Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011417.1 Corchorus capsularis cultivar CVL-1 contig11438, 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: 38302
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Found at i:3041 original size:27 final size:25
Alignment explanation
Indices: 3011--3066 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
3001 TGTGGAAAAT
*
3011 AGAAACTGTAAGTTGTGACAAAAAGAA
1 AGAAACTGTAAG--ATGACAAAAAGAA
* *
3038 AGAACCTGTCAGATGACAAAAAGAA
1 AGAAACTGTAAGATGACAAAAAGAA
3063 AGAA
1 AGAA
3067 CTAATTAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 16 0.62
27 10 0.38
ACGTcount: A:0.54, C:0.11, G:0.21, T:0.14
Consensus pattern (25 bp):
AGAAACTGTAAGATGACAAAAAGAA
Found at i:9535 original size:23 final size:24
Alignment explanation
Indices: 9509--9564 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 24
9499 ATTGGATCAA
9509 TATTTTAT-ATTATAAATATGAAT
1 TATTTTATGATTATAAATATGAAT
*
9532 TATTTTTTTGGAATTATAAATATGAAT
1 TA-TTTTAT-G-ATTATAAATATGAAT
9559 TATTTT
1 TATTTT
9565 TTTCTGGTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 2 0.07
24 5 0.18
26 4 0.14
27 17 0.61
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (24 bp):
TATTTTATGATTATAAATATGAAT
Found at i:9547 original size:27 final size:28
Alignment explanation
Indices: 9517--9591 Score: 116
Period size: 29 Copynumber: 2.7 Consensus size: 28
9507 AATATTTTAT
9517 ATTATAAATATGAATTATTTTTT-TGGA
1 ATTATAAATATGAATTATTTTTTCTGGA
*
9544 ATTATAAATATGAATTATTTTTTTCTGGT
1 ATTATAAATATGAATTA-TTTTTTCTGGA
*
9573 ATAATAAATATGAATTATT
1 ATTATAAATATGAATTATT
9592 GATACAAGCT
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
27 17 0.39
28 8 0.18
29 19 0.43
ACGTcount: A:0.39, C:0.01, G:0.09, T:0.51
Consensus pattern (28 bp):
ATTATAAATATGAATTATTTTTTCTGGA
Found at i:18216 original size:12 final size:13
Alignment explanation
Indices: 18199--18227 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
18189 CTTTTCTCTA
18199 CTTTCTTTC-TTT
1 CTTTCTTTCTTTT
18211 CTTTCTTTCTTTT
1 CTTTCTTTCTTTT
18224 CTTT
1 CTTT
18228 TTTTTAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (13 bp):
CTTTCTTTCTTTT
Found at i:18588 original size:2 final size:2
Alignment explanation
Indices: 18583--18610 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
18573 ACACACACAC
18583 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
18611 TCTTAATGGG
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:22549 original size:19 final size:19
Alignment explanation
Indices: 22525--22562 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
22515 CATTTTTCTC
*
22525 TCTTTTGCTCTTAAACTAT
1 TCTTTTGATCTTAAACTAT
22544 TCTTTTGATCTTAAACTAT
1 TCTTTTGATCTTAAACTAT
22563 ACAATTGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.24, C:0.18, G:0.05, T:0.53
Consensus pattern (19 bp):
TCTTTTGATCTTAAACTAT
Found at i:25114 original size:31 final size:32
Alignment explanation
Indices: 25076--25138 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
25066 ACCTTGTCAT
* *
25076 GTGGCATTTTT-GTCCAACTTGTCATTGCCAC
1 GTGGCATTTTTGGTCCAACGTGGCATTGCCAC
*
25107 GTGGCATTTTTGGTCCGACGTGGCATTGCCAC
1 GTGGCATTTTTGGTCCAACGTGGCATTGCCAC
25139 ATCGGTAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 11 0.39
32 17 0.61
ACGTcount: A:0.14, C:0.25, G:0.25, T:0.35
Consensus pattern (32 bp):
GTGGCATTTTTGGTCCAACGTGGCATTGCCAC
Found at i:34535 original size:161 final size:159
Alignment explanation
Indices: 34225--34540 Score: 463
Period size: 161 Copynumber: 2.0 Consensus size: 159
34215 TTACATAATT
* * * *
34225 GATTGATATAGTACTAAATCATATGTTCAAACCCCTACATAGCATAACTACCAACATCAGTGCTA
1 GATTGATATAGCACAAAATCATATGTTCAAACCACTACATAGCATAACTACCAACATCAGCGCTA
* * * ** *
34290 TATGATCTCCCTTTTGATCTAATTTTTTTAGTAGAATAAGATTTAAATTGAGCCCCTAATATAAG
66 AATGATCCCCCTTATGATCTAATTCCTTTAGTAGAATAAGATTTAAATAGAGCCCCTAATATAAG
*
34355 GTTGTAAGTCGTTATTGGCCTCTTAGATC
131 GTTGTAAGCCGTTATTGGCCTCTTAGATC
* *
34384 GATTGATATAGCACAAAATCATATGTTCAAACCATTCCATAGCATAACTACCAACATC-GACGCT
1 GATTGATATAGCACAAAATCATATGTTCAAACCACTACATAGCATAACTACCAACATCAG-CGCT
* *
34448 AAATGATCACCCCTTATGAATCTGATTCCTTTAGTAGAATAAGATTTAAATAGAGCCCCTAGTAT
65 AAATGATC-CCCCTTATG-ATCTAATTCCTTTAGTAGAATAAGATTTAAATAGAGCCCCTAATAT
34513 AAGGTTGTAAGCCGTTATTGGCCTCTTA
128 AAGGTTGTAAGCCGTTATTGGCCTCTTA
34541 TGTACTAAAA
Statistics
Matches: 139, Mismatches: 15, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
158 1 0.01
159 63 0.45
160 7 0.05
161 68 0.49
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (159 bp):
GATTGATATAGCACAAAATCATATGTTCAAACCACTACATAGCATAACTACCAACATCAGCGCTA
AATGATCCCCCTTATGATCTAATTCCTTTAGTAGAATAAGATTTAAATAGAGCCCCTAATATAAG
GTTGTAAGCCGTTATTGGCCTCTTAGATC
Found at i:35427 original size:21 final size:21
Alignment explanation
Indices: 35398--35445 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
35388 TGGGAAGAGT
* *
35398 GACGAAGACGACGACGATGAC
1 GACGGAGACGACGACGATCAC
**
35419 GACGGAGACGACGGTGATCAC
1 GACGGAGACGACGACGATCAC
35440 GACGGA
1 GACGGA
35446 AGGGTCCCGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.23, G:0.38, T:0.06
Consensus pattern (21 bp):
GACGGAGACGACGACGATCAC
Done.