Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013843.1 Corchorus capsularis cultivar CVL-1 contig13864, 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: 7707
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.35
Found at i:1495 original size:25 final size:25
Alignment explanation
Indices: 1461--1517 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
1451 TGAAAATTAC
* * *
1461 AAGTATATTACTTGGAAGTTTCTCT
1 AAGTTTATTACATGGAAGCTTCTCT
*
1486 AAGTTTATTACATGTAAGCTTCTCT
1 AAGTTTATTACATGGAAGCTTCTCT
1511 AGAGTTT
1 A-AGTTT
1518 TTTTTTGTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
25 22 0.81
26 5 0.19
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (25 bp):
AAGTTTATTACATGGAAGCTTCTCT
Found at i:1868 original size:14 final size:14
Alignment explanation
Indices: 1849--1876 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1839 GGCGGCACCA
1849 AATTAGATAATGAT
1 AATTAGATAATGAT
1863 AATTAGATAATGAT
1 AATTAGATAATGAT
1877 TAGAATGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (14 bp):
AATTAGATAATGAT
Found at i:3723 original size:49 final size:49
Alignment explanation
Indices: 3662--3761 Score: 182
Period size: 49 Copynumber: 2.0 Consensus size: 49
3652 TTTTGAGTAT
*
3662 TTCCATCATATGCAACATCATTATAGAATTTACGAAATTATTTAGGCTC
1 TTCCATCATATGCAACATCAATATAGAATTTACGAAATTATTTAGGCTC
*
3711 TTCCATCATATGCAACATCAATATAGAATTTCCGAAATTATTTAGGCTC
1 TTCCATCATATGCAACATCAATATAGAATTTACGAAATTATTTAGGCTC
3760 TT
1 TT
3762 GGATTAATGA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.37
Consensus pattern (49 bp):
TTCCATCATATGCAACATCAATATAGAATTTACGAAATTATTTAGGCTC
Found at i:4244 original size:22 final size:22
Alignment explanation
Indices: 4218--4264 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
4208 TAATTTTTAA
4218 TTAGTAGCAAATTTTGATATTT
1 TTAGTAGCAAATTTTGATATTT
4240 TTAGTAGCAAATTTTGATATTT
1 TTAGTAGCAAATTTTGATATTT
4262 TTA
1 TTA
4265 TATTGACCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.32, C:0.04, G:0.13, T:0.51
Consensus pattern (22 bp):
TTAGTAGCAAATTTTGATATTT
Found at i:4334 original size:18 final size:18
Alignment explanation
Indices: 4311--4365 Score: 82
Period size: 18 Copynumber: 3.3 Consensus size: 18
4301 ATGTCTTTTC
4311 TAGATCAATTTTAAAAAG
1 TAGATCAATTTTAAAAAG
4329 TAGATCAATTTT-AAAA-
1 TAGATCAATTTTAAAAAG
4345 T--ATCAATTTTAAAAAG
1 TAGATCAATTTTAAAAAG
4361 TAGAT
1 TAGAT
4366 TGCAGCTGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
14 9 0.27
15 4 0.12
16 2 0.06
17 4 0.12
18 14 0.42
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.36
Consensus pattern (18 bp):
TAGATCAATTTTAAAAAG
Found at i:4351 original size:14 final size:14
Alignment explanation
Indices: 4332--4358 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4322 TAAAAAGTAG
4332 ATCAATTTTAAAAT
1 ATCAATTTTAAAAT
4346 ATCAATTTTAAAA
1 ATCAATTTTAAAA
4359 AGTAGATTGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (14 bp):
ATCAATTTTAAAAT
Found at i:5868 original size:591 final size:595
Alignment explanation
Indices: 4496--6289 Score: 3203
Period size: 591 Copynumber: 3.0 Consensus size: 595
4486 GGGTAAACAT
4496 GTATTTTTATTTCATAAAAAACTATTAAGTTTTAATGGTTAATAAGTAATTTACTTCTTCTTAAA
1 GTATTTTTATTTCATAAAAAACTATTAAG-TTTAATGGTTAATAAGTAATTTACTTCTTCTTAAA
4561 ATTTTATTTAACTTTAACTTTTAAATTTTAATTGGTGGAGAACTTTTATTTAACTTTAACAAATG
65 ATTTTATTTAACTTTAACTTTTAAATTTTAATTGGTGGAGAACTTTTATTTAACTTTAACAAATG
*
4626 AAAAAATAGTAATTCATAATTCATAAAACTTCTACATATTAAAAGAAAAAAATTACATAAATCTT
130 AAAAAATAGTAATTCATAATTCATAAAACTTTTACATATTAAAAGAAAAAAATTACATAAATCTT
4691 TTGAATTTTTTTTGAGGAAAAAAATTGGAAAGGAGAAATTGGTATTAAAATTTTACAAATATAAA
195 TTGAATTTTTTTTGAGGAAAAAAATTGGAAAGGAGAAATTGGTATTAAAATTTTACAAATATAAA
*
4756 ATTGTTGAGGTCCTCCAAAATAAAAATGCCATTATTATCTACTTTCTCCTTCCTCTTCACGGCTT
260 ATTGTTGAGGTCCTCCAAAATAAAAATGCCATTATTATCTACTTTCTCCCTCCTCTTCACGGCTT
4821 AACTCCATTGGAAAATCCCGTATGCCATAAAAAGCTATCAATCCTATTCCAATTAACAACTCTCA
325 AACTCCATT-GAAAATCCCGTATGCCATAAAAAGCTATCAATCCTATTCCAATTAACAACTCTCA
4886 AACTTGATAGTTCTTCATAGTTTCAAAATGCAACTACTTTTGGATTGTAAGCTTTGAATCCTTGA
389 AACTTGATAGTTCTTCATAGTTTCAAAATGCAACTA-TTTTGGATTGTAAGCTTTGAATCCTTGA
* *
4951 TAAATCCCTTTCTATACAGTCACTATTTCCTAAAAAATCA-TTTTTGTCCCAAGAAAATTAAATA
453 TAAATCCCTTTCTATACAGTCACCATTTCCTAAAAAATCATTTTTTGTCCCAAGTAAATTAAATA
5015 ACCAGATAATCCAATCTTTTTATAAAAATATATATGCAGTTTGCAACACTTGGTGGTGGCCAATC
518 ACCAGATAATCCAATC--TTTAT----ATATATATGCAGTTTGCAACACTTGGTGGTGGCCAATC
*
5080 AATTTAAAGATTTATACTTC
577 AA-TTAAAGATTTCTACTTC
5100 GTATTTTTATTTCATAAAAAACTATTAAGCTTTAATGGTTAATAAGTAATTTACTTCTTCTTAAA
1 GTATTTTTATTTCATAAAAAACTATTAAG-TTTAATGGTTAATAAGTAATTTACTTCTTCTTAAA
*
5165 ATTTTATTTAATTTTAACTTTTAAATTTTAATTGGTGGAGAACTTTTATTTAACTTTAACAAAAT
65 ATTTTATTTAACTTTAACTTTTAAATTTTAATTGGTGGAGAACTTTTATTTAACTTTAAC-AAAT
5230 GAAAAAATAGTAATTCATAATTCATAAAACTTTTACATATT-AAAGAAAAAAATTACATAAATCT
129 GAAAAAATAGTAATTCATAATTCATAAAACTTTTACATATTAAAAGAAAAAAATTACATAAATCT
5294 TTTGAATTTTTTTTGAGGAAAAAAATTGGAAAGGAGAAATTGGTATTAAAATTTTACAAATATAA
194 TTTGAATTTTTTTTGAGGAAAAAAATTGGAAAGGAGAAATTGGTATTAAAATTTTACAAATATAA
* *
5359 AATTGTTGAGGTCCTCC-AAATAAAAATGCCCTTATTATCTACTTTCTCCCTCCTCTTCGCGGCT
259 AATTGTTGAGGTCCTCCAAAATAAAAATGCCATTATTATCTACTTTCTCCCTCCTCTTCACGGCT
*
5423 TAACTCCATT-AGAATCCCGTATGCCATAAAAAGCTATCAATCCTATTCCAATTAACAACTCTCA
324 TAACTCCATTGAAAATCCCGTATGCCATAAAAAGCTATCAATCCTATTCCAATTAACAACTCTCA
5487 AACTTGATAGTTCTTCATAGTTTCAAAATGCAACTATTTTGGATTGTAAGCTTTGAATCCTTGAT
389 AACTTGATAGTTCTTCATAGTTTCAAAATGCAACTATTTTGGATTGTAAGCTTTGAATCCTTGAT
*
5552 AAATCCCTTTCTATACAGTCACCCTTTCCTAAAAAATCATTTTTTGTCCCAAGTAAATTAAATAA
454 AAATCCCTTTCTATACAGTCACCATTTCCTAAAAAATCATTTTTTGTCCCAAGTAAATTAAATAA
*
5617 CCAGATAATCCAATC-TT-T-TATATATGCAGTTTGCAACACTTAGTGGTGGCCAATCAATTAAA
519 CCAGATAATCCAATCTTTATATATATATGCAGTTTGCAACACTTGGTGGTGGCCAATCAATTAAA
5679 GATTTCTACTTC
584 GATTTCTACTTC
*
5691 GTATTTTTATTTCATAAAAAACTATTAAGTTGTAATGGTTAATAAGTAATTTACTTCTTTTTAAA
1 GTATTTTTATTTCATAAAAAACTATTAAGTT-TAATGGTTAATAAGTAATTTACTTCTTCTTAAA
5756 ATTTTATTTAACTTTAACTTTTAAATTTTAATTGGTGGAGAACTTTTATTTAACTTTAACAAATG
65 ATTTTATTTAACTTTAACTTTTAAATTTTAATTGGTGGAGAACTTTTATTTAACTTTAACAAATG
5821 AAAAAATAGTAATTCATAATTCATAAAACTTTTACATATTAAAAG-AAAAAATTACATAAATCTT
130 AAAAAATAGTAATTCATAATTCATAAAACTTTTACATATTAAAAGAAAAAAATTACATAAATCTT
*
5885 TTGAA-TTTTTTTAAGG-AAAAAATTGGAAAGGAGAAATTGGTATTAAAATTTTACAAATATAAA
195 TTGAATTTTTTTTGAGGAAAAAAATTGGAAAGGAGAAATTGGTATTAAAATTTTACAAATATAAA
5948 ATTGTTGAGGTCCTCCAAAATAAAAATGCCATTATTATCTACTTTCTCCCTCCTCTTCACGGCTT
260 ATTGTTGAGGTCCTCCAAAATAAAAATGCCATTATTATCTACTTTCTCCCTCCTCTTCACGGCTT
6013 AACTCCATTGGAAAATCCCGTATGCCATAAAAAGCTATCAATCCTATTCCAATTAACAACTCTCA
325 AACTCCATT-GAAAATCCCGTATGCCATAAAAAGCTATCAATCCTATTCCAATTAACAACTCTCA
*
6078 AACCTGATAGTTCTTCATAGTTTCAAAATGCAACTATTTTGGATTGTAAGCTTTGAATCCTTGAT
389 AACTTGATAGTTCTTCATAGTTTCAAAATGCAACTATTTTGGATTGTAAGCTTTGAATCCTTGAT
6143 AAATCCCTTTCTATACAGTCACCATTTCCTAAAAAATCATTTTTTGTCCCAAGTAAATTAAATAA
454 AAATCCCTTTCTATACAGTCACCATTTCCTAAAAAATCATTTTTTGTCCCAAGTAAATTAAATAA
*
6208 CCAGATAATCCAATCTTTTTATAAAAATATATATGCAGTTTGCAAAACTTGGTGGTGGCCAATCA
519 CCAGATAATCCAATC--TTTAT----ATATATATGCAGTTTGCAACACTTGGTGGTGGCCAATCA
6273 ATTAAAGATTTCTACTT
578 ATTAAAGATTTCTACTT
6290 ACCATTAAAG
Statistics
Matches: 1152, Mismatches: 22, Indels: 36
0.95 0.02 0.03
Matches are distributed among these distances:
588 63 0.05
589 65 0.06
590 71 0.06
591 336 0.29
592 38 0.03
594 2 0.00
595 1 0.00
597 1 0.00
598 2 0.00
600 119 0.10
601 128 0.11
603 54 0.05
604 228 0.20
605 44 0.04
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (595 bp):
GTATTTTTATTTCATAAAAAACTATTAAGTTTAATGGTTAATAAGTAATTTACTTCTTCTTAAAA
TTTTATTTAACTTTAACTTTTAAATTTTAATTGGTGGAGAACTTTTATTTAACTTTAACAAATGA
AAAAATAGTAATTCATAATTCATAAAACTTTTACATATTAAAAGAAAAAAATTACATAAATCTTT
TGAATTTTTTTTGAGGAAAAAAATTGGAAAGGAGAAATTGGTATTAAAATTTTACAAATATAAAA
TTGTTGAGGTCCTCCAAAATAAAAATGCCATTATTATCTACTTTCTCCCTCCTCTTCACGGCTTA
ACTCCATTGAAAATCCCGTATGCCATAAAAAGCTATCAATCCTATTCCAATTAACAACTCTCAAA
CTTGATAGTTCTTCATAGTTTCAAAATGCAACTATTTTGGATTGTAAGCTTTGAATCCTTGATAA
ATCCCTTTCTATACAGTCACCATTTCCTAAAAAATCATTTTTTGTCCCAAGTAAATTAAATAACC
AGATAATCCAATCTTTATATATATATGCAGTTTGCAACACTTGGTGGTGGCCAATCAATTAAAGA
TTTCTACTTC
Done.