Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01003505.1 Corchorus capsularis cultivar CVL-1 contig03513, 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: 6110
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Found at i:74 original size:19 final size:19
Alignment explanation
Indices: 50--88 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
40 ACTTTGCAGC
50 ATGGATTTTACAATAGGAG
1 ATGGATTTTACAATAGGAG
69 ATGGATTTTACAATAGGAG
1 ATGGATTTTACAATAGGAG
88 A
1 A
89 AAAGGGGTTC
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:0.38, C:0.05, G:0.26, T:0.31
Consensus pattern (19 bp):
ATGGATTTTACAATAGGAG
Found at i:2914 original size:26 final size:26
Alignment explanation
Indices: 2838--2915 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 26
2828 ATCAGTAATC
*
2838 AGTAAAAAGAGATTAATCAGAG-TCA
1 AGTAAAAAGAGATTAATCAGAGTTAA
* *
2863 AG-GAAAA-AG--TAATC--AGTAAA
1 AGTAAAAAGAGATTAATCAGAGTTAA
2883 TCAGTAAAAAGAGATTAATCAGAGTTAA
1 --AGTAAAAAGAGATTAATCAGAGTTAA
2911 AGTAA
1 AGTAA
2916 TCAATAAATC
Statistics
Matches: 39, Mismatches: 5, Indels: 17
0.64 0.08 0.28
Matches are distributed among these distances:
19 2 0.05
20 1 0.03
21 5 0.13
22 2 0.05
23 6 0.15
24 6 0.15
25 2 0.05
26 10 0.26
28 5 0.13
ACGTcount: A:0.54, C:0.06, G:0.19, T:0.21
Consensus pattern (26 bp):
AGTAAAAAGAGATTAATCAGAGTTAA
Found at i:2942 original size:96 final size:96
Alignment explanation
Indices: 2819--3081 Score: 431
Period size: 96 Copynumber: 2.8 Consensus size: 96
2809 AAATGGGATC
* * *
2819 AATCAGTAAATCAGTAA-TCAGTAAAAAGAGATTAATCAGAGTCAAGGAAAAAGTAATCAGTAAA
1 AATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTAAA
*
2883 TCAGTAAAAAGAGATTAATCAGAGTTAA-AGT
66 TCAGTAAAAAGAGATTAATCA-AGGTAATAGT
* * *
2914 AATCAATAAATCAGTAATTAACTAAAAAGTGATTAATCAGAGTCAAGGTAATAGTAATCAGTAAA
1 AATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTAAA
2979 TCAGTAAAAAGAGATTAATCAAGGTAATAGT
66 TCAGTAAAAAGAGATTAATCAAGGTAATAGT
*
3010 AATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAGTCAGTAAA
1 AATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTAAA
3075 TCAGTAA
66 TCAGTAA
3082 TTAAGAGTCA
Statistics
Matches: 155, Mismatches: 11, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
95 21 0.14
96 134 0.86
ACGTcount: A:0.50, C:0.08, G:0.17, T:0.24
Consensus pattern (96 bp):
AATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTAAA
TCAGTAAAAAGAGATTAATCAAGGTAATAGT
Found at i:2948 original size:49 final size:49
Alignment explanation
Indices: 2819--3081 Score: 308
Period size: 47 Copynumber: 5.5 Consensus size: 49
2809 AAATGGGATC
* *
2819 AATCAGTAAATCAGT-AATCAGTAAAAAGAGATTAATCAGAG-TCAAGG
1 AATCAGTAAATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTTAAAGT
**
2866 AAAAAGT-AATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTTAAAGT
1 AATCAGTAAATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTTAAAGT
* * * * * * *
2914 AATCAATAAATCAGTAATTAACTAAAAAGTGATTAATCAGAGTCAAGGT
1 AATCAGTAAATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTTAAAGT
*
2963 AAT-AGT-AATCAGTAAATCAGTAAAAAGAGATTAATCA-AGGTAATAGT
1 AATCAGTAAATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTTAA-AGT
* * * *
3010 AATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGT
1 AATCAGTAAATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTTAAAGT
*
3059 AAT-AGT-AGTCAGTAAATCAGTAA
1 AATCAGTAAATCAGTAAATCAGTAA
3082 TTAAGAGTCA
Statistics
Matches: 180, Mismatches: 29, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
46 11 0.06
47 77 0.43
48 16 0.09
49 72 0.40
50 4 0.02
ACGTcount: A:0.50, C:0.08, G:0.17, T:0.24
Consensus pattern (49 bp):
AATCAGTAAATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTTAAAGT
Found at i:3057 original size:55 final size:54
Alignment explanation
Indices: 2873--3086 Score: 214
Period size: 49 Copynumber: 4.3 Consensus size: 54
2863 AGGAAAAAGT
* * *
2873 AATCAGTAAATCAGTAAAAAGAGATTAATCAGAGT----TAA-AGTAATCAATA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTAAGGTAATAGTAATCAGTA
* *
2922 AATCAGTAATTAACTAAAAAGTGATTAATCAGAGTCAAGGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGT-AAGGTAATAGTAATCAGTA
2977 AATC--------AGTAAAAAGAGATTAATCA-AGGTAA--T-A--GTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGA-GTAAGGTAATAGTAATCAGTA
*
3018 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAGTCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGT-AAGGTAATAGTAATCAGTA
3073 AATCAGTAATTAAG
1 AATCAGTAATTAAG
3087 AGTCAAGGGA
Statistics
Matches: 135, Mismatches: 8, Indels: 38
0.75 0.04 0.21
Matches are distributed among these distances:
41 14 0.10
43 1 0.01
44 1 0.01
46 3 0.02
47 19 0.14
49 52 0.39
50 3 0.02
52 1 0.01
53 1 0.01
54 3 0.02
55 37 0.27
ACGTcount: A:0.50, C:0.08, G:0.17, T:0.26
Consensus pattern (54 bp):
AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTAAGGTAATAGTAATCAGTA
Found at i:3455 original size:21 final size:21
Alignment explanation
Indices: 3413--3454 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
3403 GTAAGCTAAG
3413 AGTAATCAGTAAAAAGGTAAA
1 AGTAATCAGTAAAAAGGTAAA
3434 AGTAATCAGTAAAAA-GTAAA
1 AGTAATCAGTAAAAAGGTAAA
3454 A
1 A
3455 ATGGCAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.60, C:0.05, G:0.17, T:0.19
Consensus pattern (21 bp):
AGTAATCAGTAAAAAGGTAAA
Found at i:3577 original size:25 final size:25
Alignment explanation
Indices: 3549--3599 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
3539 AAAATGGTGT
3549 AGAGTAAAAAATGGTATTAAATAAA
1 AGAGTAAAAAATGGTATTAAATAAA
* *
3574 AGAGTAAAGAATGGTATTAATTAAA
1 AGAGTAAAAAATGGTATTAAATAAA
3599 A
1 A
3600 AATGGTGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.57, C:0.00, G:0.18, T:0.25
Consensus pattern (25 bp):
AGAGTAAAAAATGGTATTAAATAAA
Found at i:3599 original size:42 final size:42
Alignment explanation
Indices: 3553--3658 Score: 115
Period size: 42 Copynumber: 2.5 Consensus size: 42
3543 TGGTGTAGAG
*
3553 TAAAAAATGGTATTAAATAAAAGAGT-AAAGAATGGTATTAAT
1 TAAAAAATGGTATTAAACAAAAGAGTCAAA-AATGGTATTAAT
* * * ** *
3595 TAAAAAATGGTGTTAAGCAAAAGGGTCAAAAATGGTATCCAG
1 TAAAAAATGGTATTAAACAAAAGAGTCAAAAATGGTATTAAT
* *
3637 TAAGAGATGGTATTAAACAAAA
1 TAAAAAATGGTATTAAACAAAA
3659 ATGGTATTAA
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
42 49 0.94
43 3 0.06
ACGTcount: A:0.51, C:0.05, G:0.20, T:0.25
Consensus pattern (42 bp):
TAAAAAATGGTATTAAACAAAAGAGTCAAAAATGGTATTAAT
Found at i:3674 original size:16 final size:16
Alignment explanation
Indices: 3622--3674 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
3612 CAAAAGGGTC
**
3622 AAAAATGGTATCCAGT
1 AAAAATGGTATTAAGT
* **
3638 AAGAGATGGTATTAAAC
1 AA-AAATGGTATTAAGT
3655 AAAAATGGTATTAAGT
1 AAAAATGGTATTAAGT
3671 AAAA
1 AAAA
3675 GAGTAATAAA
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
16 17 0.61
17 11 0.39
ACGTcount: A:0.51, C:0.06, G:0.19, T:0.25
Consensus pattern (16 bp):
AAAAATGGTATTAAGT
Found at i:3698 original size:59 final size:57
Alignment explanation
Indices: 3580--3703 Score: 126
Period size: 58 Copynumber: 2.1 Consensus size: 57
3570 TAAAAGAGTA
* * **
3580 AAGAATGGTATTAATTAAAAAATGGTGTTAAGCAAAAGGGTCAAAAATGGTATCCAGT
1 AAGAATGGTATTAA-TAAAAAATGGTATTAAGCAAAAGAGTCAAAAATGGTATAAAGT
* *
3638 AAGAGATGGTATTAA-ACAAAAATGGTATTAAGTAAAAGAGTAATAAAAATGGTA-AAAGT
1 AAGA-ATGGTATTAATA-AAAAATGGTATTAAGCAAAAGAGT--CAAAAATGGTATAAAGT
*
3697 AAAAATG
1 AAGAATG
3704 ATAAAAGTAG
Statistics
Matches: 55, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
57 1 0.02
58 28 0.51
59 16 0.29
60 10 0.18
ACGTcount: A:0.51, C:0.04, G:0.21, T:0.24
Consensus pattern (57 bp):
AAGAATGGTATTAATAAAAAATGGTATTAAGCAAAAGAGTCAAAAATGGTATAAAGT
Found at i:3701 original size:15 final size:15
Alignment explanation
Indices: 3681--3712 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3671 AAAAGAGTAA
*
3681 TAAAAATGGTAAAAG
1 TAAAAATGATAAAAG
3696 TAAAAATGATAAAAG
1 TAAAAATGATAAAAG
3711 TA
1 TA
3713 GCAAAAGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.16, T:0.22
Consensus pattern (15 bp):
TAAAAATGATAAAAG
Found at i:4137 original size:33 final size:32
Alignment explanation
Indices: 4084--4187 Score: 118
Period size: 33 Copynumber: 3.2 Consensus size: 32
4074 TGGAGAACCC
*
4084 GCCACGCGACTTGGAGATGCCCGCGCAACACCG
1 GCCACGCGACATGGAGATGCCCG-GCAACACCG
* * *
4117 GCCATGTGACATGGAGATGCCCGGTCATCACCG
1 GCCACGCGACATGGAGATGCCCGG-CAACACCG
** *
4150 GCCACGCGACATGGCCATGCCCGGCCACACCCG
1 GCCACGCGACATGGAGATGCCCGGCAACA-CCG
4183 GCCAC
1 GCCAC
4188 TTGACTCGGC
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
32 4 0.07
33 55 0.93
ACGTcount: A:0.20, C:0.40, G:0.29, T:0.11
Consensus pattern (32 bp):
GCCACGCGACATGGAGATGCCCGGCAACACCG
Done.