Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015675.1 Corchorus capsularis cultivar CVL-1 contig15696, 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: 9451
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Found at i:538 original size:54 final size:55
Alignment explanation
Indices: 435--635 Score: 316
Period size: 54 Copynumber: 3.7 Consensus size: 55
425 GTTCAATAAG
*
435 ATCAGTAAATCAGTAATTATGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTA
1 ATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTA
* * *
490 ATCAGTAAATCAGTAATTAAGT-AAAAGCGATTAATCAGGGTCAAGGTAATAAT-
1 ATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTA
543 ATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTA
1 ATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTA
* * * *
598 ATCAGTAAATCAGTAATCAAGCAAAAAGATAGTAATCA
1 ATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCA
636 TTAAATTGAT
Statistics
Matches: 133, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
53 22 0.17
54 56 0.42
55 55 0.41
ACGTcount: A:0.48, C:0.09, G:0.17, T:0.25
Consensus pattern (55 bp):
ATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTA
Found at i:551 original size:108 final size:108
Alignment explanation
Indices: 429--623 Score: 354
Period size: 108 Copynumber: 1.8 Consensus size: 108
419 AATTAAGTTC
*
429 AATAAGATCAGTAAATCAGTAATTATGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCA
1 AATAAGATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCA
* *
494 GTAAATCAGTAATTAAGTAAAAGCGATTAATCAGGGTCAAGGT
66 GTAAATCAGTAATCAAGCAAAAGCGATTAATCAGGGTCAAGGT
*
537 AATAATATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCA
1 AATAAGATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCA
602 GTAAATCAGTAATCAAGCAAAA
66 GTAAATCAGTAATCAAGCAAAA
624 AGATAGTAAT
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
108 83 1.00
ACGTcount: A:0.49, C:0.09, G:0.17, T:0.25
Consensus pattern (108 bp):
AATAAGATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCA
GTAAATCAGTAATCAAGCAAAAGCGATTAATCAGGGTCAAGGT
Found at i:631 original size:34 final size:34
Alignment explanation
Indices: 592--712 Score: 104
Period size: 34 Copynumber: 3.5 Consensus size: 34
582 AGTCAAGGTA
*
592 ATAGTAATCAGTAAATCAGTAATCAAGCAAAAAG
1 ATAGTAATCAGTAAATCAGTAATAAAGCAAAAAG
* * * *
626 ATAGTAATCATTAAAT-TGATAATTAAGAGTCCAGATA-
1 ATAGTAATCAGTAAATCAG-TAA-TAA-AG--CAAAAAG
* * *
663 ATAGTAATCAGT-AATTAGTAATTAAGTAAAAAG
1 ATAGTAATCAGTAAATCAGTAATAAAGCAAAAAG
696 ATAGTAATCAGTAAATC
1 ATAGTAATCAGTAAATC
713 GATAATTAAG
Statistics
Matches: 67, Mismatches: 12, Indels: 16
0.71 0.13 0.17
Matches are distributed among these distances:
32 3 0.04
33 13 0.19
34 23 0.34
35 4 0.06
36 8 0.12
37 12 0.18
38 4 0.06
ACGTcount: A:0.50, C:0.08, G:0.14, T:0.28
Consensus pattern (34 bp):
ATAGTAATCAGTAAATCAGTAATAAAGCAAAAAG
Found at i:705 original size:70 final size:70
Alignment explanation
Indices: 580--797 Score: 271
Period size: 70 Copynumber: 3.1 Consensus size: 70
570 GAGATTAATC
* * * *
580 AGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATCAAGCAAAAAGATAGTAATCATTAAATTGA
1 AGAGTCAAGGTAATAGTAATCAGT-AATTAGTAATTAAGTAAAAAGATAGTAATCAGTAAATTGA
645 TAATTA
65 TAATTA
* * *
651 AGAGTCCAGATAATAGTAATCAGTAATTAGTAATTAAGTAAAAAGATAGTAATCAGTAAATCGAT
1 AGAGTCAAGGTAATAGTAATCAGTAATTAGTAATTAAGTAAAAAGATAGTAATCAGTAAATTGAT
716 AATTA
66 AATTA
* * *
721 AGAGTCAAGGTAAGAGATTAATCAGTAATTAAAG-AGTCTAGGT-AAAA-ATAGTAATCAGTAAA
1 AGAGTCAAGGTAATAG--TAATCAGTAATT--AGTAAT-TAAGTAAAAAGATAGTAATCAGTAAA
783 TTGATAATTA
61 TTGATAATTA
793 AGAGT
1 AGAGT
798 TAAAGTGATC
Statistics
Matches: 129, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
70 54 0.42
71 22 0.17
72 41 0.32
73 6 0.05
74 6 0.05
ACGTcount: A:0.48, C:0.07, G:0.17, T:0.28
Consensus pattern (70 bp):
AGAGTCAAGGTAATAGTAATCAGTAATTAGTAATTAAGTAAAAAGATAGTAATCAGTAAATTGAT
AATTA
Found at i:781 original size:33 final size:31
Alignment explanation
Indices: 715--781 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 31
705 AGTAAATCGA
*
715 TAATTAAGAGTCAAGGTAAGAGATTAATCAG
1 TAATTAAGAGTCAAGGTAAGAAATTAATCAG
*
746 TAATTAAAGAGTCTAGGTAA-AAATAGTAATCAG
1 TAATT-AAGAGTCAAGGTAAGAAAT--TAATCAG
779 TAA
1 TAA
782 ATTGATAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 8 0.26
32 13 0.42
33 10 0.32
ACGTcount: A:0.48, C:0.06, G:0.19, T:0.27
Consensus pattern (31 bp):
TAATTAAGAGTCAAGGTAAGAAATTAATCAG
Found at i:958 original size:24 final size:25
Alignment explanation
Indices: 921--976 Score: 87
Period size: 24 Copynumber: 2.3 Consensus size: 25
911 AATTAAGAAG
*
921 AGATTGATAATTAAAGTGGTAATTA
1 AGATTCATAATTAAAGTGGTAATTA
*
946 AGATTCAT-ATTAAAGTGGTAATTG
1 AGATTCATAATTAAAGTGGTAATTA
970 AGATTCA
1 AGATTCA
977 AAGTAAGAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 22 0.76
25 7 0.24
ACGTcount: A:0.41, C:0.04, G:0.20, T:0.36
Consensus pattern (25 bp):
AGATTCATAATTAAAGTGGTAATTA
Found at i:1160 original size:16 final size:16
Alignment explanation
Indices: 1135--1232 Score: 70
Period size: 16 Copynumber: 6.7 Consensus size: 16
1125 GTAAGATAGA
1135 AAGT-AAAATGGTATT
1 AAGTAAAAATGGTATT
*
1150 AAGTAAAAATGGCATT
1 AAGTAAAAATGGTATT
* * *
1166 AGGTCAAAATGATATT
1 AAGTAAAAATGGTATT
1182 AAGT-AAAA----A--
1 AAGTAAAAATGGTATT
* *
1191 AGGTCAAAATGGTATT
1 AAGTAAAAATGGTATT
*
1207 AAGTAAAAATGGTA-A
1 AAGTAAAAATGGTATT
1222 AAGTAAAAATG
1 AAGTAAAAATG
1233 ATAAAAGTCG
Statistics
Matches: 65, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
9 3 0.05
10 4 0.06
11 1 0.02
14 1 0.02
15 19 0.29
16 37 0.57
ACGTcount: A:0.52, C:0.03, G:0.19, T:0.26
Consensus pattern (16 bp):
AAGTAAAAATGGTATT
Found at i:1200 original size:25 final size:25
Alignment explanation
Indices: 1166--1223 Score: 91
Period size: 25 Copynumber: 2.4 Consensus size: 25
1156 AAATGGCATT
1166 AGGTCAAAATGATATTAAGTAAAAA
1 AGGTCAAAATGATATTAAGTAAAAA
*
1191 AGGTCAAAATGGTATTAAGTAAAAA
1 AGGTCAAAATGATATTAAGTAAAAA
*
1216 TGGT-AAAA
1 AGGTCAAAA
1224 GTAAAAATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 4 0.13
25 27 0.87
ACGTcount: A:0.53, C:0.03, G:0.19, T:0.24
Consensus pattern (25 bp):
AGGTCAAAATGATATTAAGTAAAAA
Found at i:1237 original size:15 final size:15
Alignment explanation
Indices: 1207--1240 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1197 AAATGGTATT
*
1207 AAGTAAAAATGGTAA
1 AAGTAAAAATGATAA
1222 AAGTAAAAATGATAA
1 AAGTAAAAATGATAA
1237 AAGT
1 AAGT
1241 CGCAAAAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.18, T:0.21
Consensus pattern (15 bp):
AAGTAAAAATGATAA
Found at i:1237 original size:24 final size:24
Alignment explanation
Indices: 1210--1260 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
1200 TGGTATTAAG
* *
1210 TAAAAATGGTAAAAGTAAAAATGA
1 TAAAAATCGCAAAAGTAAAAATGA
*
1234 TAAAAGTCGCAAAAGTAAAAATGA
1 TAAAAATCGCAAAAGTAAAAATGA
1258 TAA
1 TAA
1261 TCAGTAGGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.61, C:0.04, G:0.16, T:0.20
Consensus pattern (24 bp):
TAAAAATCGCAAAAGTAAAAATGA
Found at i:6597 original size:21 final size:21
Alignment explanation
Indices: 6571--6619 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
6561 GCACTGGAGG
* * *
6571 ACATGGGTCGCGAGGCAAACC
1 ACATGGGGCGCCAAGCAAACC
*
6592 ACATGGGGCGCCAAGCATACC
1 ACATGGGGCGCCAAGCAAACC
6613 ACATGGG
1 ACATGGG
6620 CCCCCAACTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.29, C:0.29, G:0.33, T:0.10
Consensus pattern (21 bp):
ACATGGGGCGCCAAGCAAACC
Found at i:6708 original size:21 final size:20
Alignment explanation
Indices: 6684--6725 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
6674 GAGTGCTGAG
*
6684 GCCAACGACCTGGGCGCACAA
1 GCCAACGACATGGGCGC-CAA
*
6705 GCCAACTACATGGGCGCCAA
1 GCCAACGACATGGGCGCCAA
6725 G
1 G
6726 GGGGAGTCGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.29, C:0.36, G:0.29, T:0.07
Consensus pattern (20 bp):
GCCAACGACATGGGCGCCAA
Done.