Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011549.1 Corchorus capsularis cultivar CVL-1 contig11570, 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: 26093
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Found at i:2597 original size:22 final size:22
Alignment explanation
Indices: 2572--2617 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
2562 AAACGTGGCG
2572 TTTTGAGATGGCAAACAGTTGT
1 TTTTGAGATGGCAAACAGTTGT
****
2594 TTTTTTTTTGGCAAACAGTTGT
1 TTTTGAGATGGCAAACAGTTGT
2616 TT
1 TT
2618 AAGATAACGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.22, C:0.09, G:0.22, T:0.48
Consensus pattern (22 bp):
TTTTGAGATGGCAAACAGTTGT
Found at i:3118 original size:32 final size:31
Alignment explanation
Indices: 3082--3174 Score: 107
Period size: 32 Copynumber: 2.9 Consensus size: 31
3072 ACGGGTCAGG
* *
3082 TTTGGTTCAGGCTTAAGTT-AGGTCGGGTTGAA
1 TTTGGGTCAGG-TTAA-TTCAGGTCGGGTTAAA
* *
3114 TTTGGGTCGGGTTAATTCGGGTACGGGTTAAA
1 TTTGGGTCAGGTTAATTCAGGT-CGGGTTAAA
3146 TTTGGGTCAGGTTAATTCAGGTTCGGGTT
1 TTTGGGTCAGGTTAATTCAGG-TCGGGTT
3175 CAGTTTAGGT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
30 2 0.04
31 7 0.13
32 42 0.81
33 1 0.02
ACGTcount: A:0.17, C:0.10, G:0.35, T:0.38
Consensus pattern (31 bp):
TTTGGGTCAGGTTAATTCAGGTCGGGTTAAA
Found at i:3152 original size:17 final size:15
Alignment explanation
Indices: 3102--3162 Score: 77
Period size: 16 Copynumber: 3.9 Consensus size: 15
3092 GCTTAAGTTA
3102 GGTCGGGTTGAATTTG
1 GGTCGGGTT-AATTTG
*
3118 GGTCGGGTTAATTCG
1 GGTCGGGTTAATTTG
3133 GGTACGGGTTAAATTTG
1 GGT-CGGGTT-AATTTG
*
3150 GGTCAGGTTAATT
1 GGTCGGGTTAATT
3163 CAGGTTCGGG
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
15 12 0.30
16 20 0.50
17 8 0.20
ACGTcount: A:0.18, C:0.08, G:0.38, T:0.36
Consensus pattern (15 bp):
GGTCGGGTTAATTTG
Found at i:3351 original size:16 final size:16
Alignment explanation
Indices: 3330--3397 Score: 64
Period size: 16 Copynumber: 4.2 Consensus size: 16
3320 AATTTTTGGA
*
3330 TTCGGGTTAGGGTTTT
1 TTCGGGTTCGGGTTTT
* *
3346 TTCGGGTTCTGATTTT
1 TTCGGGTTCGGGTTTT
* * *
3362 TTCCGGTTTGAGTTTT
1 TTCGGGTTCGGGTTTT
**
3378 TTCGAATTCGGGTTTT
1 TTCGGGTTCGGGTTTT
3394 TTCG
1 TTCG
3398 AATTCGGGTA
Statistics
Matches: 39, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.07, C:0.12, G:0.28, T:0.53
Consensus pattern (16 bp):
TTCGGGTTCGGGTTTT
Found at i:3398 original size:16 final size:16
Alignment explanation
Indices: 3373--3406 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
3363 TCCGGTTTGA
3373 GTTTTTTCGAATTCGG
1 GTTTTTTCGAATTCGG
3389 GTTTTTTCGAATTCGG
1 GTTTTTTCGAATTCGG
3405 GT
1 GT
3407 ATTTGACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.26, T:0.50
Consensus pattern (16 bp):
GTTTTTTCGAATTCGG
Found at i:4429 original size:1 final size:1
Alignment explanation
Indices: 4423--4448 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
4413 TCAAGAGTTG
4423 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
4449 AAAGAATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:15155 original size:658 final size:643
Alignment explanation
Indices: 14208--15508 Score: 2332
Period size: 658 Copynumber: 2.0 Consensus size: 643
14198 TATACATATA
* * *
14208 CATAATGGTTTTTATAAAAATTATTATTTTACAAGTGGGGTTGCCCCGCACTTTGCGGCCGGGTT
1 CATAATGGTTTTTATAAAAATTATTATTTTACAAGTGGGGCTGCCCCACACTTCGCGGCCGGGTT
*
14273 TTGCATAACCTTTGTAGTGTATTTTTCACGGATTCTTTGATGTATTTGTTAATTTGGATCAATTT
66 TTGCATAACCTTTGTAGTGTATTTTTCACGGATTCTTTGATGTATTTGTTAATTTGGATCAAATT
14338 TTTTTTACTTTAACATTCATACTGAAATTCACTTTTTCTCACTTAGGCAATTTCTCGAGAGTTTT
131 TTTTTTACTTTAACATTCATACTGAAATTCACTTTTTCTCACTTAGGCAATTTCTCGAGAGTTTT
* * *
14403 ATTAGCTATTTAGCAATGAAGACATTGGCTCCTCAACATATAACTTAGATTTCAATAAAGGAAAC
196 ATTAGCTATTGAGCAATGAAGACATTGACCCCTCAACATATAACTTAGATTTCAATAAAGGAAAC
* * *
14468 TGAGGACACTCGCTTCCTCACAGTGTAACTTAGATTTTAATAAAGGAAACTGTCTTCATCCATTA
261 TGAGGACACCCGCTTCCTCACAATGTAACTTAGATTTTAATAAAGGAAACTGTCTCCATCCATTA
14533 CAAATAAATATAAGTTTCATTACATATAATCCTATTTGCATAGAATATAATCATAAAACCAACAA
326 CAAATAAATATAAGTTTCATTACATATAATCCTATTTGCATAGAATATAATCATAAAACCAACAA
14598 TCTGTTGTGTTTTCCTATCCTGCTATGTATTTTCTTTTCAAATCATTCCTCCTTATAACTTTCAA
391 TCTGTTGTGTTTTCCTATCCTGCTATGTATTTTCTTTTCAAATCATTCCTCCTTATAACTTTCAA
14663 AATATAGATTTCTTCATTGTTTTGCATTATTGGTTGAATTGAGAATTCTTTCAAGTATGAGAACA
456 AATATAGATTTCTTCATTGTTTTGCATTATTGGTTGAATTGAGAATTCTTTCAAGTATGAGAACA
14728 TGCAATTACCTCCATTATACTGTGTAAGTTCGATGATTATCACATGTTTGAAGTGCAAGCTTTCT
521 TGCAATTACCTCCATTATACTGTGTAAGTTCGATGATTATCACATGTTTGAAGTGCAAGCTTTCT
14793 GCCATTAAGTGCGCCTCAGCTGTTGAGAGCCTTATCCCAGGGATCACTATCATTAGTG
586 GCCATTAAGTGCGCCTCAGCTGTTGAGAGCCTTATCCCAGGGATCACTATCATTAGTG
*
14851 CATAATGGTTTTTATAAAAATTATTATTTTACAAGTGGGGCTGCCCCACACTTCGCGGCGGGGTT
1 CATAATGGTTTTTATAAAAATTATTATTTTACAAGTGGGGCTGCCCCACACTTCGCGGCCGGGTT
*
14916 TTGCATTACCTTTGTAGTGTATTTTTCACGGATTCTTTGATGTATTTGTTAATTTGGATCAAATT
66 TTGCATAACCTTTGTAGTGTATTTTTCACGGATTCTTTGATGTATTTGTTAATTTGGATCAAATT
14981 TTTTTTACTTTAACATTCATACTAAAGTCATTCCAAATAAAATTCACTTTTTCTCACTTAGGCAA
131 TTTTTTACTTTAACATTCATACT---G------------AAATTCACTTTTTCTCACTTAGGCAA
15046 TTTCTCGAGAGTTTTATTAGCTATTGAGCAATGAAGACATTGACCCCTCAACATATAACTTAGAT
181 TTTCTCGAGAGTTTTATTAGCTATTGAGCAATGAAGACATTGACCCCTCAACATATAACTTAGAT
15111 TTCAATAAAGGAAACTGAGGACACCCGCTTCCTCACAATGTAACTTAGATTTTAATAAAGGAAAC
246 TTCAATAAAGGAAACTGAGGACACCCGCTTCCTCACAATGTAACTTAGATTTTAATAAAGGAAAC
15176 TGTCTCCATCCATTACAAATAAATATAAGTTTCATTACATATAATCCTATTTGCATAGAATATAA
311 TGTCTCCATCCATTACAAATAAATATAAGTTTCATTACATATAATCCTATTTGCATAGAATATAA
15241 TCATAAAACCAACAATCTGTTGTGTTTTCCTATCCTGCTATGTATTTTCTTTTCAAATCATTCCT
376 TCATAAAACCAACAATCTGTTGTGTTTTCCTATCCTGCTATGTATTTTCTTTTCAAATCATTCCT
*
15306 CCTTATAACTTTCAAAATATAGATTTCTTCATTGTTTTGCGTTATTGGTTGAATTGAGAATTCTT
441 CCTTATAACTTTCAAAATATAGATTTCTTCATTGTTTTGCATTATTGGTTGAATTGAGAATTCTT
* *
15371 TCAAGTATGAGAACATGCAATTACCTCCATTATATTGTGTAAGTTCGATGATTATCACCTGTTTG
506 TCAAGTATGAGAACATGCAATTACCTCCATTATACTGTGTAAGTTCGATGATTATCACATGTTTG
15436 AAGTGCAAGCTTTCTGCCATTAAGTGCGCCTCAGCTGTTGAGAGCCTTATCCCAGGGATCACTAT
571 AAGTGCAAGCTTTCTGCCATTAAGTGCGCCTCAGCTGTTGAGAGCCTTATCCCAGGGATCACTAT
15501 CATTAGTG
636 CATTAGTG
15509 GTTTATAAGC
Statistics
Matches: 628, Mismatches: 15, Indels: 15
0.95 0.02 0.02
Matches are distributed among these distances:
643 147 0.23
646 1 0.00
658 480 0.76
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (643 bp):
CATAATGGTTTTTATAAAAATTATTATTTTACAAGTGGGGCTGCCCCACACTTCGCGGCCGGGTT
TTGCATAACCTTTGTAGTGTATTTTTCACGGATTCTTTGATGTATTTGTTAATTTGGATCAAATT
TTTTTTACTTTAACATTCATACTGAAATTCACTTTTTCTCACTTAGGCAATTTCTCGAGAGTTTT
ATTAGCTATTGAGCAATGAAGACATTGACCCCTCAACATATAACTTAGATTTCAATAAAGGAAAC
TGAGGACACCCGCTTCCTCACAATGTAACTTAGATTTTAATAAAGGAAACTGTCTCCATCCATTA
CAAATAAATATAAGTTTCATTACATATAATCCTATTTGCATAGAATATAATCATAAAACCAACAA
TCTGTTGTGTTTTCCTATCCTGCTATGTATTTTCTTTTCAAATCATTCCTCCTTATAACTTTCAA
AATATAGATTTCTTCATTGTTTTGCATTATTGGTTGAATTGAGAATTCTTTCAAGTATGAGAACA
TGCAATTACCTCCATTATACTGTGTAAGTTCGATGATTATCACATGTTTGAAGTGCAAGCTTTCT
GCCATTAAGTGCGCCTCAGCTGTTGAGAGCCTTATCCCAGGGATCACTATCATTAGTG
Found at i:17749 original size:22 final size:21
Alignment explanation
Indices: 17714--17778 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
17704 CAATTGGAAT
*
17714 AATTAATA-ATTTAATCTAGATA
1 AATTAATATA-TTAAT-TACATA
*
17736 AATTAATATATTAATTTCATA
1 AATTAATATATTAATTACATA
* * *
17757 AGTTAATATATTGATTCCATA
1 AATTAATATATTAATTACATA
17778 A
1 A
17779 GTAAAATTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
21 23 0.62
22 13 0.35
23 1 0.03
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.43
Consensus pattern (21 bp):
AATTAATATATTAATTACATA
Found at i:17762 original size:21 final size:21
Alignment explanation
Indices: 17733--17780 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
17723 TTTAATCTAG
* *
17733 ATAAATTAATATATTAATTTC
1 ATAAGTTAATATATTAATTCC
*
17754 ATAAGTTAATATATTGATTCC
1 ATAAGTTAATATATTAATTCC
17775 ATAAGT
1 ATAAGT
17781 AAAATTATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (21 bp):
ATAAGTTAATATATTAATTCC
Found at i:19501 original size:58 final size:58
Alignment explanation
Indices: 19411--19554 Score: 261
Period size: 58 Copynumber: 2.5 Consensus size: 58
19401 CCTTTTGTTT
*
19411 TTAACTGACTCAATTACCCTGAATTAAGTCCTTATTACTGATTATCCTTCTTCGATTC
1 TTAACTGACTCAATTACCCTGAATTAAGTCCTTATTACTGATTATCCTTCTTAGATTC
*
19469 TTAACTGACTCAATTACCCTGAATTAAGTCCTTATTACTGATTATTCTTCTTAGATTC
1 TTAACTGACTCAATTACCCTGAATTAAGTCCTTATTACTGATTATCCTTCTTAGATTC
*
19527 TTAACTGACTCAATTACCTTGAATTAAG
1 TTAACTGACTCAATTACCCTGAATTAAG
19555 CCATTTTATT
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 83 1.00
ACGTcount: A:0.28, C:0.22, G:0.09, T:0.41
Consensus pattern (58 bp):
TTAACTGACTCAATTACCCTGAATTAAGTCCTTATTACTGATTATCCTTCTTAGATTC
Found at i:20042 original size:35 final size:35
Alignment explanation
Indices: 19590--20037 Score: 603
Period size: 35 Copynumber: 12.7 Consensus size: 35
19580 TTCTTACTAA
* * *
19590 ACTTAATTACCCTGACTTAAGTT-ACTTATTGACTC
1 ACTTAATTACCCTGAATTAAGTTGA-TTACTGACTT
* *
19625 ACTTAATTACCCTGGATTTAAGTTGATTACTGACTC
1 ACTTAATTACCCT-GAATTAAGTTGATTACTGACTT
* * *
19661 ACTTAATTATCCTGAATTAAGTTGATTAATGACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
*
19696 ACTTAATTACCCTGAATTAAGTTTATTACTGACTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
*
19731 ACTTAATCACCCTGAATTAAGTTGATTACTGACTT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
*
19766 ACTTAATTACCCTGAATTAAGTTGATTACTGAATT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
*
19801 ACTTAATTACCCTGAATTAAGTTGATTACTGACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
* *
19836 ACTTAATTACCCTGAATTAAGTTGATTATTGAATT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
* * *
19871 ACTTAATTACCCTGAATTAAGTTAATAACTGAATT
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
* *
19906 TCTTAATTACCCTGAATTAAGTT-ACTGACTGACTT
1 ACTTAATTACCCTGAATTAAGTTGA-TTACTGACTT
* *
19941 ACTTAATTACCCTGAATTAAGCTGATTACTGACTC
1 ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
** *
19976 ACTTAATCGCCCTGAATTAAGTTACTGACTTACTAACTT
1 ACTTAATTACCCTGAATTAAG-T--TGA-TTACTGACTT
20015 ACTTAATTACCCTGAATTAAGTT
1 ACTTAATTACCCTGAATTAAGTT
20038 ACTTATTACT
Statistics
Matches: 370, Mismatches: 35, Indels: 15
0.88 0.08 0.04
Matches are distributed among these distances:
34 1 0.00
35 305 0.82
36 32 0.09
37 1 0.00
38 4 0.01
39 27 0.07
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (35 bp):
ACTTAATTACCCTGAATTAAGTTGATTACTGACTT
Found at i:23442 original size:13 final size:13
Alignment explanation
Indices: 23424--23449 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
23414 AACCGGAAAG
23424 TGCTTAATGAACA
1 TGCTTAATGAACA
23437 TGCTTAATGAACA
1 TGCTTAATGAACA
23450 CAGGCTACTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGCTTAATGAACA
Found at i:24346 original size:60 final size:60
Alignment explanation
Indices: 24253--24369 Score: 234
Period size: 60 Copynumber: 1.9 Consensus size: 60
24243 AGGGCACCCA
24253 TGAAACGCTTGTCACGCCCCGACCCAGAGTCGACCACATGACAGCCGCCGTGTTACCCCG
1 TGAAACGCTTGTCACGCCCCGACCCAGAGTCGACCACATGACAGCCGCCGTGTTACCCCG
24313 TGAAACGCTTGTCACGCCCCGACCCAGAGTCGACCACATGACAGCCGCCGTGTTACC
1 TGAAACGCTTGTCACGCCCCGACCCAGAGTCGACCACATGACAGCCGCCGTGTTACC
24370 TCGTAATGCG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.22, C:0.39, G:0.23, T:0.15
Consensus pattern (60 bp):
TGAAACGCTTGTCACGCCCCGACCCAGAGTCGACCACATGACAGCCGCCGTGTTACCCCG
Found at i:24758 original size:14 final size:14
Alignment explanation
Indices: 24739--24767 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
24729 AGGGTTAACT
24739 AACATCACATTAAG
1 AACATCACATTAAG
24753 AACATCACATTAAG
1 AACATCACATTAAG
24767 A
1 A
24768 GTGAAGTGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.21, G:0.07, T:0.21
Consensus pattern (14 bp):
AACATCACATTAAG
Done.