Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005741.1 Corchorus capsularis cultivar CVL-1 contig05759, 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: 12301
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35
Found at i:1354 original size:19 final size:19
Alignment explanation
Indices: 1330--1368 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1320 TCAAATGTGC
1330 TTTCCCATGTGTATGTATG
1 TTTCCCATGTGTATGTATG
*
1349 TTTCCCATGTGTATTTATG
1 TTTCCCATGTGTATGTATG
1368 T
1 T
1369 ATATATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.15, C:0.15, G:0.18, T:0.51
Consensus pattern (19 bp):
TTTCCCATGTGTATGTATG
Found at i:1375 original size:2 final size:2
Alignment explanation
Indices: 1368--1404 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1358 TGTATTTATG
1368 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1405 ACAAAACAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2405 original size:29 final size:32
Alignment explanation
Indices: 2371--2438 Score: 83
Period size: 31 Copynumber: 2.2 Consensus size: 32
2361 TGTAAAATAC
2371 TATTATAATAT-AA-T-A-AATATAATTTTTTA
1 TATTATAATATGAATTGATAAT-TAATTTTTTA
*
2400 TATTAT-ATATGAATTGATAATTATTTTTTTA
1 TATTATAATATGAATTGATAATTAATTTTTTA
2431 TATTATAA
1 TATTATAA
2439 AGAATTATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
28 4 0.12
29 8 0.24
30 1 0.03
31 16 0.48
32 4 0.12
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (32 bp):
TATTATAATATGAATTGATAATTAATTTTTTA
Found at i:2548 original size:32 final size:32
Alignment explanation
Indices: 2510--2586 Score: 82
Period size: 32 Copynumber: 2.4 Consensus size: 32
2500 TGGAAACACA
*
2510 ACTATTTAGTGGCCCTTCTTTGAAAAAACGCC
1 ACTATTTAGTGGCCCTTCTATGAAAAAACGCC
** * *** *
2542 TTTATTTAGGGGTGTTTCTATGAGAAAACGCC
1 ACTATTTAGTGGCCCTTCTATGAAAAAACGCC
2574 ACTATTTAGTGGC
1 ACTATTTAGTGGC
2587 ATTTTTAACC
Statistics
Matches: 33, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (32 bp):
ACTATTTAGTGGCCCTTCTATGAAAAAACGCC
Found at i:4904 original size:33 final size:33
Alignment explanation
Indices: 4862--4988 Score: 127
Period size: 33 Copynumber: 3.9 Consensus size: 33
4852 TTGCCCTTAG
*
4862 CCACGGCGGAGCC-TCCCCACTAGGGCGGCTCTA
1 CCACGGCGGAGCCGT-CCCACTAGGACGGCTCTA
* *
4895 CCACGGCGGAGCC-TCCCCACGAGGACGGCTCTG
1 CCACGGCGGAGCCGT-CCCACTAGGACGGCTCTA
* *
4928 CCACGGC-TAGCCGTCCCACTAGGATGGCT-TA
1 CCACGGCGGAGCCGTCCCACTAGGACGGCTCTA
* * *
4959 GCCACGGCAGAGCCGTCCGACTAGGGCGGC
1 -CCACGGCGGAGCCGTCCCACTAGGACGGC
4989 AAGGCTATTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
31 1 0.01
32 24 0.30
33 55 0.69
ACGTcount: A:0.17, C:0.39, G:0.32, T:0.12
Consensus pattern (33 bp):
CCACGGCGGAGCCGTCCCACTAGGACGGCTCTA
Found at i:5315 original size:15 final size:15
Alignment explanation
Indices: 5279--5315 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
5269 CGTCGTTTTG
5279 TATA-ATATATATTA
1 TATATATATATATTA
5293 TA-ATTATATATATTA
1 TATA-TATATATATTA
5308 TATATATA
1 TATATATA
5316 AAATAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
13 1 0.05
14 2 0.10
15 16 0.80
16 1 0.05
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TATATATATATATTA
Found at i:5337 original size:9 final size:9
Alignment explanation
Indices: 5309--5348 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
5299 TATATATTAT
5309 ATATATAAA
1 ATATATAAA
*
5318 ATA-AAAAA
1 ATATATAAA
5326 ATATATAAA
1 ATATATAAA
*
5335 ATATTTAAA
1 ATATATAAA
5344 ATATA
1 ATATA
5349 AATACCTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
8 7 0.27
9 19 0.73
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
ATATATAAA
Found at i:5460 original size:19 final size:18
Alignment explanation
Indices: 5419--5453 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
5409 TAGAGAAACC
5419 AAAA-AGGAAAGAAAAAA
1 AAAAGAGGAAAGAAAAAA
5436 AAAAGAGGAAAGTAAAAA
1 AAAAGAGGAAAG-AAAAA
5454 TAGAAGAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 7 0.44
19 5 0.31
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (18 bp):
AAAAGAGGAAAGAAAAAA
Found at i:7752 original size:33 final size:33
Alignment explanation
Indices: 7670--7767 Score: 92
Period size: 32 Copynumber: 3.0 Consensus size: 33
7660 ACTTTTGCCT
* *
7670 TTAGCCACGGCGGAGCCTCCCCATTAGGACGGC
1 TTAGCCACGGCGGAGCCGCCCCACTAGGACGGC
** * * *
7703 TCT-GCCGTGGC-TAGCCGCCCCACTGGGATGGC
1 T-TAGCCACGGCGGAGCCGCCCCACTAGGACGGC
* *
7735 TTAGCCACGGCGGAGCCGCCCGACTAGGGCGGC
1 TTAGCCACGGCGGAGCCGCCCCACTAGGACGGC
7768 AAGGCTATTT
Statistics
Matches: 48, Mismatches: 14, Indels: 6
0.71 0.21 0.09
Matches are distributed among these distances:
31 1 0.02
32 23 0.48
33 23 0.48
34 1 0.02
ACGTcount: A:0.14, C:0.37, G:0.35, T:0.14
Consensus pattern (33 bp):
TTAGCCACGGCGGAGCCGCCCCACTAGGACGGC
Found at i:7805 original size:25 final size:25
Alignment explanation
Indices: 7771--7838 Score: 127
Period size: 25 Copynumber: 2.7 Consensus size: 25
7761 GGGCGGCAAG
7771 GCTATTTTTTTTTTAAAAAAAATTA
1 GCTATTTTTTTTTTAAAAAAAATTA
*
7796 GCTATTTTTTTTTAAAAAAAAATTA
1 GCTATTTTTTTTTTAAAAAAAATTA
7821 GCTATTTTTTTTTTAAAA
1 GCTATTTTTTTTTTAAAA
7839 TTAGGTTTAG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.53
Consensus pattern (25 bp):
GCTATTTTTTTTTTAAAAAAAATTA
Found at i:10783 original size:3 final size:3
Alignment explanation
Indices: 10777--10810 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
10767 AAACCTTTAA
10777 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA- AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
10811 AAAAGAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:10816 original size:12 final size:14
Alignment explanation
Indices: 10775--10819 Score: 67
Period size: 15 Copynumber: 3.3 Consensus size: 14
10765 AAAAACCTTT
10775 AAAAGAAGAAGAAG
1 AAAAGAAGAAGAAG
10789 AAGAAGAAGAAGAAG
1 AA-AAGAAGAAGAAG
10804 AAAAGAA-AA-AAG
1 AAAAGAAGAAGAAG
10816 AAAA
1 AAAA
10820 AAAAAGCTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.23
13 2 0.07
14 7 0.23
15 14 0.47
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (14 bp):
AAAAGAAGAAGAAG
Found at i:11333 original size:13 final size:13
Alignment explanation
Indices: 11300--11335 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
11290 TGTGACAAGC
*
11300 TTAGTTACAGATG
1 TTAGTGACAGATG
11313 TT-GTGACAGATG
1 TTAGTGACAGATG
11325 TTAGTGACAGA
1 TTAGTGACAGA
11336 ACACTTTCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.31, C:0.08, G:0.28, T:0.33
Consensus pattern (13 bp):
TTAGTGACAGATG
Found at i:11334 original size:25 final size:24
Alignment explanation
Indices: 11288--11335 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
11278 TTATGTAAAA
*
11288 GTTGTGACAAGCTTAGTTACAGAT
1 GTTGTGACAAGCTTAGTGACAGAT
11312 GTTGTGACAGATG-TTAGTGACAGA
1 GTTGTGACA-A-GCTTAGTGACAGA
11336 ACACTTTCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 9 0.43
25 11 0.52
26 1 0.05
ACGTcount: A:0.29, C:0.10, G:0.29, T:0.31
Consensus pattern (24 bp):
GTTGTGACAAGCTTAGTGACAGAT
Found at i:11693 original size:3 final size:3
Alignment explanation
Indices: 11685--11756 Score: 62
Period size: 3 Copynumber: 24.3 Consensus size: 3
11675 TTAGGTAACT
* *
11685 TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TAAA TTT TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA T-TA TTA TTA TTA TTA
*
11731 TT- TT- TTA TT- TTA TTA TAA TTTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA T
11757 GTAATAATTT
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
2 8 0.14
3 42 0.74
4 7 0.12
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:11729 original size:25 final size:25
Alignment explanation
Indices: 11684--11756 Score: 69
Period size: 25 Copynumber: 2.9 Consensus size: 25
11674 TTTAGGTAAC
*
11684 TTTATTATTATTATTATTATTATTA
1 TTTATTATAATTATTATTATTATTA
* *
11709 TTTATTATAAATTTTTA-TATTATTT
1 TTTATTAT-AATTATTATTATTATTA
* *
11734 TTTATT-TTATTATAATTTATTAT
1 TTTATTATAATTATTA-TTATTAT
11757 GTAATAATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
23 5 0.13
24 1 0.03
25 27 0.69
26 6 0.15
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (25 bp):
TTTATTATAATTATTATTATTATTA
Done.