Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016309.1 Corchorus capsularis cultivar CVL-1 contig16330, 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: 30549
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:505 original size:9 final size:9
Alignment explanation
Indices: 493--585 Score: 52
Period size: 9 Copynumber: 10.3 Consensus size: 9
483 TATTTATGAT
493 ATATATATA
1 ATATATATA
502 ATATACT-TA
1 ATATA-TATA
*
511 ATTATTTATGA
1 A-TATATAT-A
*
522 CATATATAAA
1 -ATATATATA
*
532 ATATATGTA
1 ATATATATA
*
541 AAATATATA
1 ATATATATA
550 A-AT-TAT-
1 ATATATATA
*
556 ATTTAT-TA
1 ATATATATA
*
564 TATATATAAA
1 -ATATATATA
574 ATATATATA
1 ATATATATA
583 ATA
1 ATA
586 AATTATTTTT
Statistics
Matches: 63, Mismatches: 11, Indels: 20
0.67 0.12 0.21
Matches are distributed among these distances:
6 1 0.02
7 5 0.08
8 3 0.05
9 40 0.63
10 7 0.11
11 6 0.10
12 1 0.02
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (9 bp):
ATATATATA
Found at i:542 original size:11 final size:11
Alignment explanation
Indices: 523--583 Score: 63
Period size: 11 Copynumber: 5.7 Consensus size: 11
513 TATTTATGAC
523 ATATATAAAAT
1 ATATATAAAAT
*
534 ATATGT-AAA-
1 ATATATAAAAT
*
543 ATATATAAATT
1 ATATATAAAAT
* **
554 ATATTTATTAT
1 ATATATAAAAT
565 ATATATAAAAT
1 ATATATAAAAT
576 ATATATAA
1 ATATATAA
584 TAAATTATTT
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
9 5 0.13
10 5 0.13
11 28 0.74
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (11 bp):
ATATATAAAAT
Found at i:548 original size:20 final size:21
Alignment explanation
Indices: 523--588 Score: 71
Period size: 22 Copynumber: 3.1 Consensus size: 21
513 TATTTATGAC
523 ATATATAAAATATATGTA-AA
1 ATATATAAAATATATGTATAA
* * *
543 ATATATAAATTATATTTATTAT
1 ATATATAAAATATATGTA-TAA
*
565 ATATATAAAATATATATAATAA
1 ATATATAAAATATATGT-ATAA
587 AT
1 AT
589 TATTTTTATT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
20 16 0.43
22 20 0.54
23 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (21 bp):
ATATATAAAATATATGTATAA
Found at i:8314 original size:15 final size:15
Alignment explanation
Indices: 8294--8323 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
8284 ACCATTTCAC
8294 GTAAAAAGTTATCTG
1 GTAAAAAGTTATCTG
8309 GTAAAAAGTTATCTG
1 GTAAAAAGTTATCTG
8324 AATACCTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (15 bp):
GTAAAAAGTTATCTG
Found at i:12252 original size:19 final size:19
Alignment explanation
Indices: 12228--12266 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
12218 ATTGCATAGA
12228 GCAGCAGCTACCAGGTTTT
1 GCAGCAGCTACCAGGTTTT
12247 GCAGCAGCTACCAGGTTTT
1 GCAGCAGCTACCAGGTTTT
12266 G
1 G
12267 AAGAGGAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.26, G:0.28, T:0.26
Consensus pattern (19 bp):
GCAGCAGCTACCAGGTTTT
Done.