Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009892.1 Corchorus capsularis cultivar CVL-1 contig09913, 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: 32687
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:1718 original size:4 final size:4
Alignment explanation
Indices: 1704--1736 Score: 57
Period size: 4 Copynumber: 8.0 Consensus size: 4
1694 CTAATGAGTA
1704 TATT GTATT TATT TATT TATT TATT TATT TATT
1 TATT -TATT TATT TATT TATT TATT TATT TATT
1737 CATTCATTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 24 0.86
5 4 0.14
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:16375 original size:38 final size:38
Alignment explanation
Indices: 16324--16434 Score: 160
Period size: 38 Copynumber: 3.0 Consensus size: 38
16314 CCATAGCCTT
16324 AATACTAGCTCTTCTGGAGCTTTCAATCAAATTTGCAC
1 AATACTAGCTCTTCTGGAGCTTTCAATCAAATTTGCAC
*
16362 AATACTAGCTCTTCCGGAGCTTTCAATCAAATTT--A-
1 AATACTAGCTCTTCTGGAGCTTTCAATCAAATTTGCAC
16397 AATACT-GACTCTTCTGGAG-TCTTCAATCAAATTTGCAC
1 AATACTAG-CTCTTCTGGAGCT-TTCAATCAAATTTGCAC
16435 TATCCGATAT
Statistics
Matches: 66, Mismatches: 2, Indels: 10
0.85 0.03 0.13
Matches are distributed among these distances:
34 2 0.03
35 29 0.44
36 1 0.02
37 1 0.02
38 33 0.50
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (38 bp):
AATACTAGCTCTTCTGGAGCTTTCAATCAAATTTGCAC
Found at i:17923 original size:33 final size:34
Alignment explanation
Indices: 17881--17977 Score: 135
Period size: 33 Copynumber: 2.8 Consensus size: 34
17871 TATTTCTTTT
*
17881 ATGTGACAACTTCAGGTGTCACTAATATGT-TTG-
1 ATGTGACAACTTCAGGTGCCACTAATAT-TCTTGA
17914 ATGTGACAACTTCAGGTGCCACTAATATTCTTGA
1 ATGTGACAACTTCAGGTGCCACTAATATTCTTGA
*
17948 TCATGTGACAACTTCAGGAGCCACTAATAT
1 --ATGTGACAACTTCAGGTGCCACTAATAT
17978 ACAAGGTAGT
Statistics
Matches: 58, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
32 1 0.02
33 30 0.52
36 27 0.47
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.32
Consensus pattern (34 bp):
ATGTGACAACTTCAGGTGCCACTAATATTCTTGA
Found at i:18052 original size:33 final size:32
Alignment explanation
Indices: 18010--18072 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 32
18000 GTAATTTTTA
*
18010 ATGATAAAGAAAGGTAGAAGGAGGAGATTATGC
1 ATGATAAAGAAAGGTAGAA-GAAGAGATTATGC
18043 ATGATAAAGAAAGGTAGAAGAAGAGATTAT
1 ATGATAAAGAAAGGTAGAAGAAGAGATTAT
18073 ACATATTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 10 0.34
33 19 0.66
ACGTcount: A:0.49, C:0.02, G:0.30, T:0.19
Consensus pattern (32 bp):
ATGATAAAGAAAGGTAGAAGAAGAGATTATGC
Found at i:22999 original size:17 final size:16
Alignment explanation
Indices: 22977--23018 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
22967 AAATTGCATA
*
22977 GAAAGGAAGTAGGGAAG
1 GAAAGGAAATA-GGAAG
22994 GAAAGGAAATAGGAAG
1 GAAAGGAAATAGGAAG
23010 G-AAGGAAAT
1 GAAAGGAAAT
23019 GATCCTATAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 8 0.33
16 6 0.25
17 10 0.42
ACGTcount: A:0.52, C:0.00, G:0.40, T:0.07
Consensus pattern (16 bp):
GAAAGGAAATAGGAAG
Found at i:29554 original size:30 final size:30
Alignment explanation
Indices: 29518--29585 Score: 100
Period size: 30 Copynumber: 2.3 Consensus size: 30
29508 GAGTCGCCCA
29518 CCATATGGGAAAGTCGTATATTATAAGTAC
1 CCATATGGGAAAGTCGTATATTATAAGTAC
* * *
29548 CCATATGGGGAAGTTGTATATTATAAGTAT
1 CCATATGGGAAAGTCGTATATTATAAGTAC
*
29578 CCGTATGG
1 CCATATGG
29586 ACTATGGAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (30 bp):
CCATATGGGAAAGTCGTATATTATAAGTAC
Found at i:32551 original size:4 final size:4
Alignment explanation
Indices: 32542--32570 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
32532 GATTCACAGA
32542 ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
32571 AATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:32579 original size:2 final size:2
Alignment explanation
Indices: 32572--32601 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
32562 ACATACATAA
32572 AT 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 AT
32602 CAAGGGCGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.