Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01003908.1 Corchorus capsularis cultivar CVL-1 contig03916, 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: 1799
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.37
Found at i:409 original size:2 final size:2
Alignment explanation
Indices: 397--481 Score: 55
Period size: 2 Copynumber: 47.5 Consensus size: 2
387 TTAGTTTTAT
* * *
397 TA TA T- TA TA TA TA TA TA AA TA -A T- TA AA TA TA TA CA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
435 TA TA -A TA TA TA TA AA TA -A T- TA AA TA TA TA -A TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
472 TA -A TA TA TA T
1 TA TA TA TA TA T
482 TAATAATAGA
Statistics
Matches: 64, Mismatches: 9, Indels: 20
0.69 0.10 0.22
Matches are distributed among these distances:
1 10 0.16
2 54 0.84
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (2 bp):
TA
Found at i:426 original size:25 final size:26
Alignment explanation
Indices: 398--483 Score: 70
Period size: 28 Copynumber: 3.2 Consensus size: 26
388 TAGTTTTATT
398 ATATTATATATATATAAATAAT-TAA
1 ATATTATATATATATAAATAATATAA
*
423 ATA-TATACA-ATATATAATATATATAA
1 ATATTATATATATATA-AATA-ATATAA
* * *
449 ATAATTAAATATATAATATATAATAATAT
1 AT-ATTATATATAT-ATAAATAAT-ATAA
478 ATATTA
1 ATATTA
484 ATAATAGAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 13
0.73 0.08 0.20
Matches are distributed among these distances:
23 5 0.10
24 9 0.19
25 5 0.10
26 5 0.10
27 1 0.02
28 10 0.21
29 10 0.21
30 3 0.06
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (26 bp):
ATATTATATATATATAAATAATATAA
Found at i:428 original size:16 final size:17
Alignment explanation
Indices: 400--488 Score: 94
Period size: 18 Copynumber: 5.1 Consensus size: 17
390 GTTTTATTAT
400 ATTATATATATATAAATA
1 ATTA-ATATATATAAATA
418 ATTAA-ATATATACAAT-
1 ATTAATATATATA-AATA
434 ATATAATATATATAAATA
1 AT-TAATATATATAAATA
452 ATTAA-ATATATAATATA
1 ATTAATATATATAA-ATA
* *
469 TAATAATATATATTAATA
1 -ATTAATATATATAAATA
487 AT
1 AT
489 AGAAACTTTC
Statistics
Matches: 61, Mismatches: 3, Indels: 15
0.77 0.04 0.19
Matches are distributed among these distances:
16 17 0.28
17 17 0.28
18 20 0.33
19 7 0.11
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (17 bp):
ATTAATATATATAAATA
Found at i:448 original size:34 final size:35
Alignment explanation
Indices: 397--488 Score: 136
Period size: 34 Copynumber: 2.7 Consensus size: 35
387 TTAGTTTTAT
*
397 TATATTAT-ATATATATAAATAATTAAATATATACA
1 TATATAATAATATATATAAATAATTAAATATATA-A
432 -ATAT-ATAATATATATAAATAATTAAATATATAA
1 TATATAATAATATATATAAATAATTAAATATATAA
*
465 TATATAATAATATATATTAATAAT
1 TATATAATAATATATATAAATAAT
489 AGAAACTTTC
Statistics
Matches: 53, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
33 3 0.06
34 33 0.62
35 17 0.32
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (35 bp):
TATATAATAATATATATAAATAATTAAATATATAA
Found at i:489 original size:16 final size:16
Alignment explanation
Indices: 405--489 Score: 91
Period size: 17 Copynumber: 5.0 Consensus size: 16
395 ATTATATTAT
405 ATATATATAAATAATTA
1 ATATATATAAATAA-TA
422 A-ATATATACAATATATA
1 ATATATATA-AATA-ATA
439 ATATATATAAATAATTAA
1 ATATATATAAATAA-T-A
*
457 ATATATAATATATAATA
1 ATATAT-ATAAATAATA
*
474 ATATATATTAATAATA
1 ATATATATAAATAATA
490 GAAACTTTCT
Statistics
Matches: 59, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
16 16 0.27
17 20 0.34
18 16 0.27
19 7 0.12
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATATATAAATAATA
Done.