Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007057.1 Corchorus capsularis cultivar CVL-1 contig07078, 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: 67661
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1589 original size:289 final size:291
Alignment explanation
Indices: 1069--1629 Score: 1081
Period size: 289 Copynumber: 1.9 Consensus size: 291
1059 TCAAGATTTC
1069 AATATTTTTAATATATATTTAGCAGTTGAAAATATTATGTATCAAACATATAGTTAAAAATATTA
1 AATATTTTTAATATATATTTAGCAGTTGAAAATATTATGTATCAAACATATAGTTAAAAATATTA
1134 AATTAACACCAAATTTGACATGCATAATCTATGTGATTAGAATTTAAGTTTCAACCGTCAGATTA
66 AATTAACACCAAATTTGACATGCATAATCTATGTGATTAGAATTTAAGTTTCAACCGTCAGATTA
*
1199 GCCAAATTTAAATTCTACAAAATGTATAAAAGAGCATATAGAGGGTGTAACTTACATCGGGTGTA
131 GCCAAATTTAAATTCTACAAAATGTATAAAAGAGCACATAGAGGGTGTAACTTACATCGGGTGTA
1264 AATTGATTCCTCCCTTTAGTTAAAAGTGAG-AAAAAAAATCATATAGATATATCAATTATGAATG
196 AATTGATTCCTCCCTTTAGTTAAAAGTGAGAAAAAAAAATCATATAGATATATCAATTATGAATG
1328 TGTTAAAAGTTTTCAATATTTCAATATTTTT
261 TGTTAAAAGTTTTCAATATTTCAATATTTTT
*
1359 AATATTTTTAATATATATTTAGCAGTTGAAAATATTATGTATCAAACATATAGTT-AAAATCTTA
1 AATATTTTTAATATATATTTAGCAGTTGAAAATATTATGTATCAAACATATAGTTAAAAATATTA
*
1423 AATTAACACCAAATTTGACATGCATAATCTATGTGATTAGAATTTAAGTTTCAACTGTCAGATTA
66 AATTAACACCAAATTTGACATGCATAATCTATGTGATTAGAATTTAAGTTTCAACCGTCAGATTA
1488 GCCAAATTTAAATTCTACAAAATGTATAAAAGAGCACATAGAGGGTGTAACTTACATCGGGTGTA
131 GCCAAATTTAAATTCTACAAAATGTATAAAAGAGCACATAGAGGGTGTAACTTACATCGGGTGTA
1553 AATTGATTCCTCCCTTTAGTTAAAAGTGAGAAAAAAAAATCATATAGATATATCAATTATGAATG
196 AATTGATTCCTCCCTTTAGTTAAAAGTGAGAAAAAAAAATCATATAGATATATCAATTATGAATG
1618 TGTTAAAAGTTT
261 TGTTAAAAGTTT
1630 ATTTTGACGT
Statistics
Matches: 267, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
289 166 0.62
290 101 0.38
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (291 bp):
AATATTTTTAATATATATTTAGCAGTTGAAAATATTATGTATCAAACATATAGTTAAAAATATTA
AATTAACACCAAATTTGACATGCATAATCTATGTGATTAGAATTTAAGTTTCAACCGTCAGATTA
GCCAAATTTAAATTCTACAAAATGTATAAAAGAGCACATAGAGGGTGTAACTTACATCGGGTGTA
AATTGATTCCTCCCTTTAGTTAAAAGTGAGAAAAAAAAATCATATAGATATATCAATTATGAATG
TGTTAAAAGTTTTCAATATTTCAATATTTTT
Found at i:5929 original size:13 final size:13
Alignment explanation
Indices: 5911--5937 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5901 ACCCATATTA
5911 TCTTTTCTTCTTC
1 TCTTTTCTTCTTC
5924 TCTTTTCTTCTTC
1 TCTTTTCTTCTTC
5937 T
1 T
5938 TCTTCTTCCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (13 bp):
TCTTTTCTTCTTC
Found at i:7765 original size:147 final size:147
Alignment explanation
Indices: 7498--7794 Score: 594
Period size: 147 Copynumber: 2.0 Consensus size: 147
7488 ACCGCAAGTG
7498 GATCATGAGAGCAATGGGTAGAGTAAGTTCGAGTTAGGGGTTGAACGTTGACGCCAAAAAGTAAA
1 GATCATGAGAGCAATGGGTAGAGTAAGTTCGAGTTAGGGGTTGAACGTTGACGCCAAAAAGTAAA
7563 GACCCGTCAAATAATGCAATTTGATAGTGTAATTGATCCATTAGATACTTTTTGCACCCTTAATT
66 GACCCGTCAAATAATGCAATTTGATAGTGTAATTGATCCATTAGATACTTTTTGCACCCTTAATT
7628 AGTTAATTTCCACAAGA
131 AGTTAATTTCCACAAGA
7645 GATCATGAGAGCAATGGGTAGAGTAAGTTCGAGTTAGGGGTTGAACGTTGACGCCAAAAAGTAAA
1 GATCATGAGAGCAATGGGTAGAGTAAGTTCGAGTTAGGGGTTGAACGTTGACGCCAAAAAGTAAA
7710 GACCCGTCAAATAATGCAATTTGATAGTGTAATTGATCCATTAGATACTTTTTGCACCCTTAATT
66 GACCCGTCAAATAATGCAATTTGATAGTGTAATTGATCCATTAGATACTTTTTGCACCCTTAATT
7775 AGTTAATTTCCACAAGA
131 AGTTAATTTCCACAAGA
7792 GAT
1 GAT
7795 TAATGGAGAT
Statistics
Matches: 150, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
147 150 1.00
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (147 bp):
GATCATGAGAGCAATGGGTAGAGTAAGTTCGAGTTAGGGGTTGAACGTTGACGCCAAAAAGTAAA
GACCCGTCAAATAATGCAATTTGATAGTGTAATTGATCCATTAGATACTTTTTGCACCCTTAATT
AGTTAATTTCCACAAGA
Found at i:17265 original size:3 final size:3
Alignment explanation
Indices: 17259--17295 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
17249 TTTCTTCTAC
*
17259 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
17296 ATATGAATCA
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:18485 original size:13 final size:12
Alignment explanation
Indices: 18463--18497 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 12
18453 GCTAACTCAC
18463 AAAA-AAAAAAA
1 AAAACAAAAAAA
18474 AAAACGAAAAAAA
1 AAAAC-AAAAAAA
18487 AAAACAAAAAA
1 AAAACAAAAAA
18498 CACTAGCACT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 4 0.18
12 6 0.27
13 12 0.55
ACGTcount: A:0.91, C:0.06, G:0.03, T:0.00
Consensus pattern (12 bp):
AAAACAAAAAAA
Found at i:19140 original size:17 final size:16
Alignment explanation
Indices: 19088--19136 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
19078 CACCCCATAT
*
19088 ATCACTAGTGATCTAAG
1 ATCACCAGTGATC-AAG
19105 ATCACCAGTGATGCAAG
1 ATCACCAGTGAT-CAAG
*
19122 ATCACCGGTGATCAA
1 ATCACCAGTGATCAA
19137 AGATTACATG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 3 0.10
17 25 0.86
18 1 0.03
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.22
Consensus pattern (16 bp):
ATCACCAGTGATCAAG
Found at i:20264 original size:17 final size:17
Alignment explanation
Indices: 20230--20265 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
20220 TTGTAAAATA
**
20230 AATTTTAATTTTTTTTT
1 AATTTTAATTTTGATTT
20247 AATTTTAATTTTGATTT
1 AATTTTAATTTTGATTT
20264 AA
1 AA
20266 AATAGATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (17 bp):
AATTTTAATTTTGATTT
Found at i:28911 original size:20 final size:18
Alignment explanation
Indices: 28886--28925 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
28876 TTTTGTAGTC
*
28886 CTGCCATCTTTTGCTTCCTT
1 CTGCCAT-TTTAGCTT-CTT
28906 CTGCCATTTTAGCTTCTT
1 CTGCCATTTTAGCTTCTT
28924 CT
1 CT
28926 AAAGTCTCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 7 0.37
20 7 0.37
ACGTcount: A:0.07, C:0.33, G:0.10, T:0.50
Consensus pattern (18 bp):
CTGCCATTTTAGCTTCTT
Found at i:39462 original size:9 final size:9
Alignment explanation
Indices: 39450--39509 Score: 51
Period size: 8 Copynumber: 7.2 Consensus size: 9
39440 AAAGAAGGAT
39450 AAGAG-AAA
1 AAGAGAAAA
39458 AA-AGAAAA
1 AAGAGAAAA
*
39466 AACAG-AAA
1 AAGAGAAAA
39474 AAGA-AAAA
1 AAGAGAAAA
39482 AAGA-AAAGA
1 AAGAGAAA-A
*
39491 AAG-GAATA
1 AAGAGAAAA
39499 AAGAGAAAA
1 AAGAGAAAA
39508 AA
1 AA
39510 AATAAAAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
7 2 0.05
8 27 0.63
9 14 0.33
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (9 bp):
AAGAGAAAA
Found at i:39480 original size:14 final size:14
Alignment explanation
Indices: 39456--39492 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
39446 GGATAAGAGA
39456 AAAAAGAAAAAACAG
1 AAAAAGAAAAAA-AG
39471 AAAAAGAAAAAAAG
1 AAAAAGAAAAAAAG
39485 -AAAAGAAA
1 AAAAAGAAA
39493 GGAATAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 8 0.36
14 2 0.09
15 12 0.55
ACGTcount: A:0.84, C:0.03, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAAAG
Found at i:40439 original size:117 final size:120
Alignment explanation
Indices: 40264--40494 Score: 353
Period size: 117 Copynumber: 1.9 Consensus size: 120
40254 CGTTTTCTAC
* *
40264 TTTGATAATTCTTTTTTTTTCGTTTAAGATATTTTTTTAAAAAAAATCTAAAATATCCTCCTCAT
1 TTTGACAATTCTTTTTTTATCGTTTAAGATATTTTTTT-AAAAAAATCTAAAATATCCTCCTCAT
40329 TTTTTAATATGTGTGTTAGAGAAAATAATAATAAATCAACTAAAAAAATGTGTGTTT
65 TTTTTAATATGTGTGTTAGAGAAAA-AATAATAAATCAACTAAAAAAATGTGTGTTT
** * *
40386 TTTGACAATTC-TTTTTTAT-GTTTAAGAT-TTTTTTT-TCAAAATCTGAAATATCCTCGTCATT
1 TTTGACAATTCTTTTTTTATCGTTTAAGATATTTTTTTAAAAAAATCTAAAATATCCTCCTCATT
*
40447 TTTTAATATGTGTGTTAGAGAAAAAATAATAAATCAAGTAAAAAAATG
66 TTTTAATATGTGTGTTAGAGAAAAAATAATAAATCAACTAAAAAAATG
40495 CAGTTGATAT
Statistics
Matches: 102, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
116 23 0.23
117 46 0.45
119 7 0.07
120 9 0.09
121 7 0.07
122 10 0.10
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (120 bp):
TTTGACAATTCTTTTTTTATCGTTTAAGATATTTTTTTAAAAAAATCTAAAATATCCTCCTCATT
TTTTAATATGTGTGTTAGAGAAAAAATAATAAATCAACTAAAAAAATGTGTGTTT
Found at i:42768 original size:2 final size:2
Alignment explanation
Indices: 42761--42785 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
42751 GATCATCTTA
42761 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
42786 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:43031 original size:24 final size:22
Alignment explanation
Indices: 42988--43033 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
42978 TGATAACAAA
* *
42988 ATGTCATTATATTTTGTTTCTT
1 ATGTCATTATATTATATTTCTT
43010 ATGTCAATTACTATTATATTTCTT
1 ATGTC-ATTA-TATTATATTTCTT
43034 TGTGCAAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.25
23 4 0.20
24 11 0.55
ACGTcount: A:0.24, C:0.11, G:0.07, T:0.59
Consensus pattern (22 bp):
ATGTCATTATATTATATTTCTT
Found at i:45395 original size:24 final size:24
Alignment explanation
Indices: 45368--45423 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
45358 AAGAAAAGTA
45368 AGAAGAAGAGCAAT-AAGGCTGAAG
1 AGAAGAAGAGCAATGAA-GCTGAAG
* *
45392 AGAACAAGAGCAGTGAAGCTGAAG
1 AGAAGAAGAGCAATGAAGCTGAAG
45416 AGAAGAAG
1 AGAAGAAG
45424 GCGGTGGACC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 26 0.93
25 2 0.07
ACGTcount: A:0.50, C:0.09, G:0.34, T:0.07
Consensus pattern (24 bp):
AGAAGAAGAGCAATGAAGCTGAAG
Found at i:45461 original size:60 final size:60
Alignment explanation
Indices: 45392--45619 Score: 330
Period size: 60 Copynumber: 3.8 Consensus size: 60
45382 AAGGCTGAAG
* * * * *
45392 AGAACAAGAGCAGTGAAGCTGAAGAGAAGAAGGCGGTGGACCAAATTGAGGAGAAAAGCA
1 AGAAGAAGAGCAATAAAGCTGAAGAGAACAAGGCTGTGGACCAAATTGAGGAGAAAAGCA
* * *
45452 AGAAGAAGAGCAATGAAGCTGAAGGGAACAAGGCTGTGGACCAATTTGAGGAGAAAAGCA
1 AGAAGAAGAGCAATAAAGCTGAAGAGAACAAGGCTGTGGACCAAATTGAGGAGAAAAGCA
* * **
45512 AGAAGAAGAGCAATAAAGCTGAAGGGAACAAGGCTGTGGACCAGATTGACAAGAAAAGCA
1 AGAAGAAGAGCAATAAAGCTGAAGAGAACAAGGCTGTGGACCAAATTGAGGAGAAAAGCA
* *
45572 AGAAGAAGAGCAAAAAAGCTGAAGAGCACAAGGCTGTGGACCAAATTG
1 AGAAGAAGAGCAATAAAGCTGAAGAGAACAAGGCTGTGGACCAAATTG
45620 TGGACAAGAA
Statistics
Matches: 153, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 153 1.00
ACGTcount: A:0.45, C:0.13, G:0.32, T:0.10
Consensus pattern (60 bp):
AGAAGAAGAGCAATAAAGCTGAAGAGAACAAGGCTGTGGACCAAATTGAGGAGAAAAGCA
Found at i:58088 original size:2 final size:2
Alignment explanation
Indices: 58083--58113 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
58073 TGTGTGTGTG
58083 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
58114 TGTACATAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:63855 original size:2 final size:2
Alignment explanation
Indices: 63848--63898 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
63838 AAGTAATTTC
63848 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
63890 GA GA GA GA G
1 GA GA GA GA G
63899 TTTCAACAGG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:64690 original size:14 final size:14
Alignment explanation
Indices: 64673--64703 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
64663 AACCACAAAT
*
64673 GAAAAGAACAGAAA
1 GAAAAGAAAAGAAA
64687 GAAAAGAAAAGAAA
1 GAAAAGAAAAGAAA
64701 GAA
1 GAA
64704 CCTCAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.74, C:0.03, G:0.23, T:0.00
Consensus pattern (14 bp):
GAAAAGAAAAGAAA
Done.