Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017046.1 Corchorus olitorius cultivar O-4 contig17079, 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: 52800
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:6512 original size:2 final size:2
Alignment explanation
Indices: 6505--6529 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6495 TATTTTTCAT
6505 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
6530 TTAAGGGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13290 original size:7 final size:7
Alignment explanation
Indices: 13278--13329 Score: 77
Period size: 7 Copynumber: 7.4 Consensus size: 7
13268 TTCTTTCACA
13278 ACATCCT
1 ACATCCT
13285 ACATCCT
1 ACATCCT
**
13292 GTATCCT
1 ACATCCT
*
13299 GCATCCT
1 ACATCCT
13306 ACATCCT
1 ACATCCT
13313 ACATCCT
1 ACATCCT
13320 ACATCCT
1 ACATCCT
13327 ACA
1 ACA
13330 ATATTATTGC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 41 1.00
ACGTcount: A:0.27, C:0.40, G:0.04, T:0.29
Consensus pattern (7 bp):
ACATCCT
Found at i:15295 original size:34 final size:34
Alignment explanation
Indices: 15252--15320 Score: 113
Period size: 34 Copynumber: 2.0 Consensus size: 34
15242 TGTCACCCTT
*
15252 GCACAAATTATTTAATCTGATATT-ACTTGATACA
1 GCACAAATTATTTAATCT-ATATTCAATTGATACA
15286 GCACAAATTATTTAATCTATATTCAATTGATACA
1 GCACAAATTATTTAATCTATATTCAATTGATACA
15320 G
1 G
15321 AAGTTACCTC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
33 5 0.15
34 28 0.85
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38
Consensus pattern (34 bp):
GCACAAATTATTTAATCTATATTCAATTGATACA
Found at i:17794 original size:19 final size:19
Alignment explanation
Indices: 17772--17808 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
17762 AATTGAATAG
*
17772 AAGATATAAGGTTAATACT
1 AAGATATAAGATTAATACT
17791 AAGATATAAGATTAATAC
1 AAGATATAAGATTAATAC
17809 CAAAAGGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.05, G:0.14, T:0.30
Consensus pattern (19 bp):
AAGATATAAGATTAATACT
Found at i:22125 original size:10 final size:10
Alignment explanation
Indices: 22095--22152 Score: 73
Period size: 10 Copynumber: 5.6 Consensus size: 10
22085 GATTTGGGTA
22095 TGTTTTTTTT
1 TGTTTTTTTT
22105 TGTTCTGTTTTGT
1 TGTT-T-TTTT-T
*
22118 TTTTTTTTTT
1 TGTTTTTTTT
22128 TGTTTTTTTT
1 TGTTTTTTTT
22138 TGTTTTTTTT
1 TGTTTTTTTT
22148 T-TTTT
1 TGTTTT
22153 GAGTTCTTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
9 4 0.09
10 25 0.58
11 5 0.12
12 5 0.12
13 4 0.09
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.88
Consensus pattern (10 bp):
TGTTTTTTTT
Found at i:22127 original size:23 final size:23
Alignment explanation
Indices: 22097--22151 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
22087 TTTGGGTATG
22097 TTTTTTTTTGTTCTGTTTTGTTT
1 TTTTTTTTTGTTCTGTTTTGTTT
* *
22120 TTTTTTTTTGTTTTTTTTTGTTT
1 TTTTTTTTTGTTCTGTTTTGTTT
22143 TTTTTTTTT
1 TTTTTTTTT
22152 TGAGTTCTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.00, C:0.02, G:0.09, T:0.89
Consensus pattern (23 bp):
TTTTTTTTTGTTCTGTTTTGTTT
Found at i:22171 original size:1 final size:1
Alignment explanation
Indices: 22097--22152 Score: 58
Period size: 1 Copynumber: 56.0 Consensus size: 1
22087 TTTGGGTATG
* * * * * *
22097 TTTTTTTTTGTTCTGTTTTGTTTTTTTTTTTTGTTTTTTTTTGTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
22153 GAGTTCTTTA
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.00, C:0.02, G:0.09, T:0.89
Consensus pattern (1 bp):
T
Found at i:28558 original size:437 final size:434
Alignment explanation
Indices: 27589--28630 Score: 1272
Period size: 437 Copynumber: 2.4 Consensus size: 434
27579 AATATATTAT
* * * *
27589 CAATCGAAATCACAAAATTTCA-AAAGTATTTTTTAAAATTTAAACATGAAAATTAGCTTTTGAG
1 CAATCGAAACCACAAAATTT-AGAAAGCATTTTTT-AAATTAAAACATAAAAATT-GCTTTTGAG
* * * *
27653 TTCTTTCATGAAAGAGTTGTAGATCATAAAATTACTTTTTAATAGACACTTGAATTACCTTAATT
63 TTC-TTCATGAAA-A-TTGTAGATCATGAAATTACCTTTTAATAGACACTTGAATCAACTTAATT
* *
27718 GGACAAATAGAACATAGAAAATAAAAAATGAAA-CGTTAAATCGAGTAAGATAGAATTTGTAAAG
125 GGACAAATAGAACAAAGAATA-AAAAAAT-AAATCGTTAAATCGAGTAAGATAGAATTTGTAAAG
* * *
27782 AACTAAGTAGCATAAATATATAAAATAGAAAAGTATGAGGGTCATTTGATAACTAATTCAAATAA
188 AACTAAGTAG-------ATATAAAATAGAAAAATATGAGGGTCATTTGATAAATAATCCAAATAA
* * * *
27847 GAAATTATTTTTTAATGGATATCTTGAAACATAAAAATTCCCTTCTGAACCCTTCATGAAACTCG
246 GAAAATATTTGTTAATGGAGATCTTGAAACATAAAAACTCCCTTCTGAACCCTTCATGAAACTCG
* * * * *
27912 TAGCTCAAACTAACTTTCGGGTTCTTCATGAAAGTCGTAGATCATACAGTAACCTTTTAACCGAC
311 TAGATCAAACTAACTTTCGGGTCCTTCAAGAAAGTCGTAAATCATACAATAACCTTTTAACCGAC
* * * *
27977 ACTTGAATAACTTTAATCGGACATGTGGATCAAAAATTATATGGTATTAAATAGACCAA
376 ACTTCAATAACTTCAATCGGACATGTGGATCAAAAATTATACGATATTAAATAGACCAA
* *
28036 CAATCGAAACGACCAAATTTAGAAAGCATTTTTTTAAATTAAAACATAAAAATTTGCTTTTGAGT
1 CAATCGAAACCACAAAATTTAGAAAGCA-TTTTTTAAATTAAAACATAAAAA-TTGCTTTTGAGT
* * * * *
28101 CCTTCATGAAAGTTGTAGATCATGAAATTACCTTTTAATAGACACATGAATCAATTTAATCGGAC
64 TCTTCATGAAAATTGTAGATCATGAAATTACCTTTTAATAGACACTTGAATCAACTTAATTGGAC
28166 AAATAGAACAAAGAATAAAAAAATAAATC-TTAAA-CGTTAGATGAAGATAGAATTTGTAAAGAA
129 AAATAGAACAAAGAATAAAAAAATAAATCGTTAAATCG--AG-T-AAGATAGAATTTGTAAAGAA
* * * * *
28229 CTAAGTAG-TATAAAGTAGAAAAATATTAGGGTTATTTGATAAATAATCCAAATACGAAAATGTT
190 CTAAGTAGATATAAAATAGAAAAATATGAGGGTCATTTGATAAATAATCCAAATAAGAAAATATT
* * *
28293 TGTTAATGGAGATCTTGAAGCATAAAAACTCCCTTTTGAGCCCTTCATGAAACTCGTAGATCAAA
255 TGTTAATGGAGATCTTGAAACATAAAAACTCCCTTCTGAACCCTTCATGAAACTCGTAGATCAAA
* * * *
28358 TTTAGCTTTCGGGTCCTTTAAGAAAGTCGTAAATCATGCAATAACCTTTTAACCGACACTTCAAT
320 -CTAACTTTCGGGTCCTTCAAGAAAGTCGTAAATCATACAATAACCTTTTAACCGACACTTCAAT
* **
28423 AACTTCAATCGGATATGTGGA-CAAAAAATTATACGATATTAAATTA-ACCGG
384 AACTTCAATCGGACATGTGGATC-AAAAATTATACGATATTAAA-TAGACCAA
* * * * *
28474 CAATCAAAACCACAAAATTTTGGAAGCATTTTTTAGAATCAAAACATTAAAATTGCTTTTGAGTT
1 CAATCGAAACCACAAAATTTAGAAAGCATTTTTTA-AATTAAAACATAAAAATTGCTTTTGAGTT
* *
28539 CTTCATGAAAATTGTAGATCATGAAATAACCTTTTAATAGACACTTGAATCAGCTTAATTGGACA
65 CTTCATGAAAATTGTAGATCATGAAATTACCTTTTAATAGACACTTGAATCAACTTAATTGGACA
* * *
28604 AATAGGAA-AAAAAATACAAATATAAAT
130 AATA-GAACAAAGAATAAAAAAATAAAT
28631 GTTTAATTGG
Statistics
Matches: 517, Mismatches: 65, Indels: 36
0.84 0.11 0.06
Matches are distributed among these distances:
437 204 0.39
438 135 0.26
439 2 0.00
441 2 0.00
442 8 0.02
443 10 0.02
444 62 0.12
445 28 0.05
446 10 0.02
447 48 0.09
448 8 0.02
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (434 bp):
CAATCGAAACCACAAAATTTAGAAAGCATTTTTTAAATTAAAACATAAAAATTGCTTTTGAGTTC
TTCATGAAAATTGTAGATCATGAAATTACCTTTTAATAGACACTTGAATCAACTTAATTGGACAA
ATAGAACAAAGAATAAAAAAATAAATCGTTAAATCGAGTAAGATAGAATTTGTAAAGAACTAAGT
AGATATAAAATAGAAAAATATGAGGGTCATTTGATAAATAATCCAAATAAGAAAATATTTGTTAA
TGGAGATCTTGAAACATAAAAACTCCCTTCTGAACCCTTCATGAAACTCGTAGATCAAACTAACT
TTCGGGTCCTTCAAGAAAGTCGTAAATCATACAATAACCTTTTAACCGACACTTCAATAACTTCA
ATCGGACATGTGGATCAAAAATTATACGATATTAAATAGACCAA
Found at i:28637 original size:40 final size:40
Alignment explanation
Indices: 28593--28672 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
28583 TTGAATCAGC
28593 TTAATTGGACAAATAGGAAAAAAAATACAAATATAAATGT
1 TTAATTGGACAAATAGGAAAAAAAATACAAATATAAATGT
28633 TTAATTGGACAAATAGGAAAAAAAATACAAATATAAATGT
1 TTAATTGGACAAATAGGAAAAAAAATACAAATATAAATGT
28673 GAACGCGTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.57, C:0.05, G:0.12, T:0.25
Consensus pattern (40 bp):
TTAATTGGACAAATAGGAAAAAAAATACAAATATAAATGT
Found at i:29281 original size:31 final size:29
Alignment explanation
Indices: 29221--29287 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 29
29211 GAGAGTTTAG
*
29221 GGGGGCAAAACGTCCAAAATTAAAGTTCA
1 GGGGGCAAAACGTCCAAAAGTAAAGTTCA
*
29250 GGGGGCAAAACGTCCAAACCGTACAAGTTCA
1 GGGGGCAAAACGTCCAAA-AGTA-AAGTTCA
*
29281 GGAGGCA
1 GGGGGCA
29288 GAAAATGTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 18 0.55
30 2 0.06
31 13 0.39
ACGTcount: A:0.37, C:0.21, G:0.28, T:0.13
Consensus pattern (29 bp):
GGGGGCAAAACGTCCAAAAGTAAAGTTCA
Found at i:35317 original size:8 final size:8
Alignment explanation
Indices: 35299--35343 Score: 54
Period size: 8 Copynumber: 5.4 Consensus size: 8
35289 AATGAAAGTC
35299 TTTCTTTTT
1 TTTC-TTTT
35308 TTTCTTTT
1 TTTCTTTT
*
35316 TTTCTTTA
1 TTTCTTTT
35324 TTTCTTTT
1 TTTCTTTT
*
35332 CTTCTTCTT
1 TTTCTT-TT
35341 TTT
1 TTT
35344 TTGTATTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
8 23 0.74
9 8 0.26
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTCTTTT
Found at i:35342 original size:25 final size:25
Alignment explanation
Indices: 35299--35351 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
35289 AATGAAAGTC
*
35299 TTTCTTTTTTTTCTTTTTTTCTT-TA
1 TTTCTTTTTCTTCTTTTTTT-TTGTA
35324 TTTC-TTTTCTTCTTCTTTTTTTGTA
1 TTTCTTTTTCTTCTT-TTTTTTTGTA
35349 TTT
1 TTT
35352 TTTCCTTGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 11 0.44
25 14 0.56
ACGTcount: A:0.04, C:0.13, G:0.02, T:0.81
Consensus pattern (25 bp):
TTTCTTTTTCTTCTTTTTTTTTGTA
Found at i:39741 original size:35 final size:35
Alignment explanation
Indices: 39691--39757 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
39681 TAATGGCCAA
*
39691 AAATATAGAGCTTACATGAGGATGGCACCTCACTT
1 AAATATAGAGCTTACAAGAGGATGGCACCTCACTT
*
39726 AAATATAGAGTTTACAAGAGGATGGCACCTCA
1 AAATATAGAGCTTACAAGAGGATGGCACCTCA
39758 GGACAATTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (35 bp):
AAATATAGAGCTTACAAGAGGATGGCACCTCACTT
Found at i:46007 original size:2 final size:2
Alignment explanation
Indices: 46000--46029 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
45990 TCACTTCAAC
46000 AT AT 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 AT AT
46030 TAATATTTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46436 original size:46 final size:46
Alignment explanation
Indices: 46369--46462 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
46359 ACTGGGAAAA
46369 GCCATTATGTTACACAAGAACTGGGCAAGTTGTAATAGATTATGAT
1 GCCATTATGTTACACAAGAACTGGGCAAGTTGTAATAGATTATGAT
46415 GCCATTATGTTACACAAGAACTGGGCAAGTTGTAATAGATTATGAT
1 GCCATTATGTTACACAAGAACTGGGCAAGTTGTAATAGATTATGAT
46461 GC
1 GC
46463 GAGGAGCTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (46 bp):
GCCATTATGTTACACAAGAACTGGGCAAGTTGTAATAGATTATGAT
Done.