220 TCAAAA-TTCTATAAG-GAGGTCTA
1 TCAAAATTTC-ATAAGAG-GGT-TA
* * ***
48243 TCAAAATTTTATAGGAAAATTTA
1 TCAAAATTTCATAAG-AGGGTTA
48266 TCAAAATTTCATAACGA-GGTTA
1 TCAAAATTTCATAA-GAGGGTTA
*
48288 TCACAATTTCATA
1 TCAAAATTTCATA
48301 CACTTGTAGT
Statistics
Matches: 154, Mismatches: 27, Indels: 54
0.66 0.11 0.23
Matches are distributed among these distances:
16 9 0.06
18 3 0.02
19 3 0.02
20 1 0.01
21 12 0.08
22 80 0.52
23 34 0.22
24 11 0.07
25 1 0.01
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.32
Consensus pattern (22 bp):
TCAAAATTTCATAAGAGGGTTA
Found at i:48142 original size:44 final size:44
Alignment explanation
Indices: 48028--48143 Score: 118
Period size: 44 Copynumber: 2.7 Consensus size: 44
48018 TTATGGAGTA
* *
48028 ATCAAAATTTC--AGGGAAGA-TATCAAAATTTCATAGTTTCGTT
1 ATCAAAATTTCATAGGG-AGATTATCAAAATTTCATAGTATCGTG
*
48070 TTCAAAATTTCATAAGAGG-G-TTATCAAAATTTCATAGTAT-GTAG
1 ATCAAAATTTCAT-AG-GGAGATTATCAAAATTTCATAGTATCGT-G
*
48114 ATCAAAATTTCATAGGGAGATTAACAAAAT
1 ATCAAAATTTCATAGGGAGATTATCAAAAT
48144 CTCAAAAATG
Statistics
Matches: 61, Mismatches: 5, Indels: 14
0.76 0.06 0.17
Matches are distributed among these distances:
42 12 0.20
43 5 0.08
44 40 0.66
45 2 0.03
46 2 0.03
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (44 bp):
ATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGTATCGTG
Found at i:50496 original size:40 final size:40
Alignment explanation
Indices: 50440--50528 Score: 169
Period size: 40 Copynumber: 2.2 Consensus size: 40
50430 ATTAGTTCTA
50440 TAAGATCTACCACTAATAATACACATCTTAACCTTTTGATT
1 TAAGAT-TACCACTAATAATACACATCTTAACCTTTTGATT
50481 TAAGATTACCACTAATAATACACATCTTAACCTTTTGATT
1 TAAGATTACCACTAATAATACACATCTTAACCTTTTGATT
50521 TAAGATTA
1 TAAGATTA
50529 AATTAAGATT
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 42 0.88
41 6 0.12
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (40 bp):
TAAGATTACCACTAATAATACACATCTTAACCTTTTGATT
Done.