Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014145.1 Corchorus olitorius cultivar O-4 contig14178, 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: 43383
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:38 original size:3 final size:3
Alignment explanation
Indices: 24--222 Score: 362
Period size: 3 Copynumber: 65.0 Consensus size: 3
14 AATTATGTGA
24 AAT AATT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
70 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT AAT AAAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT -AAT AAT AAT
117 AAAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
163 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
211 AAT AAT AAT AAT
1 AAT AAT AAT AAT
223 TGTAATTAAT
Statistics
Matches: 192, Mismatches: 0, Indels: 8
0.96 0.00 0.04
Matches are distributed among these distances:
3 180 0.94
4 12 0.06
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:10741 original size:30 final size:30
Alignment explanation
Indices: 10705--10762 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
10695 ATTAATAAGC
10705 CATTAAAATTTGAGGGTATAAGAGGAAAAT
1 CATTAAAATTTGAGGGTATAAGAGGAAAAT
10735 CATTAAAATTTGAGGGTATAAGAGGAAA
1 CATTAAAATTTGAGGGTATAAGAGGAAA
10763 GTCAAGATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.24, T:0.26
Consensus pattern (30 bp):
CATTAAAATTTGAGGGTATAAGAGGAAAAT
Found at i:12422 original size:3 final size:3
Alignment explanation
Indices: 12416--12457 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
12406 TTCCTTCTTC
12416 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
12458 CCTCTTTTCC
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:13293 original size:14 final size:15
Alignment explanation
Indices: 13268--13302 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
13258 TTTTTTTTGG
13268 TTTTTCTCTTCTTGC
1 TTTTTCTCTTCTTGC
*
13283 TTTTTCT-TTCTTTC
1 TTTTTCTCTTCTTGC
13297 TTTTTC
1 TTTTTC
13303 CAACTACAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.00, C:0.23, G:0.03, T:0.74
Consensus pattern (15 bp):
TTTTTCTCTTCTTGC
Found at i:18001 original size:25 final size:26
Alignment explanation
Indices: 17969--18035 Score: 100
Period size: 28 Copynumber: 2.5 Consensus size: 26
17959 ATTGTTAATT
17969 TTATATTTTTTTCTTTTTTT-GTGAA
1 TTATATTTTTTTCTTTTTTTGGTGAA
*
17994 TTATATTTATTTATTTTTTTTTGGTGAA
1 TTATATTT-TTT-TCTTTTTTTGGTGAA
18022 TTATATTTTTTTCT
1 TTATATTTTTTTCT
18036 CAAGTAGCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
25 8 0.22
26 5 0.14
27 11 0.30
28 13 0.35
ACGTcount: A:0.18, C:0.03, G:0.07, T:0.72
Consensus pattern (26 bp):
TTATATTTTTTTCTTTTTTTGGTGAA
Found at i:18691 original size:8 final size:8
Alignment explanation
Indices: 18678--18712 Score: 70
Period size: 8 Copynumber: 4.4 Consensus size: 8
18668 AATAATAATT
18678 CTATCTTA
1 CTATCTTA
18686 CTATCTTA
1 CTATCTTA
18694 CTATCTTA
1 CTATCTTA
18702 CTATCTTA
1 CTATCTTA
18710 CTA
1 CTA
18713 CTATATAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.49
Consensus pattern (8 bp):
CTATCTTA
Found at i:23465 original size:14 final size:14
Alignment explanation
Indices: 23446--23472 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
23436 TAAAAAAACC
23446 ATTGAATTAATACG
1 ATTGAATTAATACG
23460 ATTGAATTAATAC
1 ATTGAATTAATAC
23473 ATTTGTATGT
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:0.44, C:0.07, G:0.11, T:0.37
Consensus pattern (14 bp):
ATTGAATTAATACG
Found at i:32543 original size:24 final size:26
Alignment explanation
Indices: 32516--32567 Score: 70
Period size: 29 Copynumber: 1.9 Consensus size: 26
32506 ATAATAATAC
32516 TTTT-ATTAGTTTATATTATAATTTTT
1 TTTTAATTAGTTTATATTATAA-TTTT
32542 TTTTCAAATTAGTTTATATTATAATT
1 TTTT--AATTAGTTTATATTATAATT
32568 GAAATGGGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 4 0.17
28 2 0.09
29 17 0.74
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (26 bp):
TTTTAATTAGTTTATATTATAATTTT
Found at i:38150 original size:19 final size:19
Alignment explanation
Indices: 38114--38151 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
38104 AATTTCAAAC
*
38114 TTTATTTTAAAATTAATAT
1 TTTATTTTAAAATAAATAT
38133 TTTATTTTTAAAA-AAATAT
1 TTTA-TTTTAAAATAAATAT
38152 GGGCGGATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTATTTTAAAATAAATAT
Found at i:41509 original size:439 final size:434
Alignment explanation
Indices: 40653--41517 Score: 1056
Period size: 439 Copynumber: 2.0 Consensus size: 434
40643 GTGGGCCCAT
* * *
40653 TCTCCATAAAGAAATATTTTTTTTGGATTATTTATCGAATGATACTCATACTTTTATGTTTTATG
1 TCTCCATAAACAAATATTTTTTTTGGATTATTTATCAAATGATACTCATACTTTTATGCTTTATG
* * *
40718 CTATTTAATCCTTTACAATTATGGGTTGGACAATTTAACACGTCGGCTTTTATTTTTATATTTTT
66 CTATTTAATCCTTTACAATTATGGGTTGGACAATTTAACACATCGACTTCTATTTTTATATTTTT
* * * * * *
40783 TGTTCTATTTGTCCAATTAAGGTGATTTAATAACTATTAAAAGGTAATTTTATGATCTACAACTT
131 TGTCCTATTTATCCAATTAAGATGATTCAATAACTATTAAAAAGTAATTTCATGATCTACAACTT
* * * *
40848 TCATGAAGAACTCAGAAGCCAATTTTAATGGTTTGATTTTAAAAAATACTTATGAAATTTTGTGG
196 TCATGAAAAACTCAGAAGCCAATTTTAATGGTTTAATTCTAAAAAATACTTATGAAATTTTATGG
* * * *
40913 TCTCGATTTTCGGTCTATTTAATATTGTATAATATTTGGTCTACTTGTCCGATTAAGATTGTTCA
261 TCTCGATTCTCGGTCTATTTAATATCGTATAATATTTGATCCACTTGTCCGATTAAGATTGTTCA
* * * * ** * * *
40978 AGTGTCGGTTAAATGTTTATTATGTGATTTATGACTTTCGTCAAGGGCCTGAAAGCTGAATTTGA
326 AGTGTCGATTAAAAGGTTATTATGTGATCTACAACTTTCATCAAGGGCCTAAAAGCTAAATTTGA
* * * *
41043 TTAATGAGTTTCGTGGAGAGTTCAAAATGGAATTTTTATGTTTGG
391 TTAA-GAGTTTCATGAAGAGCTCAAAATGAAATTTTTATGTTTGG
* *
41088 TCTCCATAAACAAATATTTTTTTACTGGATTATTTATCAAATGATCCTCATAGTTTTATGCTTTA
1 TCTCCATAAACAAATATTTTTTT--TGGATTATTTATCAAATGATACTCATACTTTTATGCTTTA
* ** * *
41153 TGCTATTTAATCCTTTACAATTATGGGTTGGACGATTTAATGCATTGACTTCTATTTTTGTAGTT
64 TGCTATTTAATCCTTTACAATTATGGGTTGGACAATTTAACACATCGACTTCTATTTTTATA-TT
* * * ** *
41218 TTTTGTCCTATTTATCCGATTGAGATGATTCATGTGTCTATTAAAAAGTAATTTCATTATCTACA
128 TTTTGTCCTATTTATCCAATTAAGATGATTCA-ATAACTATTAAAAAGTAATTTCATGATCTACA
* ** ** * *
41283 ACTTTCATGAAAAACTCAGGAGCCGGTTTTAATTTTTTAATTCTAAAAAATGCTTCTGAAATTTT
192 ACTTTCATGAAAAACTCAGAAGCCAATTTTAATGGTTTAATTCTAAAAAATACTTATGAAATTTT
* * *
41348 ATGGTTTTGATTGCT-GGTCTATTTAATATCGTATAAT-TTTCGATCCACTTGTCTGATTGAAG-
257 ATGGTCTCGATT-CTCGGTCTATTTAATATCGTATAATATTT-GATCCACTTGTCCGATT-AAGA
* * *
41410 TTGTTCACGTGTCGATTAAAAGGTTATTGTGTGATCTACAACTTTCATGAAGGGTCC-AAAAGCT
319 TTGTTCAAGTGTCGATTAAAAGGTTATTATGTGATCTACAACTTTCATCAAGGG-CCTAAAAGCT
*
41474 AAATTTGATCTACA-AGTTTCATGAAGGGCTCAAAATGAAATTTT
383 AAATTTGAT-TA-AGAGTTTCATGAAGAGCTCAAAATGAAATTTT
41518 GATTAGTTAT
Statistics
Matches: 360, Mismatches: 60, Indels: 16
0.83 0.14 0.04
Matches are distributed among these distances:
435 22 0.06
437 90 0.25
438 31 0.09
439 208 0.58
440 8 0.02
441 1 0.00
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.43
Consensus pattern (434 bp):
TCTCCATAAACAAATATTTTTTTTGGATTATTTATCAAATGATACTCATACTTTTATGCTTTATG
CTATTTAATCCTTTACAATTATGGGTTGGACAATTTAACACATCGACTTCTATTTTTATATTTTT
TGTCCTATTTATCCAATTAAGATGATTCAATAACTATTAAAAAGTAATTTCATGATCTACAACTT
TCATGAAAAACTCAGAAGCCAATTTTAATGGTTTAATTCTAAAAAATACTTATGAAATTTTATGG
TCTCGATTCTCGGTCTATTTAATATCGTATAATATTTGATCCACTTGTCCGATTAAGATTGTTCA
AGTGTCGATTAAAAGGTTATTATGTGATCTACAACTTTCATCAAGGGCCTAAAAGCTAAATTTGA
TTAAGAGTTTCATGAAGAGCTCAAAATGAAATTTTTATGTTTGG
Found at i:41628 original size:22 final size:22
Alignment explanation
Indices: 41601--41654 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
41591 CCCCAAGCCC
** *
41601 TTTGGGTTTGAGACTAGTCCCT
1 TTTGGGTCGGAGACTAATCCCT
*
41623 TTTGGGGCGGAGACTAATCCCT
1 TTTGGGTCGGAGACTAATCCCT
41645 TTTGGGTCGG
1 TTTGGGTCGG
41655 GAGCGTATAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.13, C:0.19, G:0.33, T:0.35
Consensus pattern (22 bp):
TTTGGGTCGGAGACTAATCCCT
Done.