Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013778.1 Corchorus olitorius cultivar O-4 contig13811, 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: 72864
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1119 original size:46 final size:46
Alignment explanation
Indices: 1062--1180 Score: 202
Period size: 46 Copynumber: 2.6 Consensus size: 46
1052 CATGAAATGG
* *
1062 TAAGTGTTTTATGAAGTTTTTGAATTAGGAATTTACAATTCATAAC
1 TAAGTGCTTTATGAAGTTTTTGAATTAGGAATTTACAATACATAAC
1108 TAAGTGCTTTATGAAGTTTTTGAATTAGGAATTTACAATACATAAC
1 TAAGTGCTTTATGAAGTTTTTGAATTAGGAATTTACAATACATAAC
*
1154 TAAGTGCTTTATGAATGGTTTTGAATT
1 TAAGTGCTTTATGAA-GTTTTTGAATT
1181 TATGCAGAGC
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
46 59 0.86
47 10 0.14
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.43
Consensus pattern (46 bp):
TAAGTGCTTTATGAAGTTTTTGAATTAGGAATTTACAATACATAAC
Found at i:1504 original size:14 final size:14
Alignment explanation
Indices: 1485--1511 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1475 CTGCAGAAAA
1485 TTATAGGCTCACTG
1 TTATAGGCTCACTG
1499 TTATAGGCTCACT
1 TTATAGGCTCACT
1512 TTTGCTTATC
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:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (14 bp):
TTATAGGCTCACTG
Found at i:1904 original size:14 final size:14
Alignment explanation
Indices: 1885--1911 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1875 CTGCAGAAAA
1885 TTATAGGCTCACTG
1 TTATAGGCTCACTG
1899 TTATAGGCTCACT
1 TTATAGGCTCACT
1912 TTTGCTTATC
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:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (14 bp):
TTATAGGCTCACTG
Found at i:2098 original size:400 final size:398
Alignment explanation
Indices: 1359--2140 Score: 1458
Period size: 400 Copynumber: 2.0 Consensus size: 398
1349 GACTACTGAT
* *
1359 CGTATGATTGTTGAGTTTTAGGAGTAAGTTGACTTTATATATCTGGTTTAAAGTTTCATATTGAT
1 CGTATGATTGTTGAGTTTTAGGAGTAAATTGACTTTATATATCTGGTTGAAAGTTTCATATTGAT
1424 GCCAAGAATTAAAAGAATAAAAAAAATGAGAGTGAATATTGGTTACTAACACTGCAGAAAATTAT
66 GCCAAGAATTAAAAGAATAAAAAAAATGAGAGTGAATATTGGTTACTAACACTGCAGAAAATTAT
1489 AGGCTCACTGTTATAGGCTCACTTTTGCTTATCTAAATTTTTATTAGAGTTTTATCTTAGAAATA
131 AGGCTCACTGTTATAGGCTCACTTTTGCTTATCTAAATTTTTATTAGAGTTTTATCTTAGAAATA
1554 TAAGAATCTATCACGAAAGAGAGCTGCTGATGTTTATTCTTACTTACTATGCCTTAAGTACGTAT
196 TAAGAATCTATCACGAAAGAGAGCTGCTGATGTTTATTCTTACTTACTATGCCTTAAGTACGTAT
1619 AGCTTTGAGTATTTAGACATTGGCATAGTTGCACCTTGAATATGCTATTGAGTGGTTTCTTCATT
261 AGCTTTGAGTATTTAGACATTGGCATAGTTGCACCTTGAATATGCTATTGAGTGGTTTCTTCATT
*
1684 GCCTAAATGTTCATGTATGATGTAAAATTGTTGTAATTGTTGCTGGTATCCTTGGTAATTGCAAT
326 GCCTAAAGGTTCATGTATGATGTAAAATTGTTGTAATTGTTGCTGGTATCCTTGGTAATTGCAAT
1749 AGGGTTCA
391 AGGGTTCA
1757 CGTATGATTGTTGAGTTTTAGGAGTAAATTGACTTTATATATCTGGTTGAAAGTTTCATATTGAT
1 CGTATGATTGTTGAGTTTTAGGAGTAAATTGACTTTATATATCTGGTTGAAAGTTTCATATTGAT
1822 GCCAAGAATTAAAAGAATAAAAAAAGAATGAGAGTGAATATTGGTTACTAACACTGCAGAAAATT
66 GCCAAGAATTAAAAGAAT-AAAAAA-AATGAGAGTGAATATTGGTTACTAACACTGCAGAAAATT
1887 ATAGGCTCACTGTTATAGGCTCACTTTTGCTTATCTAAATTTTTATTAGAGTTTTATCTTAGAAA
129 ATAGGCTCACTGTTATAGGCTCACTTTTGCTTATCTAAATTTTTATTAGAGTTTTATCTTAGAAA
1952 TATAAGAATCTATCACGAAAGAGAGCTGCTGATGTTTATTCTTACTTACTATGCCTTAAGTACGT
194 TATAAGAATCTATCACGAAAGAGAGCTGCTGATGTTTATTCTTACTTACTATGCCTTAAGTACGT
* *
2017 ATAGCTTTGAGTATTTAGACTTTGGCATAGTTGCACCTTGAGTATGCTATTGAGTGGTTTCTTCA
259 ATAGCTTTGAGTATTTAGACATTGGCATAGTTGCACCTTGAATATGCTATTGAGTGGTTTCTTCA
* * *
2082 TTGCAGT-AGGGTTCATGTATGATGTAATATTGTTGTAATTGTTGCTGGTATCCTTGGTA
324 TTGC-CTAAAGGTTCATGTATGATGTAAAATTGTTGTAATTGTTGCTGGTATCCTTGGTA
2141 CCAATCTTTA
Statistics
Matches: 373, Mismatches: 8, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
398 81 0.22
399 6 0.02
400 285 0.76
401 1 0.00
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (398 bp):
CGTATGATTGTTGAGTTTTAGGAGTAAATTGACTTTATATATCTGGTTGAAAGTTTCATATTGAT
GCCAAGAATTAAAAGAATAAAAAAAATGAGAGTGAATATTGGTTACTAACACTGCAGAAAATTAT
AGGCTCACTGTTATAGGCTCACTTTTGCTTATCTAAATTTTTATTAGAGTTTTATCTTAGAAATA
TAAGAATCTATCACGAAAGAGAGCTGCTGATGTTTATTCTTACTTACTATGCCTTAAGTACGTAT
AGCTTTGAGTATTTAGACATTGGCATAGTTGCACCTTGAATATGCTATTGAGTGGTTTCTTCATT
GCCTAAAGGTTCATGTATGATGTAAAATTGTTGTAATTGTTGCTGGTATCCTTGGTAATTGCAAT
AGGGTTCA
Found at i:7211 original size:3 final size:3
Alignment explanation
Indices: 7203--7234 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
7193 ACCTTTATAC
7203 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
7235 TACTAAATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:18207 original size:3 final size:3
Alignment explanation
Indices: 18195--18239 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
18185 AATCTAATGT
18195 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
18240 GTTATTATTA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:18247 original size:3 final size:3
Alignment explanation
Indices: 18241--18302 Score: 58
Period size: 3 Copynumber: 21.0 Consensus size: 3
18231 AATAATAATG
* * *
18241 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA CATA TTA TTT TTC TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
18286 -TA TATA TTA TT- TTA TTA
1 TTA T-TA TTA TTA TTA TTA
18303 AATTAAAACT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
2 6 0.12
3 39 0.78
4 5 0.10
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:18264 original size:18 final size:17
Alignment explanation
Indices: 18241--18307 Score: 64
Period size: 18 Copynumber: 3.8 Consensus size: 17
18231 AATAATAATG
18241 TTATTATTATTATTATTA
1 TTATTATTA-TATTATTA
*
18259 TTATTATTATACATATTA
1 TTATTATTATA-TTATTA
* *
18277 TTTTTCTTATATATATTA
1 TTATTATTATAT-TATTA
*
18295 TT-TTATTAAATTA
1 TTATTATTATATTA
18308 AAACTAATTA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
16 2 0.05
17 9 0.22
18 30 0.73
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (17 bp):
TTATTATTATATTATTA
Found at i:25745 original size:16 final size:14
Alignment explanation
Indices: 25710--25740 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
25700 ATCCAAATGA
25710 TATTCTACTATTAT
1 TATTCTACTATTAT
25724 TATTCTACTA-TAT
1 TATTCTACTATTAT
25737 TATT
1 TATT
25741 ATTCTTTGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.29, C:0.13, G:0.00, T:0.58
Consensus pattern (14 bp):
TATTCTACTATTAT
Found at i:26723 original size:17 final size:16
Alignment explanation
Indices: 26680--26738 Score: 66
Period size: 16 Copynumber: 3.7 Consensus size: 16
26670 TTTGGTTGGG
26680 AGGAAA-GAAATAGGA
1 AGGAAAGGAAATAGGA
* *
26695 AGGAAAGAAAATAGTA
1 AGGAAAGGAAATAGGA
*
26711 AGAGAAAGGAAATAGGG
1 AG-GAAAGGAAATAGGA
*
26728 AGGAAGGGAAA
1 AGGAAAGGAAA
26739 GGAAGTCACA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
15 6 0.17
16 17 0.47
17 13 0.36
ACGTcount: A:0.58, C:0.00, G:0.36, T:0.07
Consensus pattern (16 bp):
AGGAAAGGAAATAGGA
Found at i:35228 original size:41 final size:40
Alignment explanation
Indices: 35192--35271 Score: 126
Period size: 41 Copynumber: 2.0 Consensus size: 40
35182 TTTATCCTTA
35192 TGAAATATT-TATAAACTAGTTCTTTTATATAATTATCAT
1 TGAAATATTATATAAACTAGTTCTTTTATATAATTATCAT
* *
35231 TGAAATTTTCATATAAACTAGTTCTTTTATATAATCATCAT
1 TGAAATATT-ATATAAACTAGTTCTTTTATATAATTATCAT
35272 CCAAATTTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 8 0.22
41 29 0.78
ACGTcount: A:0.38, C:0.10, G:0.05, T:0.47
Consensus pattern (40 bp):
TGAAATATTATATAAACTAGTTCTTTTATATAATTATCAT
Found at i:35278 original size:41 final size:41
Alignment explanation
Indices: 35201--35283 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
35191 ATGAAATATT
* **
35201 TATAAACTAGTTCTTTTATATAATTATCATTGAAATTTTCA
1 TATAAACTAGTTCTTTTATATAATCATCATCCAAATTTTCA
35242 TATAAACTAGTTCTTTTATATAATCATCATCCAAATTTTCA
1 TATAAACTAGTTCTTTTATATAATCATCATCCAAATTTTCA
35283 T
1 T
35284 TAATTTCTCT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.36, C:0.13, G:0.04, T:0.47
Consensus pattern (41 bp):
TATAAACTAGTTCTTTTATATAATCATCATCCAAATTTTCA
Found at i:42345 original size:2 final size:2
Alignment explanation
Indices: 42338--42388 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
42328 GCAGCAGGCT
42338 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
42380 TC TC TC TC T
1 TC TC TC TC T
42389 TACTGTGTTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:44759 original size:81 final size:81
Alignment explanation
Indices: 44666--44828 Score: 290
Period size: 81 Copynumber: 2.0 Consensus size: 81
44656 TTATTCTATT
* *
44666 AAAAACTCTATTTTCATTTAACTAAATCTAATATTTTATAATTATTTTATTTTTATCATTTTATT
1 AAAAACTCTATTTTCATTTAACTAAATCTAATATTTTATAATTATTTTATTTTCATCATTTTAAT
*
44731 TTGAAAAGTTATTGTG
66 TTAAAAAGTTATTGTG
*
44747 AAAAGCTCTATTTTCATTTAACTAAATCTAATATTTTATAATTATTTTATTTTCATCATTTTAAT
1 AAAAACTCTATTTTCATTTAACTAAATCTAATATTTTATAATTATTTTATTTTCATCATTTTAAT
44812 TTAAAAAGTTATTGTG
66 TTAAAAAGTTATTGTG
44828 A
1 A
44829 TTGACATCTT
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
81 78 1.00
ACGTcount: A:0.36, C:0.08, G:0.05, T:0.52
Consensus pattern (81 bp):
AAAAACTCTATTTTCATTTAACTAAATCTAATATTTTATAATTATTTTATTTTCATCATTTTAAT
TTAAAAAGTTATTGTG
Found at i:45462 original size:32 final size:33
Alignment explanation
Indices: 45398--45475 Score: 140
Period size: 33 Copynumber: 2.4 Consensus size: 33
45388 TTAGGACAAA
45398 ATTAGTAGTATGCATTTTTTTTTTGGTAAAAAC
1 ATTAGTAGTATGCATTTTTTTTTTGGTAAAAAC
*
45431 ATTAGTAGTATGCATTTTTTTTTT-GTTAAAAC
1 ATTAGTAGTATGCATTTTTTTTTTGGTAAAAAC
45463 ATTAGTAGTATGC
1 ATTAGTAGTATGC
45476 TTAAGATTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 20 0.45
33 24 0.55
ACGTcount: A:0.29, C:0.06, G:0.15, T:0.49
Consensus pattern (33 bp):
ATTAGTAGTATGCATTTTTTTTTTGGTAAAAAC
Found at i:52090 original size:33 final size:33
Alignment explanation
Indices: 52026--52090 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
52016 AGCAAAGAGA
* * *
52026 GAAGGTGGCAAAAAGGAGGGAAAAGGTGAGAAG
1 GAAGGTGGAAAAAAGGAGGCAAAAGGAGAGAAG
*
52059 GAAGGTTGAAAAAAGGA-GCAAAAGAGAGAGAA
1 GAAGGTGGAAAAAAGGAGGCAAAAG-GAGAGAA
52091 TTGTTTTTGG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 6 0.22
33 21 0.78
ACGTcount: A:0.51, C:0.03, G:0.40, T:0.06
Consensus pattern (33 bp):
GAAGGTGGAAAAAAGGAGGCAAAAGGAGAGAAG
Found at i:71377 original size:10 final size:10
Alignment explanation
Indices: 71341--71387 Score: 58
Period size: 10 Copynumber: 4.6 Consensus size: 10
71331 TTTTCAGGGC
71341 CAATATCAGT
1 CAATATCAGT
* * *
71351 CAATTTAAGCC
1 CAATATCAG-T
71362 CAATATCAGT
1 CAATATCAGT
71372 CAATATCAGT
1 CAATATCAGT
71382 CAATAT
1 CAATAT
71388 ATAACCAACA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
10 23 0.77
11 7 0.23
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (10 bp):
CAATATCAGT
Done.