Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010821.1 Corchorus capsularis cultivar CVL-1 contig10842, 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: 7242
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Found at i:586 original size:55 final size:55
Alignment explanation
Indices: 472--699 Score: 319
Period size: 55 Copynumber: 4.3 Consensus size: 55
462 CATCAAGGGC
* *
472 AAATCAGTAATTAAGTAAGAAGAGATTAATCAGAGT-----TAA-GGTAAT-AGT
1 AAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGT
* *
520 AAAGCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGAAATCAGT
1 AAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGT
* *
575 AAATCGGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAGTAGTAATCAGT
1 AAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGT
* *
630 AAATCAGTAATTAAGTAAAAAAAGATTAATCAGAGTCAAGGTAATAGTAATCAGT
1 AAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGT
685 AAATC-GATAATTAAG
1 AAATCAG-TAATTAAG
700 AGTTAAAATG
Statistics
Matches: 160, Mismatches: 12, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
48 34 0.21
53 3 0.02
54 5 0.03
55 118 0.74
ACGTcount: A:0.50, C:0.07, G:0.18, T:0.25
Consensus pattern (55 bp):
AAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGT
Found at i:616 original size:26 final size:26
Alignment explanation
Indices: 532--617 Score: 70
Period size: 26 Copynumber: 3.2 Consensus size: 26
522 AGCAGTAATT
532 AAGTAAAAAGAGATTAATCAGAGTCA
1 AAGTAAAAAGAGATTAATCAGAGTCA
* * *
558 AAGTAATAGAA-ATCAGTAAATC-G-GTAA
1 AAGTAA-A-AAGA-GA-TTAATCAGAGTCA
585 TTAAGTAAAAAGAGATTAATCAGAGTCA
1 --AAGTAAAAAGAGATTAATCAGAGTCA
613 AAGTA
1 AAGTA
618 GTAGTAATCA
Statistics
Matches: 45, Mismatches: 6, Indels: 18
0.65 0.09 0.26
Matches are distributed among these distances:
26 16 0.36
27 9 0.20
28 9 0.20
29 11 0.24
ACGTcount: A:0.52, C:0.07, G:0.19, T:0.22
Consensus pattern (26 bp):
AAGTAAAAAGAGATTAATCAGAGTCA
Found at i:620 original size:29 final size:29
Alignment explanation
Indices: 533--620 Score: 78
Period size: 29 Copynumber: 3.1 Consensus size: 29
523 GCAGTAATTA
533 AGTAAAAAGAGATTAATCAGAGTCAAAGT
1 AGTAAAAAGAGATTAATCAGAGTCAAAGT
* ** * *
562 AATAGAAATCAG-TAAATC-G-GT--AATT
1 AGTA-AAAAGAGATTAATCAGAGTCAAAGT
587 AAGTAAAAAGAGATTAATCAGAGTCAAAGT
1 -AGTAAAAAGAGATTAATCAGAGTCAAAGT
617 AGTA
1 AGTA
621 GTAATCAGTA
Statistics
Matches: 42, Mismatches: 10, Indels: 14
0.64 0.15 0.21
Matches are distributed among these distances:
25 8 0.19
26 8 0.19
27 3 0.07
28 3 0.07
29 12 0.29
30 8 0.19
ACGTcount: A:0.51, C:0.07, G:0.19, T:0.23
Consensus pattern (29 bp):
AGTAAAAAGAGATTAATCAGAGTCAAAGT
Found at i:1005 original size:22 final size:22
Alignment explanation
Indices: 930--1210 Score: 107
Period size: 21 Copynumber: 12.6 Consensus size: 22
920 AAATGGTAAT
*
930 TAGTAATCAATAAAAAGTAAGAA
1 TAGTAATCAGTAAAAAGTAA-AA
* *
953 -GGTAATCA--ACAAGAGTAAAA
1 TAGTAATCAGTA-AAAAGTAAAA
* **
973 TAATAGGCAGTAAAAAGTAAAA
1 TAGTAATCAGTAAAAAGTAAAA
**
995 TAGTAATCAGT-ATGAGTAAAA
1 TAGTAATCAGTAAAAAGTAAAA
* * *
1016 AAGGTAATAAGTAAGAAGTAAAA
1 TA-GTAATCAGTAAAAAGTAAAA
* * *
1039 GTA-AAATCAGT-AAGAGTAAGA
1 -TAGTAATCAGTAAAAAGTAAAA
* * *
1060 -AGATGATTAGTAAAGAGTAAAAA
1 TAG-TAATCAGTAAAAAGT-AAAA
* *
1083 AAGCTAATCAGCAAGAAA-TAAAA
1 TAG-TAATCAGTAA-AAAGTAAAA
*
1106 -AGGTAATCAGTAAAAAGCAAAA
1 TA-GTAATCAGTAAAAAGTAAAA
* *
1128 -GGCAATCAGTAAAAAGTAAAA
1 TAGTAATCAGTAAAAAGTAAAA
* *
1149 GAGTAATCAGCAAAAAAGGAGCATAAAA
1 TAGTAATCAG--TAAAA--AG--TAAAA
*
1177 TAGTAATCAGTAAAGAGT-AAA
1 TAGTAATCAGTAAAAAGTAAAA
* *
1198 TGGTGATCAGTAA
1 TAGTAATCAGTAA
1211 TTCAAAGAGT
Statistics
Matches: 192, Mismatches: 44, Indels: 46
0.68 0.16 0.16
Matches are distributed among these distances:
19 1 0.01
20 3 0.02
21 67 0.35
22 66 0.34
23 17 0.09
24 17 0.09
25 2 0.01
26 5 0.03
28 14 0.07
ACGTcount: A:0.56, C:0.06, G:0.20, T:0.19
Consensus pattern (22 bp):
TAGTAATCAGTAAAAAGTAAAA
Found at i:2752 original size:33 final size:33
Alignment explanation
Indices: 2712--2808 Score: 122
Period size: 33 Copynumber: 2.9 Consensus size: 33
2702 AGCACAAGTG
**
2712 ACTGGCCATGCGACTTGGAGATGTTCGGCCAAC
1 ACTGGCCATGCGACTTGGAGATGCCCGGCCAAC
*
2745 ACTGGCCATGCGACTTGGAGATGCCCGGCCATC
1 ACTGGCCATGCGACTTGGAGATGCCCGGCCAAC
* * * **
2778 ACCGGCCACGCGACATGGTCATGCCCGGCCA
1 ACTGGCCATGCGACTTGGAGATGCCCGGCCA
2809 CAACCGGCCA
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.20, C:0.34, G:0.30, T:0.16
Consensus pattern (33 bp):
ACTGGCCATGCGACTTGGAGATGCCCGGCCAAC
Found at i:2817 original size:10 final size:10
Alignment explanation
Indices: 2802--2853 Score: 50
Period size: 10 Copynumber: 4.9 Consensus size: 10
2792 ATGGTCATGC
2802 CCGGCCACAA
1 CCGGCCACAA
2812 CCGGCCACATGA
1 CCGGCCACA--A
***
2824 CTCGGCCATGC
1 C-CGGCCACAA
2835 CCGGCCACAA
1 CCGGCCACAA
2845 CCGGCCACA
1 CCGGCCACA
2854 TGATCCTTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
10 24 0.73
11 1 0.03
12 2 0.06
13 6 0.18
ACGTcount: A:0.23, C:0.48, G:0.23, T:0.06
Consensus pattern (10 bp):
CCGGCCACAA
Found at i:2854 original size:33 final size:33
Alignment explanation
Indices: 2765--2856 Score: 125
Period size: 33 Copynumber: 2.8 Consensus size: 33
2755 CGACTTGGAG
** *
2765 ATGCCCGGCCATC-ACCGGCCACGCGACATGGTC
1 ATGCCCGGCCA-CAACCGGCCACATGACATGGCC
2798 ATGCCCGGCCACAACCGGCCACATGAC-TCGGCC
1 ATGCCCGGCCACAACCGGCCACATGACAT-GGCC
2831 ATGCCCGGCCACAACCGGCCACATGA
1 ATGCCCGGCCACAACCGGCCACATGA
2857 TCCTTTATCT
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
32 2 0.04
33 52 0.96
ACGTcount: A:0.22, C:0.43, G:0.25, T:0.10
Consensus pattern (33 bp):
ATGCCCGGCCACAACCGGCCACATGACATGGCC
Found at i:6326 original size:33 final size:32
Alignment explanation
Indices: 6239--6412 Score: 159
Period size: 33 Copynumber: 5.3 Consensus size: 32
6229 AAAGGATCGT
* * * **
6239 GTGGCCGGTTGTGGCCGGGCAAGGCCGAGTCAA
1 GTGGCCGG-TGTGGCCGGGCATGACCAAGTCGC
* * *
6272 GTGGCCGGGTGTGACCGGGCATGGCCATGTCGC
1 GTGGCC-GGTGTGGCCGGGCATGACCAAGTCGC
** *
6305 GTGGCCGGTGATGGCCGGGCATCTCCATGTCGC
1 GTGGCCGGTG-TGGCCGGGCATGACCAAGTCGC
* * *
6338 ATGGCCGGTGTTGCACGGGCATTACCAAGTCGC
1 GTGGCCGGTGTGGC-CGGGCATGACCAAGTCGC
* *
6371 GTGGCCGGTGTTGCACGGGCATTACCAAGTCGC
1 GTGGCCGGTGTGGC-CGGGCATGACCAAGTCGC
6404 GTGGCCGGT
1 GTGGCCGGT
6413 CATTCTCGCC
Statistics
Matches: 123, Mismatches: 15, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
32 7 0.06
33 114 0.93
34 2 0.02
ACGTcount: A:0.13, C:0.27, G:0.41, T:0.20
Consensus pattern (32 bp):
GTGGCCGGTGTGGCCGGGCATGACCAAGTCGC
Done.