Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013563.1 Corchorus capsularis cultivar CVL-1 contig13584, 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: 33839
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Found at i:488 original size:17 final size:17
Alignment explanation
Indices: 466--504 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
456 GAAATTTAAT
*
466 TTTTTTTTCTTCTTT-TA
1 TTTTTTTCCTT-TTTCTA
483 TTTTTTTCCTTTTTCTA
1 TTTTTTTCCTTTTTCTA
500 TTTTT
1 TTTTT
505 GGGAGGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTTTCCTTTTTCTA
Found at i:1132 original size:30 final size:31
Alignment explanation
Indices: 1072--1141 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
1062 AAATTTGGTG
1072 AGGGACCCAATTACTCAATTAACTCAACTTC
1 AGGGACCCAATTACTCAATTAACTCAACTTC
* * *
1103 AGGGACTCAATTGCTC-ATTAAGTTC-ACTTC
1 AGGGACCCAATTACTCAATTAA-CTCAACTTC
*
1133 AAGGACCCA
1 AGGGACCCA
1142 TTTGCACATT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
30 17 0.52
31 16 0.48
ACGTcount: A:0.33, C:0.27, G:0.14, T:0.26
Consensus pattern (31 bp):
AGGGACCCAATTACTCAATTAACTCAACTTC
Found at i:2497 original size:17 final size:16
Alignment explanation
Indices: 2463--2501 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2453 GAATTTAATT
*
2463 TTTTTTTCTTCTTTTA
1 TTTTTTCCTTCTTTTA
*
2479 TTTTTTCCTTTTTTCTA
1 TTTTTTCCTTCTTT-TA
2496 TTTTTT
1 TTTTTT
2502 GGGAGGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTTTCCTTCTTTTA
Found at i:2582 original size:16 final size:15
Alignment explanation
Indices: 2541--2582 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
2531 CCAAAAAAAG
* *
2541 TTTTTAAAAATTTGT
1 TTTTTAAAAAATTAT
2556 TTTTTAAAAAATTAT
1 TTTTTAAAAAATTAT
2571 TTTTTAATAAAA
1 TTTTTAA-AAAA
2583 AAATATGGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 20 0.83
16 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (15 bp):
TTTTTAAAAAATTAT
Found at i:11099 original size:34 final size:34
Alignment explanation
Indices: 11056--11124 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
11046 AACAATTCTA
11056 ATCAGAAACAAACAGAGATATCAATTAGATCTGG
1 ATCAGAAACAAACAGAGATATCAATTAGATCTGG
* *
11090 ATCAGAAACAAGCAGAGATATCAATTAGATTTGG
1 ATCAGAAACAAACAGAGATATCAATTAGATCTGG
11124 A
1 A
11125 AACATGGTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.46, C:0.13, G:0.19, T:0.22
Consensus pattern (34 bp):
ATCAGAAACAAACAGAGATATCAATTAGATCTGG
Found at i:13702 original size:7 final size:7
Alignment explanation
Indices: 13685--13715 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
13675 GCCTGCTCGT
13685 CAAAAAA
1 CAAAAAA
13692 -AAAAAA
1 CAAAAAA
13698 CAAAAAA
1 CAAAAAA
13705 CAAAAAA
1 CAAAAAA
13712 CAAA
1 CAAA
13716 CAAAAACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (7 bp):
CAAAAAA
Found at i:13709 original size:14 final size:13
Alignment explanation
Indices: 13685--13721 Score: 56
Period size: 14 Copynumber: 2.7 Consensus size: 13
13675 GCCTGCTCGT
13685 CAAAAAAAAAAAA
1 CAAAAAAAAAAAA
13698 CAAAAAACAAAAAA
1 CAAAAAA-AAAAAA
13712 CAAACAAAAA
1 CAAA-AAAAA
13722 CAAAGAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 7 0.32
14 12 0.55
15 3 0.14
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (13 bp):
CAAAAAAAAAAAA
Found at i:13711 original size:18 final size:17
Alignment explanation
Indices: 13688--13725 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
13678 TGCTCGTCAA
13688 AAAAAAAAAACAAAAAAC
1 AAAAAAAAAAC-AAAAAC
*
13706 AAAAAACAAACAAAAAC
1 AAAAAAAAAACAAAAAC
13723 AAA
1 AAA
13726 GAAAGAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAACAAAAAC
Found at i:18089 original size:21 final size:22
Alignment explanation
Indices: 18063--18200 Score: 115
Period size: 22 Copynumber: 6.3 Consensus size: 22
18053 TTGGTAATAA
18063 AAAATTTCATAGGAAGGTTA-C
1 AAAATTTCATAGGAAGGTTATC
*
18084 AAAATTTCATAGGAAGGTTTATT
1 AAAATTTCATAGGAAGG-TTATC
**
18107 AAAATTTCATAGTTAGGTTATC
1 AAAATTTCATAGGAAGGTTATC
* * *
18129 TAAGTTTCATATGG-AGTTTATC
1 AAAATTTCATA-GGAAGGTTATC
*
18151 ACAATTTCATAGGTAA--TTATC
1 AAAATTTCATAGG-AAGGTTATC
* * *
18172 AAAATTTTATAACG-TGGTTATC
1 AAAATTTCAT-AGGAAGGTTATC
18194 AAAATTT
1 AAAATTT
18201 AATAAAAATA
Statistics
Matches: 94, Mismatches: 15, Indels: 15
0.76 0.12 0.12
Matches are distributed among these distances:
21 32 0.34
22 45 0.48
23 17 0.18
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.39
Consensus pattern (22 bp):
AAAATTTCATAGGAAGGTTATC
Found at i:18297 original size:2 final size:2
Alignment explanation
Indices: 18292--18397 Score: 63
Period size: 2 Copynumber: 53.0 Consensus size: 2
18282 GATATGTGTG
* * * * * * *
18292 TA TA TA TA TA TA TA TA TA TA TT TA AA AA TGA TA AA GA TA TG CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA
* * * * * *
18335 TA TA TA TA TA TA TA TA TT TA -A AA TGA TA AA GA TA TG CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA
18377 TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
18398 CTAATACAGG
Statistics
Matches: 79, Mismatches: 21, Indels: 8
0.73 0.19 0.07
Matches are distributed among these distances:
1 2 0.03
2 73 0.92
3 4 0.05
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (2 bp):
TA
Found at i:19906 original size:2 final size:2
Alignment explanation
Indices: 19895--19927 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
19885 TAGTCTTAAT
19895 TA TA -A TA TA TA TA TA TA TA TA TA TA CTA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA T
19928 TATTTTTAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 26 0.90
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:24266 original size:24 final size:25
Alignment explanation
Indices: 24211--24273 Score: 65
Period size: 26 Copynumber: 2.5 Consensus size: 25
24201 TTAAAAAAAC
*
24211 ATAAATATATATTTATTATTTTGCAA
1 ATAAATATATATTTATCATTTT-CAA
* *
24237 AGAAATATATATTTATCCTTTT-AA
1 ATAAATATATATTTATCATTTTCAA
*
24261 TTAAATAGTATAT
1 ATAAATA-TATAT
24274 ATTTAATATA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 7 0.23
25 5 0.16
26 19 0.61
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (25 bp):
ATAAATATATATTTATCATTTTCAA
Found at i:24286 original size:19 final size:21
Alignment explanation
Indices: 24267--24307 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
24257 TTAATTAAAT
24267 AGTATATATT-TAATATAATA
1 AGTATATATTATAATATAATA
*
24287 ATTATATATTCATAATATAAT
1 AGTATATATT-ATAATATAAT
24308 TCCCGTTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
22 9 0.50
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (21 bp):
AGTATATATTATAATATAATA
Found at i:24929 original size:19 final size:19
Alignment explanation
Indices: 24902--24942 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
24892 GTACTATGGG
24902 TTGAATCTT-GTGTTGTATT
1 TTGAATCTTCG-GTTGTATT
*
24921 TTGATTCTTCGGTTGTATT
1 TTGAATCTTCGGTTGTATT
24940 TTG
1 TTG
24943 TTGACTATGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 19 0.95
20 1 0.05
ACGTcount: A:0.12, C:0.07, G:0.22, T:0.59
Consensus pattern (19 bp):
TTGAATCTTCGGTTGTATT
Found at i:26602 original size:2 final size:2
Alignment explanation
Indices: 26595--26620 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
26585 TGAGTAAGAC
26595 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
26621 CCTACATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28063 original size:27 final size:27
Alignment explanation
Indices: 28012--28063 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
28002 TACTCAACTT
* **
28012 TTCCTACTCCTTTACATTACCAAACGA
1 TTCCTACTCCTTAACAACACCAAACGA
*
28039 TTCCTACTCCTTAACAACACTAAAC
1 TTCCTACTCCTTAACAACACCAAAC
28064 TACACCAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.33, C:0.35, G:0.02, T:0.31
Consensus pattern (27 bp):
TTCCTACTCCTTAACAACACCAAACGA
Found at i:28317 original size:19 final size:19
Alignment explanation
Indices: 28277--28313 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
28267 AATTTTTAAG
*
28277 TAAAAATGTAATATATAAA
1 TAAAAATATAATATATAAA
28296 TAAAAATATAATAT-TAAA
1 TAAAAATATAATATATAAA
28314 ATAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:28561 original size:16 final size:15
Alignment explanation
Indices: 28529--28574 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
28519 TTGAAGGATA
*
28529 TTTAAGAATATATTTT
1 TTTAAGGATATA-TTT
*
28545 TTTAAAGGATTTATTT
1 TTT-AAGGATATATTT
28561 TTTAAGGATATATT
1 TTTAAGGATATATT
28575 ATAGATGATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
15 10 0.38
16 9 0.35
17 7 0.27
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (15 bp):
TTTAAGGATATATTT
Done.