Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01002557.1 Corchorus capsularis cultivar CVL-1 contig02565, 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, 601
Length: 1003
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Found at i:228 original size:15 final size:15
Alignment explanation
Indices: 195--228 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
185 TCCTTTCCCC
**
195 TTTTTTATCATTTTT
1 TTTTTTATCATTTCA
210 TTTTTTATCATTTCA
1 TTTTTTATCATTTCA
225 TTTT
1 TTTT
229 CCTCCTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTTATCATTTCA
Found at i:532 original size:30 final size:30
Alignment explanation
Indices: 498--742 Score: 204
Period size: 30 Copynumber: 7.4 Consensus size: 30
488 TTTGATTTCA
498 TTCTATTTCATTATATGGTATTACATAATT
1 TTCTATTTCATTATATGGTATTACATAATT
528 TTCTATTTCATTATATGGTATTACATAATT
1 TTCTATTTCATTATATGGTATTACATAATT
**
558 TTCTATTTCATTATATGGTATTATGTAATT
1 TTCTATTTCATTATATGGTATTACATAATT
* *
588 TTGATTTCATTCTATGTTCATTATATGGTATTACATAATT
1 TT-CTAT--TTC-A--TT-A-T--ATGGTATTACATAATT
*
628 TTGATTTCATTCTATTTCATTATATGGTATTACATAATT
1 T---TC------TATTTCATTATATGGTATTACATAATT
667 TTCTATGTTCATTATATGGTATTACATAATTT
1 TTCTAT-TTCATTATATGGTATTACATAA-TT
*
699 CATTCTATGTTCATTATATGATATTACATAATT
1 --TTCTAT-TTCATTATATGGTATTACATAATT
*
732 TT-GATTTCATT
1 TTCTATTTCATT
743 CTATTTCATT
Statistics
Matches: 181, Mismatches: 11, Indels: 47
0.76 0.05 0.20
Matches are distributed among these distances:
29 6 0.03
30 65 0.36
31 26 0.14
32 2 0.01
33 5 0.03
34 29 0.16
36 3 0.02
37 1 0.01
38 1 0.01
39 17 0.09
40 15 0.08
41 1 0.01
42 1 0.01
43 3 0.02
45 1 0.01
46 3 0.02
48 2 0.01
ACGTcount: A:0.29, C:0.10, G:0.08, T:0.53
Consensus pattern (30 bp):
TTCTATTTCATTATATGGTATTACATAATT
Found at i:579 original size:15 final size:15
Alignment explanation
Indices: 501--579 Score: 68
Period size: 15 Copynumber: 5.3 Consensus size: 15
491 GATTTCATTC
501 TATTTCATTATATGG
1 TATTTCATTATATGG
* * * **
516 TATTACATAATTTTC
1 TATTTCATTATATGG
531 TATTTCATTATATGG
1 TATTTCATTATATGG
* * * **
546 TATTACATAATTTTC
1 TATTTCATTATATGG
561 TATTTCATTATATGG
1 TATTTCATTATATGG
576 TATT
1 TATT
580 ATGTAATTTT
Statistics
Matches: 44, Mismatches: 20, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
15 44 1.00
ACGTcount: A:0.29, C:0.09, G:0.08, T:0.54
Consensus pattern (15 bp):
TATTTCATTATATGG
Found at i:608 original size:40 final size:39
Alignment explanation
Indices: 558--762 Score: 251
Period size: 40 Copynumber: 5.6 Consensus size: 39
548 TTACATAATT
**
558 TTCTATTTCATTATATGGTATTATGTAATTTTGATTTCA
1 TTCTATTTCATTATATGGTATTACATAATTTTGATTTCA
597 TTCTATGTTCATTATATGGTATTACATAATTTTGATTTCA
1 TTCTAT-TTCATTATATGGTATTACATAATTTTGATTTCA
637 TTCTATTTCATTATATGGTATTACAT-A-----A-TT--
1 TTCTATTTCATTATATGGTATTACATAATTTTGATTTCA
667 TTCTATGTTCATTATATGGTATTACATAA-TTT-----CA
1 TTCTAT-TTCATTATATGGTATTACATAATTTTGATTTCA
*
701 TTCTATGTTCATTATATGATATTACATAATTTTGATTTCA
1 TTCTAT-TTCATTATATGGTATTACATAATTTTGATTTCA
741 TTCTATTTCATTATATGGTATT
1 TTCTATTTCATTATATGGTATT
763 TTGAATTGGC
Statistics
Matches: 148, Mismatches: 4, Indels: 28
0.82 0.02 0.16
Matches are distributed among these distances:
30 6 0.04
31 20 0.14
32 3 0.02
33 1 0.01
34 28 0.19
35 3 0.02
38 1 0.01
39 41 0.28
40 45 0.30
ACGTcount: A:0.28, C:0.10, G:0.09, T:0.54
Consensus pattern (39 bp):
TTCTATTTCATTATATGGTATTACATAATTTTGATTTCA
Found at i:609 original size:70 final size:69
Alignment explanation
Indices: 528--762 Score: 262
Period size: 70 Copynumber: 3.3 Consensus size: 69
518 TTACATAATT
* *
528 TTCTATTTCATTATATGGTATTACATAATTTTCTATTTCATTATATGGTATTATGTAATTTTGAT
1 TTCTATTTCATTATATGGTATTACATAATTTTCTATTTCATTATATGATATTATATAATTTTGAT
593 TTCA
66 TTCA
* * * ** *
597 TTCTATGTTCATTATATGGTATTACATAATTTT-GATTTCATTCTAT-TTCATTATATGGTATTA
1 TTCTAT-TTCATTATATGGTATTACATAATTTTCTATTTCATTATATGAT-ATTATATAAT-TTT
*
660 CATAATT--
63 GAT--TTCA
*
667 TTCTATGTTCATTATATGGTATTACATAATTTCATTCTATGTTCATTATATGATATTACATAATT
1 TTCTAT-TTCATTATATGGTATTACATAA-TT--TTCTAT-TTCATTATATGATATTATATAATT
732 TTGATTTCA
61 TTGATTTCA
741 TTCTATTTCATTATATGGTATT
1 TTCTATTTCATTATATGGTATT
763 TTGAATTGGC
Statistics
Matches: 137, Mismatches: 16, Indels: 22
0.78 0.09 0.13
Matches are distributed among these distances:
68 1 0.01
69 24 0.18
70 59 0.43
71 2 0.01
72 4 0.03
73 18 0.13
74 12 0.09
75 16 0.12
76 1 0.01
ACGTcount: A:0.28, C:0.10, G:0.09, T:0.54
Consensus pattern (69 bp):
TTCTATTTCATTATATGGTATTACATAATTTTCTATTTCATTATATGATATTATATAATTTTGAT
TTCA
Found at i:679 original size:31 final size:31
Alignment explanation
Indices: 637--733 Score: 151
Period size: 34 Copynumber: 3.1 Consensus size: 31
627 TTTGATTTCA
637 TTCTAT-TTCATTATATGGTATTACATAATT
1 TTCTATGTTCATTATATGGTATTACATAATT
667 TTCTATGTTCATTATATGGTATTACATAATTT
1 TTCTATGTTCATTATATGGTATTACATAA-TT
*
699 CATTCTATGTTCATTATATGATATTACATAATT
1 --TTCTATGTTCATTATATGGTATTACATAATT
732 TT
1 TT
734 GATTTCATTC
Statistics
Matches: 62, Mismatches: 1, Indels: 7
0.89 0.01 0.10
Matches are distributed among these distances:
30 6 0.10
31 24 0.39
32 2 0.03
33 2 0.03
34 28 0.45
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (31 bp):
TTCTATGTTCATTATATGGTATTACATAATT
Found at i:731 original size:104 final size:105
Alignment explanation
Indices: 528--762 Score: 384
Period size: 104 Copynumber: 2.2 Consensus size: 105
518 TTACATAATT
*
528 TTCTATTTCATTATATGGTATTACATAATTTTCTATTTCATTATATGGTATTATGTAATTTTGAT
1 TTCTATTTCATTATATGGTATTACATAATTTTCTATTTCATTATATGGTATTA--TAA--TTAAT
*
593 TTCATTCTATGTTCATTATATGGTATTACATAATTTTGATTTCA
62 TTCATTCTATGTTCATTATATGATATTACATAATTTTGATTTCA
*
637 TTCTATTTCATTATATGGTATTACATAATTTTCTATGTTCATTATATGGTATTA-CA-TAATTTC
1 TTCTATTTCATTATATGGTATTACATAATTTTCTAT-TTCATTATATGGTATTATAATTAATTTC
700 ATTCTATGTTCATTATATGATATTACATAATTTTGATTTCA
65 ATTCTATGTTCATTATATGATATTACATAATTTTGATTTCA
741 TTCTATTTCATTATATGGTATT
1 TTCTATTTCATTATATGGTATT
763 TTGAATTGGC
Statistics
Matches: 122, Mismatches: 3, Indels: 7
0.92 0.02 0.05
Matches are distributed among these distances:
104 68 0.56
107 1 0.01
109 36 0.30
110 17 0.14
ACGTcount: A:0.28, C:0.10, G:0.09, T:0.54
Consensus pattern (105 bp):
TTCTATTTCATTATATGGTATTACATAATTTTCTATTTCATTATATGGTATTATAATTAATTTCA
TTCTATGTTCATTATATGATATTACATAATTTTGATTTCA
Done.