Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008443.1 Corchorus capsularis cultivar CVL-1 contig08464, 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: 35495
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:397 original size:2 final size:2
Alignment explanation
Indices: 390--417 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
380 AGCATGCAAC
390 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
418 TATTAGAGTA
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:2032 original size:25 final size:27
Alignment explanation
Indices: 1980--2032 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
1970 TTACTCAACT
**
1980 AAAAACTCTATTTTTATTTTTCTGTAA
1 AAAAACTCTATTTTTATTTTAATGTAA
2007 AAAAACTCTATTTTTA-TTTAAT-TAA
1 AAAAACTCTATTTTTATTTTAATGTAA
2032 A
1 A
2033 TCTAATATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 4 0.17
27 16 0.67
ACGTcount: A:0.40, C:0.09, G:0.02, T:0.49
Consensus pattern (27 bp):
AAAAACTCTATTTTTATTTTAATGTAA
Found at i:4305 original size:386 final size:384
Alignment explanation
Indices: 3594--4364 Score: 1400
Period size: 386 Copynumber: 2.0 Consensus size: 384
3584 TATTAAATAG
3594 ACCGACAATCGAAACCGCCAAATTTGAGAAGCATTTTTTTTAATTGAAACATAAAAATTGACTTT
1 ACCGACAATCGAAACCGCCAAATTTGAGAAGCATTTTTTTTAATTGAAACATAAAAATTGACTTT
3659 TGAGTCATTAATGAAAGTTGTAAATCATGAAATTATCTTTTAATAGACACCTTAATCGGACAAAT
66 TGAGTCATTAATGAAAGTTGTAAATCATGAAATTATCTTTTAATAGACACCTTAATCGGACAAAT
* *
3724 ATAACAAAAAAAATCTGAAACGTTAAATCGATTAAGATAGAATTAGTAAATGACTAAGTAGTATA
131 ATAACAAAAAAAATCTAAAACGTTAAATCGATTAAGATAGAATTAGTAAAGGACTAAGTAGTATA
* *
3789 AAATACTAAAATATGAGAATCATTTGAAAAATAATCCAAATAAGAAAATATTTGTTGATGGAGAT
196 AAATACTAAAATATGAGAATCATTTGAAAAATAATCCAAATAAGAAAATAATTGTTAATGGAGAT
3854 CTTACAACATAAAAACTCCCTTTTGAGCCCTTCATGAAACTCGTAAATCAAATTTAGCATTCGGG
261 CTTACAACATAAAAACTCCCTTTTGAGCCCTTCATGAAACTCGTAAATCAAATTTAGCATTCGGG
* *
3919 TCCTTCATGAAAGATGTAGATCATGCAATAATCTTCTAACTGACACTTTAATAACTTTA
326 TCCTTCATAAAAGACGTAGATCATGCAATAATCTTCTAACTGACACTTTAATAACTTTA
* *
3978 ACCGACAATTGAAACCGTCAAATTTGAGAAGCATTTTTTTTAATTGAAACATAAAAATTGACTTT
1 ACCGACAATCGAAACCGCCAAATTTGAGAAGCATTTTTTTTAATTGAAACATAAAAATTGACTTT
* *
4043 TGAGTCATTAATGAAAGTTGTAGATCATGAAATTATCTTTTAATAGATACCTTAATCGGACAAAT
66 TGAGTCATTAATGAAAGTTGTAAATCATGAAATTATCTTTTAATAGACACCTTAATCGGACAAAT
4108 ATAACCAAAAAAAAATCTAAAACGTTAAATCGATTAAGATAGAATTAGTAAAGGACTAAGTAGTA
131 ATAA-C-AAAAAAAATCTAAAACGTTAAATCGATTAAGATAGAATTAGTAAAGGACTAAGTAGTA
* *
4173 TAAAATACTAAACTATGAGGATCATTTGAAAAATAATCCAAATAAGAAAATAATTGTTAATGGAG
194 TAAAATACTAAAATATGAGAATCATTTGAAAAATAATCCAAATAAGAAAATAATTGTTAATGGAG
4238 ATCTTACAACATAAAAACTCCCTTTTGAGCCCCTT-ATGAAACTCGTAAATCAAATTTAGCATTC
259 ATCTTACAACATAAAAACTCCCTTTTGAG-CCCTTCATGAAACTCGTAAATCAAATTTAGCATTC
4302 GGGTCCTTCATAAAAGACGTAGATCATGCAATAATCTTCTAACTGACACTTTAATAACTTTA
323 GGGTCCTTCATAAAAGACGTAGATCATGCAATAATCTTCTAACTGACACTTTAATAACTTTA
4364 A
1 A
4365 TCGGACATAT
Statistics
Matches: 372, Mismatches: 12, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
384 130 0.35
385 1 0.00
386 236 0.63
387 5 0.01
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.31
Consensus pattern (384 bp):
ACCGACAATCGAAACCGCCAAATTTGAGAAGCATTTTTTTTAATTGAAACATAAAAATTGACTTT
TGAGTCATTAATGAAAGTTGTAAATCATGAAATTATCTTTTAATAGACACCTTAATCGGACAAAT
ATAACAAAAAAAATCTAAAACGTTAAATCGATTAAGATAGAATTAGTAAAGGACTAAGTAGTATA
AAATACTAAAATATGAGAATCATTTGAAAAATAATCCAAATAAGAAAATAATTGTTAATGGAGAT
CTTACAACATAAAAACTCCCTTTTGAGCCCTTCATGAAACTCGTAAATCAAATTTAGCATTCGGG
TCCTTCATAAAAGACGTAGATCATGCAATAATCTTCTAACTGACACTTTAATAACTTTA
Found at i:5439 original size:180 final size:180
Alignment explanation
Indices: 5133--5465 Score: 621
Period size: 180 Copynumber: 1.9 Consensus size: 180
5123 GACTATCAAG
*
5133 GACAAATGATGCTTTCTACACTTACTCATCTTTTTGGGTTTTTTGTGTGTGAGAAATCTATACTC
1 GACAAATGATGCTTTCTACACTTACTCATCTTTTTGGGTTTTTTGTATGTGAGAAATCTATACTC
*
5198 ATCTAACTCTATTAATAGTATGAAAATGACTAATCGGTTACTGGGTCTAAAATTTTAAATTCATT
66 ATCTAACTCTATTAATAGTATGAAAATGACTAATCGGTTACTGGGTCTAAAATTCTAAATTCATT
5263 GAGCCCAAATATGGTATGATGTGTCTGTGCATGTGTGTGTTTGTGTGTGT
131 GAGCCCAAATATGGTATGATGTGTCTGTGCATGTGTGTGTTTGTGTGTGT
*
5313 GACAAATGATTCTTTCTACACTTACTCATCTTTTTGGGTTTTTTGTATGTGAGAAATCTATACTC
1 GACAAATGATGCTTTCTACACTTACTCATCTTTTTGGGTTTTTTGTATGTGAGAAATCTATACTC
* *
5378 ATCTAACTCTATTAGTAGTGTGAAAATGACTAATCGGTTACTGGGTCTAAAATTCTAAATTCATT
66 ATCTAACTCTATTAATAGTATGAAAATGACTAATCGGTTACTGGGTCTAAAATTCTAAATTCATT
5443 GAGCCCAAATATGGTATGATGTG
131 GAGCCCAAATATGGTATGATGTG
5466 AACAACCGAA
Statistics
Matches: 148, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
180 148 1.00
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.40
Consensus pattern (180 bp):
GACAAATGATGCTTTCTACACTTACTCATCTTTTTGGGTTTTTTGTATGTGAGAAATCTATACTC
ATCTAACTCTATTAATAGTATGAAAATGACTAATCGGTTACTGGGTCTAAAATTCTAAATTCATT
GAGCCCAAATATGGTATGATGTGTCTGTGCATGTGTGTGTTTGTGTGTGT
Found at i:6178 original size:2 final size:2
Alignment explanation
Indices: 6171--6236 Score: 64
Period size: 2 Copynumber: 34.0 Consensus size: 2
6161 AAGGACTTTA
* * *
6171 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT GT GT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
6212 GT GT GT AT -T AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
6237 GTATGTATGT
Statistics
Matches: 60, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
1 2 0.03
2 58 0.97
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (2 bp):
AT
Found at i:6241 original size:4 final size:4
Alignment explanation
Indices: 6234--6268 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
6224 TATATATATA
6234 TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TAT
6269 AAGTATGAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:8880 original size:27 final size:27
Alignment explanation
Indices: 8850--8905 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
8840 GGATTGGGCT
*
8850 AATTGCTCAAGTAGCGGGATCTGAAGA
1 AATTGCTCAAGTAACGGGATCTGAAGA
8877 AATTGCTCAAGTAACGGGATCTGAAGA
1 AATTGCTCAAGTAACGGGATCTGAAGA
8904 AA
1 AA
8906 ATCTGATTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.38, C:0.14, G:0.27, T:0.21
Consensus pattern (27 bp):
AATTGCTCAAGTAACGGGATCTGAAGA
Found at i:10730 original size:13 final size:15
Alignment explanation
Indices: 10702--10733 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
10692 AATTTCATTC
10702 CTTTTGTATCTATTT
1 CTTTTGTATCTATTT
10717 CTTTTGT-T-TATTT
1 CTTTTGTATCTATTT
10730 CTTT
1 CTTT
10734 CCTTTAGGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.53
14 1 0.06
15 7 0.41
ACGTcount: A:0.09, C:0.12, G:0.06, T:0.72
Consensus pattern (15 bp):
CTTTTGTATCTATTT
Found at i:12841 original size:19 final size:20
Alignment explanation
Indices: 12795--12842 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
12785 TGTGGCACAC
*
12795 CACATGTACCAAAAAGTCATGC
1 CACATGTACCAAAAAG--ATGA
12817 CACATGTACCAAAAAG-TGA
1 CACATGTACCAAAAAGATGA
12836 CACATGT
1 CACATGT
12843 CACGCCACGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 9 0.36
22 16 0.64
ACGTcount: A:0.42, C:0.25, G:0.15, T:0.19
Consensus pattern (20 bp):
CACATGTACCAAAAAGATGA
Found at i:12859 original size:53 final size:53
Alignment explanation
Indices: 12762--12864 Score: 143
Period size: 53 Copynumber: 1.9 Consensus size: 53
12752 GACGTGGCAC
* ** *
12762 GCCACGTGTACCAAAAAGTGACATGTGGCACACCACATGTACCAAAAAGTCAT
1 GCCACATGTACCAAAAAGTGACACATGGCACACCACATGCACCAAAAAGTCAT
* * *
12815 GCCACATGTACCAAAAAGTGACACATGTCACGCCACGTGCACCAAAAAGT
1 GCCACATGTACCAAAAAGTGACACATGGCACACCACATGCACCAAAAAGT
12865 GACACGTTGC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
53 43 1.00
ACGTcount: A:0.38, C:0.28, G:0.18, T:0.16
Consensus pattern (53 bp):
GCCACATGTACCAAAAAGTGACACATGGCACACCACATGCACCAAAAAGTCAT
Found at i:12881 original size:31 final size:31
Alignment explanation
Indices: 12812--12911 Score: 94
Period size: 31 Copynumber: 3.2 Consensus size: 31
12802 ACCAAAAAGT
* *
12812 CATGCCACATGTACCAAAAAGTGACAC-ATG
1 CATGCCACATGCACCAAAAAGTGACACGTTG
* *
12842 TCACGCCACGTGCACCAAAAAGTGACACGTTG
1 -CATGCCACATGCACCAAAAAGTGACACGTTG
*** * * *
12874 CATGCCACATGTTTCAAAAAATGGCACGTGG
1 CATGCCACATGCACCAAAAAGTGACACGTTG
12905 CATGCCA
1 CATGCCA
12912 TGTGCACAAA
Statistics
Matches: 56, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
31 54 0.96
32 2 0.04
ACGTcount: A:0.34, C:0.28, G:0.20, T:0.18
Consensus pattern (31 bp):
CATGCCACATGCACCAAAAAGTGACACGTTG
Found at i:20547 original size:2 final size:2
Alignment explanation
Indices: 20540--20572 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
20530 TTTGCTTCGT
*
20540 TA TA TA TA CA 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 TA T
20573 TTCTTCACGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:23384 original size:45 final size:45
Alignment explanation
Indices: 23334--23426 Score: 186
Period size: 45 Copynumber: 2.1 Consensus size: 45
23324 AATGATTAGC
23334 TTGAGCATTTTCCTTTTCCTTTTTCCCTTTAACAACATCAATACG
1 TTGAGCATTTTCCTTTTCCTTTTTCCCTTTAACAACATCAATACG
23379 TTGAGCATTTTCCTTTTCCTTTTTCCCTTTAACAACATCAATACG
1 TTGAGCATTTTCCTTTTCCTTTTTCCCTTTAACAACATCAATACG
23424 TTG
1 TTG
23427 TGTATATATA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.22, C:0.26, G:0.08, T:0.45
Consensus pattern (45 bp):
TTGAGCATTTTCCTTTTCCTTTTTCCCTTTAACAACATCAATACG
Found at i:24548 original size:33 final size:33
Alignment explanation
Indices: 24502--24567 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
24492 CATTATACCC
*
24502 TTATTTTTTAAACATATTTCTTAAATGACATTG
1 TTATTTTTCAAACATATTTCTTAAATGACATTG
24535 TTATTTTTCAAACATATTTCTTAAATGACATTG
1 TTATTTTTCAAACATATTTCTTAAATGACATTG
24568 CTTAACTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.33, C:0.11, G:0.06, T:0.50
Consensus pattern (33 bp):
TTATTTTTCAAACATATTTCTTAAATGACATTG
Done.