Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009987.1 Corchorus capsularis cultivar CVL-1 contig10008, 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: 20165
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:4957 original size:2 final size:2
Alignment explanation
Indices: 4952--4986 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
4942 GCATTACAAC
4952 AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
4987 TATTTTTGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5020 original size:43 final size:43
Alignment explanation
Indices: 4972--5057 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
4962 ATATATATAT
*
4972 ATATATACTATATATTATTTTTGTCCCCTATGGAATTTACTAA
1 ATATATACTATATATTATTTTTGTCCCCTATGAAATTTACTAA
5015 ATATATACTATATATTATTTTTGTCCCCTATGAAATTTACTAA
1 ATATATACTATATATTATTTTTGTCCCCTATGAAATTTACTAA
5058 CAAGCCCTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.34, C:0.14, G:0.06, T:0.47
Consensus pattern (43 bp):
ATATATACTATATATTATTTTTGTCCCCTATGAAATTTACTAA
Found at i:5184 original size:11 final size:11
Alignment explanation
Indices: 5168--5211 Score: 61
Period size: 11 Copynumber: 4.0 Consensus size: 11
5158 TATACTATAT
*
5168 CTAATTAATAG
1 CTAATTAATAA
*
5179 CTAATTAATAT
1 CTAATTAATAA
5190 CTAATTAATAA
1 CTAATTAATAA
*
5201 TTAATTAATAA
1 CTAATTAATAA
5212 TGAATAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (11 bp):
CTAATTAATAA
Found at i:5189 original size:22 final size:22
Alignment explanation
Indices: 5164--5210 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
5154 CCATTATACT
*
5164 ATATCTAATTAATAGCTAATTA
1 ATATCTAATTAATAACTAATTA
*
5186 ATATCTAATTAATAATTAATTA
1 ATATCTAATTAATAACTAATTA
5208 ATA
1 ATA
5211 ATGAATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (22 bp):
ATATCTAATTAATAACTAATTA
Found at i:6404 original size:16 final size:16
Alignment explanation
Indices: 6392--6470 Score: 90
Period size: 16 Copynumber: 5.0 Consensus size: 16
6382 TTTTCGGCTT
6392 ATTCGGGTTTCGGGTC
1 ATTCGGGTTTCGGGTC
*
6408 A-TCTGGGTTT-GGGTT
1 ATTC-GGGTTTCGGGTC
* *
6423 ATTCGGATTTTGGGTC
1 ATTCGGGTTTCGGGTC
*
6439 ATTCGGGTCTCGGGTC
1 ATTCGGGTTTCGGGTC
*
6455 ATTCGGGTTTCAGGTC
1 ATTCGGGTTTCGGGTC
6471 TACCGAGTCT
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
15 12 0.23
16 40 0.77
ACGTcount: A:0.09, C:0.16, G:0.35, T:0.39
Consensus pattern (16 bp):
ATTCGGGTTTCGGGTC
Found at i:6426 original size:31 final size:32
Alignment explanation
Indices: 6385--6470 Score: 95
Period size: 31 Copynumber: 2.7 Consensus size: 32
6375 GATTGTTTTT
*
6385 TCGGCTTATTCGGGTTTCGGGTCA-TCTGGGT-
1 TCGGGTTATTCGGGTTTCGGGTCATTC-GGGTC
* * *
6416 TTGGGTTATTCGGATTTTGGGTCATTCGGGTC
1 TCGGGTTATTCGGGTTTCGGGTCATTCGGGTC
* *
6448 TCGGGTCATTCGGGTTTCAGGTC
1 TCGGGTTATTCGGGTTTCGGGTC
6471 TACCGAGTCT
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
31 24 0.55
32 20 0.45
ACGTcount: A:0.08, C:0.17, G:0.35, T:0.40
Consensus pattern (32 bp):
TCGGGTTATTCGGGTTTCGGGTCATTCGGGTC
Found at i:6759 original size:41 final size:41
Alignment explanation
Indices: 6712--6791 Score: 133
Period size: 41 Copynumber: 2.0 Consensus size: 41
6702 AGATATTAAT
* *
6712 TTTGAATATTAAATACATAATTGATTATCAGGTGAGGTAGG
1 TTTGAATATTAAATAAATAATTAATTATCAGGTGAGGTAGG
*
6753 TTTGAATATTAAATAAATAATTAATTATCAGGTGGGGTA
1 TTTGAATATTAAATAAATAATTAATTATCAGGTGAGGTA
6792 TGTGTCAACA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.39, C:0.04, G:0.20, T:0.38
Consensus pattern (41 bp):
TTTGAATATTAAATAAATAATTAATTATCAGGTGAGGTAGG
Found at i:7367 original size:32 final size:32
Alignment explanation
Indices: 7327--7418 Score: 114
Period size: 32 Copynumber: 2.9 Consensus size: 32
7317 TCGGGTCACA
* * *
7327 GGTCATTCGGGTTTCGGTTTATCTGGGTTACG
1 GGTCATTCGGGTCTCGGGTCATCTGGGTTACG
* * *
7359 GGTTATTCGGGTCTCGGGTCATTTGGGTTACT
1 GGTCATTCGGGTCTCGGGTCATCTGGGTTACG
7391 GGTCATTCGGGTCTCGGGTTCATC-GGGT
1 GGTCATTCGGGTCTCGGG-TCATCTGGGT
7419 GCCGTGTCGG
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
32 47 0.92
33 4 0.08
ACGTcount: A:0.09, C:0.17, G:0.36, T:0.38
Consensus pattern (32 bp):
GGTCATTCGGGTCTCGGGTCATCTGGGTTACG
Found at i:7370 original size:16 final size:16
Alignment explanation
Indices: 7317--7402 Score: 68
Period size: 16 Copynumber: 5.4 Consensus size: 16
7307 CATATGGGTC
* *
7317 TCGGGTCACAGGTCAT
1 TCGGGTTACGGGTCAT
* * *
7333 TCGGGTTTCGGTTTA-
1 TCGGGTTACGGGTCAT
*
7348 TCTGGGTTACGGGTTAT
1 TC-GGGTTACGGGTCAT
7365 TCGGGTCT-CGGGTCAT
1 TCGGGT-TACGGGTCAT
* *
7381 TTGGGTTACTGGTCAT
1 TCGGGTTACGGGTCAT
7397 TCGGGT
1 TCGGGT
7403 CTCGGGTTCA
Statistics
Matches: 55, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
15 3 0.05
16 49 0.89
17 3 0.05
ACGTcount: A:0.10, C:0.17, G:0.35, T:0.37
Consensus pattern (16 bp):
TCGGGTTACGGGTCAT
Found at i:8348 original size:16 final size:16
Alignment explanation
Indices: 8329--8380 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
8319 GTCAGGTTCG
8329 GGTTAAATTTGGGTCA
1 GGTTAAATTTGGGTCA
* * * *
8345 GGTT-TATTCAGGTTCG
1 GGTTAAATT-TGGGTCA
8361 GGTTAAATTTGGGTCA
1 GGTTAAATTTGGGTCA
8377 GGTT
1 GGTT
8381 GATACGGGTT
Statistics
Matches: 26, Mismatches: 8, Indels: 4
0.68 0.21 0.11
Matches are distributed among these distances:
15 3 0.12
16 20 0.77
17 3 0.12
ACGTcount: A:0.19, C:0.08, G:0.33, T:0.40
Consensus pattern (16 bp):
GGTTAAATTTGGGTCA
Found at i:8359 original size:32 final size:32
Alignment explanation
Indices: 8315--8428 Score: 138
Period size: 32 Copynumber: 3.6 Consensus size: 32
8305 GGGTTCGGGC
*
8315 TTAAGTCAGGTTCGGGTTAAATTTGGGTCAGG
1 TTAATTCAGGTTCGGGTTAAATTTGGGTCAGG
*
8347 TTTATTCAGGTTCGGGTTAAATTTGGGTCAGG
1 TTAATTCAGGTTCGGGTTAAATTTGGGTCAGG
* * * * * *
8379 TTGATACGGGTTCGAGTCAATTTTGGGTCAGG
1 TTAATTCAGGTTCGGGTTAAATTTGGGTCAGG
* *
8411 TTAATTCGGGATCGGGTT
1 TTAATTCAGGTTCGGGTT
8429 CGGGCTGGGT
Statistics
Matches: 69, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 69 1.00
ACGTcount: A:0.19, C:0.11, G:0.33, T:0.37
Consensus pattern (32 bp):
TTAATTCAGGTTCGGGTTAAATTTGGGTCAGG
Found at i:8594 original size:20 final size:20
Alignment explanation
Indices: 8569--8607 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
8559 TATAGATGAA
*
8569 ATTTTCAAAAATTATTATTT
1 ATTTTCAAAAATTAGTATTT
*
8589 ATTTTCAAATATTAGTATT
1 ATTTTCAAAAATTAGTATT
8608 GAATTCGGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (20 bp):
ATTTTCAAAAATTAGTATTT
Found at i:8646 original size:10 final size:10
Alignment explanation
Indices: 8611--8651 Score: 55
Period size: 10 Copynumber: 3.9 Consensus size: 10
8601 TAGTATTGAA
8611 TTCGGGTTTT
1 TTCGGGTTTT
*
8621 TTCAGGTTTAT
1 TTCGGGTTT-T
8632 GTTCGGGTTTT
1 -TTCGGGTTTT
8643 TTCGGGTTT
1 TTCGGGTTT
8652 CAAATTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 17 0.63
11 2 0.07
12 8 0.30
ACGTcount: A:0.05, C:0.10, G:0.29, T:0.56
Consensus pattern (10 bp):
TTCGGGTTTT
Found at i:11784 original size:11 final size:10
Alignment explanation
Indices: 11766--11799 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
11756 AAAGTTCGTG
11766 TTTTGAAGAT
1 TTTTGAAGAT
11776 TTCTTGAAGAT
1 TT-TTGAAGAT
11787 ATTTTGAAGAT
1 -TTTTGAAGAT
11798 TT
1 TT
11800 GAAGAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50
Consensus pattern (10 bp):
TTTTGAAGAT
Found at i:13626 original size:37 final size:34
Alignment explanation
Indices: 13555--13628 Score: 85
Period size: 37 Copynumber: 2.1 Consensus size: 34
13545 GCGACGATAA
* *
13555 AAAATAAAAAATTTTCTTTTCCGTTTTTCCTTTT
1 AAAATAAAAAATTTTATTTTCCGTTTTGCCTTTT
* *
13589 AAAATAAAAAATATTTTTATTTTCTGTTTTGCTTTTT
1 AAAAT-AAAAA-A-TTTTATTTTCCGTTTTGCCTTTT
13626 AAA
1 AAA
13629 TTTTTTATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
34 5 0.15
35 5 0.15
36 1 0.03
37 22 0.67
ACGTcount: A:0.34, C:0.09, G:0.04, T:0.53
Consensus pattern (34 bp):
AAAATAAAAAATTTTATTTTCCGTTTTGCCTTTT
Found at i:19979 original size:375 final size:374
Alignment explanation
Indices: 19290--20038 Score: 1399
Period size: 375 Copynumber: 2.0 Consensus size: 374
19280 CCGAGCTCTA
* * * *
19290 CAACTTTTCTTTGAAGTGCAAAGCCCAGATCTGCCATTTTCAAGCCCGAATCTCAAGTCGAAGTT
1 CAACTTTCCCTTGAAGTGCAAAGCCCAGATCTGCCATCTTCAAGCCCGAATCTCAAGTCCAAGTT
*
19355 TCTGTAGAAATCTAGAAAATTCCAGGATCCTATTTTGACTTGGATTCTACTCTAGGAAGACATCT
66 TCTGTAGAAATCCAGAAAATTCCAGGATCCTATTTTGACTTGGATTCTACTCTAGGAAGACATCT
*
19420 AATCCAACTGGGAGTCTAGTCAAGGCTAAACCGTTCTACCCCTATTTCTCCACTATAAATAGCCA
131 AATCCAACTGGGAGTCTAGTCAAGGCTAAACCGTCCTACCCCTATTTCTCCACTATAAATAGCCA
19485 CCTCCTGTATCACAAATCACATACTACACAATTTTTCTCTCATATACTTTTATTCTCTTTTTCTA
196 CCTCCTGTATCACAAATCACATACTACACAATTTTTCTCTCATATACTTTTATTCTCTTTTTCTA
*
19550 CCTTTCTTTAGTTTAGGTTTTTCTCTAGTTTTAGAAGGGGGAAGTCGACACCCTCTTTAGCCATA
261 CCTTTCTTTAGTTTAGGTTTTTCTCTAGTTTTAGAAGGGGGAAGTCGACACCCTCTCTAGCCATA
19615 GAGGGGTGCAACAACCCTAGGTTTTCAAGGAGGAGAAATCGTTCCTCCC
326 GAGGGGTGCAACAACCCTAGGTTTTCAAGGAGGAGAAATCGTTCCTCCC
*
19664 CAACTTTCCCTTGAAGTGCAAAGCCCAGATTTGCCATCTTCAAGCCCGAATCTCAAGTCCAAGTT
1 CAACTTTCCCTTGAAGTGCAAAGCCCAGATCTGCCATCTTCAAGCCCGAATCTCAAGTCCAAGTT
19729 TCTGTAGAAATCCAGAAAATTCCAGGATCCTATTTTGACTTGGATTCTACTCTAGGAAGACATCT
66 TCTGTAGAAATCCAGAAAATTCCAGGATCCTATTTTGACTTGGATTCTACTCTAGGAAGACATCT
*
19794 AATCCAACTTGGAGTCTAAGTCAAGGCTAAACCGTCCTACCCCTATTTCTCCACTATAAATAGCC
131 AATCCAACTGGGAGTCT-AGTCAAGGCTAAACCGTCCTACCCCTATTTCTCCACTATAAATAGCC
19859 ACCTCCTGTATCACAAATCACATACTACACAATTTTTCTCTCATATACTTTTATTCTCTTTTTCT
195 ACCTCCTGTATCACAAATCACATACTACACAATTTTTCTCTCATATACTTTTATTCTCTTTTTCT
19924 ACCTTTCTTTAGTTTAGGTTTTTCTCTAGTTTTAGAAGGGGGAAGTCGACACCCTCTCTAGCCAT
260 ACCTTTCTTTAGTTTAGGTTTTTCTCTAGTTTTAGAAGGGGGAAGTCGACACCCTCTCTAGCCAT
*
19989 AGAGGGGTGCGACAACCCTAGGTTTTCAAGGAGGAGAAATCGTTCCTCCC
325 AGAGGGGTGCAACAACCCTAGGTTTTCAAGGAGGAGAAATCGTTCCTCCC
20039 TAGTTCTGTA
Statistics
Matches: 364, Mismatches: 10, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
374 140 0.38
375 224 0.62
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (374 bp):
CAACTTTCCCTTGAAGTGCAAAGCCCAGATCTGCCATCTTCAAGCCCGAATCTCAAGTCCAAGTT
TCTGTAGAAATCCAGAAAATTCCAGGATCCTATTTTGACTTGGATTCTACTCTAGGAAGACATCT
AATCCAACTGGGAGTCTAGTCAAGGCTAAACCGTCCTACCCCTATTTCTCCACTATAAATAGCCA
CCTCCTGTATCACAAATCACATACTACACAATTTTTCTCTCATATACTTTTATTCTCTTTTTCTA
CCTTTCTTTAGTTTAGGTTTTTCTCTAGTTTTAGAAGGGGGAAGTCGACACCCTCTCTAGCCATA
GAGGGGTGCAACAACCCTAGGTTTTCAAGGAGGAGAAATCGTTCCTCCC
Done.