Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009669.1 Corchorus capsularis cultivar CVL-1 contig09690, 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: 63958
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:500 original size:2 final size:2
Alignment explanation
Indices: 493--517 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
483 GAATTCATGC
493 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
518 AGATCTCGCA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15463 original size:33 final size:33
Alignment explanation
Indices: 15419--15499 Score: 101
Period size: 33 Copynumber: 2.5 Consensus size: 33
15409 TTTTTACACT
* *
15419 AGCCTCTCCACTAGGACGGCTCCA-CCACGGCGG
1 AGCCTCCCCACTAGGACGGCT-CAGCCACGACGG
*
15452 AGCCTCCCCACTAGGACGGCTCAGCCATGACGG
1 AGCCTCCCCACTAGGACGGCTCAGCCACGACGG
* *
15485 AGCCGCCCTACTAGG
1 AGCCTCCCCACTAGG
15500 GCGACTAGGC
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
32 2 0.05
33 40 0.95
ACGTcount: A:0.20, C:0.41, G:0.27, T:0.12
Consensus pattern (33 bp):
AGCCTCCCCACTAGGACGGCTCAGCCACGACGG
Found at i:17317 original size:12 final size:12
Alignment explanation
Indices: 17277--17311 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
17267 TCACAAATGG
*
17277 CTTCCGCCACCA
1 CTTCCACCACCA
17289 CTTCCACCACCA
1 CTTCCACCACCA
17301 CTTCCACCACC
1 CTTCCACCACC
17312 CTTTCCCTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.20, C:0.60, G:0.03, T:0.17
Consensus pattern (12 bp):
CTTCCACCACCA
Found at i:30298 original size:48 final size:48
Alignment explanation
Indices: 30244--30338 Score: 156
Period size: 48 Copynumber: 2.0 Consensus size: 48
30234 GAGGATAAGA
30244 TATAAATATAGTTTAAATATAAGAAAATGTGAAAATAGCCAA-ATTTTT
1 TATAAATATAGTTTAAATATAA-AAAATGTGAAAATAGCCAATATTTTT
* *
30292 TATAAATATAGTTTAAATATCAAATATGTGAAAATAGCCAATATTTT
1 TATAAATATAGTTTAAATATAAAAAATGTGAAAATAGCCAATATTTT
30339 ATGGGGTCAA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
47 18 0.41
48 26 0.59
ACGTcount: A:0.48, C:0.05, G:0.09, T:0.37
Consensus pattern (48 bp):
TATAAATATAGTTTAAATATAAAAAATGTGAAAATAGCCAATATTTTT
Found at i:37252 original size:16 final size:16
Alignment explanation
Indices: 37231--37264 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
37221 CAAGAATCCA
37231 TTTCCTATTAGGATTC
1 TTTCCTATTAGGATTC
37247 TTTCCTATTAGGATTC
1 TTTCCTATTAGGATTC
37263 TT
1 TT
37265 GTCCACCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.18, C:0.18, G:0.12, T:0.53
Consensus pattern (16 bp):
TTTCCTATTAGGATTC
Found at i:43830 original size:14 final size:14
Alignment explanation
Indices: 43813--43847 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
43803 AGAAAGCTTA
43813 TACAGTCTTTTCGT
1 TACAGTCTTTTCGT
*
43827 TACAGTCTTTTTGT
1 TACAGTCTTTTCGT
43841 TACAGTC
1 TACAGTC
43848 GCAATTGTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.17, C:0.20, G:0.14, T:0.49
Consensus pattern (14 bp):
TACAGTCTTTTCGT
Found at i:45603 original size:18 final size:18
Alignment explanation
Indices: 45580--45615 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
45570 GTTTGGTTGA
*
45580 GCTTTTGACACGTTTGGG
1 GCTTTTGACACGGTTGGG
*
45598 GCTTTTGGCACGGTTGGG
1 GCTTTTGACACGGTTGGG
45616 AGTCCCAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.08, C:0.17, G:0.39, T:0.36
Consensus pattern (18 bp):
GCTTTTGACACGGTTGGG
Found at i:53822 original size:31 final size:31
Alignment explanation
Indices: 53786--53845 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
53776 TATCTTTTAT
53786 AGACAAATAAGTCTCTTCATAATTGTTCATA
1 AGACAAATAAGTCTCTTCATAATTGTTCATA
53817 AGACAAATAAGTCTCTTCATAATTGTTCA
1 AGACAAATAAGTCTCTTCATAATTGTTCA
53846 CTTATGAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (31 bp):
AGACAAATAAGTCTCTTCATAATTGTTCATA
Found at i:55565 original size:26 final size:25
Alignment explanation
Indices: 55527--55578 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
55517 TTTCTCACAA
55527 AAATAATAGAAATAAACATTAGATAT
1 AAATAATAGAAATAAAC-TTAGATAT
* * * *
55553 AAATCATATAAATGAACTTATATAT
1 AAATAATAGAAATAAACTTAGATAT
55578 A
1 A
55579 TCTCATTGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.31
Consensus pattern (25 bp):
AAATAATAGAAATAAACTTAGATAT
Found at i:56344 original size:31 final size:31
Alignment explanation
Indices: 56308--56367 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
56298 TATCTTTTAT
56308 AGACAAATAAGTCTCTTCATAATTGTTCATA
1 AGACAAATAAGTCTCTTCATAATTGTTCATA
56339 AGACAAATAAGTCTCTTCATAATTGTTCA
1 AGACAAATAAGTCTCTTCATAATTGTTCA
56368 CTTATGAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (31 bp):
AGACAAATAAGTCTCTTCATAATTGTTCATA
Found at i:59023 original size:13 final size:13
Alignment explanation
Indices: 59000--59034 Score: 61
Period size: 13 Copynumber: 2.6 Consensus size: 13
58990 AAAAAAATAT
59000 TAGTACAATACATG
1 TAGT-CAATACATG
59014 TAGTCAATACATG
1 TAGTCAATACATG
59027 TAGTCAAT
1 TAGTCAAT
59035 GTCTCATTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 17 0.81
14 4 0.19
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.31
Consensus pattern (13 bp):
TAGTCAATACATG
Done.