Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020846.1 Corchorus olitorius cultivar O-4 contig20879, 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: 106714
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.28
Found at i:454 original size:26 final size:26
Alignment explanation
Indices: 416--465 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
406 AAAAGAGAAA
* *
416 GAGTTTAGGCAGAAATTTTAATTACG
1 GAGTTCAGGCAGAAAATTTAATTACG
*
442 GAGTTCAGTCAGAAAATTTAATTA
1 GAGTTCAGGCAGAAAATTTAATTA
466 GAAATAAATG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.38, C:0.08, G:0.20, T:0.34
Consensus pattern (26 bp):
GAGTTCAGGCAGAAAATTTAATTACG
Found at i:615 original size:26 final size:26
Alignment explanation
Indices: 585--641 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
575 CCAATTTTTC
*
585 AATTTAGTATTACA-AATATAAAAACA
1 AATTT-GTATGACAGAATATAAAAACA
* *
611 AATTTTTATGAGAGGAATATAAAAACA
1 AATTTGTATGACA-GAATATAAAAACA
638 AATT
1 AATT
642 AATAAATGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 5 0.19
26 5 0.19
27 16 0.62
ACGTcount: A:0.54, C:0.05, G:0.09, T:0.32
Consensus pattern (26 bp):
AATTTGTATGACAGAATATAAAAACA
Found at i:10978 original size:18 final size:18
Alignment explanation
Indices: 10951--10985 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
10941 TTCTCCGCAT
* *
10951 TCTTCTTCTAATTTTTCC
1 TCTTCCTCTAATATTTCC
10969 TCTTCCTCTAATATTTC
1 TCTTCCTCTAATATTTC
10986 TTTACCGAGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.29, G:0.00, T:0.57
Consensus pattern (18 bp):
TCTTCCTCTAATATTTCC
Found at i:25374 original size:30 final size:29
Alignment explanation
Indices: 25340--25396 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
25330 CCTGTTTGCC
25340 TTGGC-CCAAAGTTATGAGGGGTTTTTTTTT
1 TTGGCACC-AAGTTATGA-GGGTTTTTTTTT
*
25370 TTGGCATCAAGTTATGAGGGTTTTTTT
1 TTGGCACCAAGTTATGAGGGTTTTTTT
25397 ATTGCGTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 10 0.40
30 14 0.56
31 1 0.04
ACGTcount: A:0.18, C:0.09, G:0.26, T:0.47
Consensus pattern (29 bp):
TTGGCACCAAGTTATGAGGGTTTTTTTTT
Found at i:25875 original size:18 final size:18
Alignment explanation
Indices: 25852--25888 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
25842 GATAAGAAAC
25852 TACAACATTCATTTGATA
1 TACAACATTCATTTGATA
25870 TACAACATTCATTTGATA
1 TACAACATTCATTTGATA
25888 T
1 T
25889 GAAATATGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.41
Consensus pattern (18 bp):
TACAACATTCATTTGATA
Found at i:37515 original size:21 final size:21
Alignment explanation
Indices: 37454--37518 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
37444 CTAAATATGG
37454 TAAGATAATGACTCGATATAA
1 TAAGATAATGACTCGATATAA
* * *
37475 TCA-ATAAAGGA--AGACT-TAA
1 TAAGAT-AATGACTCGA-TATAA
37494 TAAGATAATGACTCGATATAA
1 TAAGATAATGACTCGATATAA
37515 TAAG
1 TAAG
37519 TAGCAAATAC
Statistics
Matches: 32, Mismatches: 6, Indels: 12
0.64 0.12 0.24
Matches are distributed among these distances:
19 11 0.34
20 6 0.19
21 15 0.47
ACGTcount: A:0.49, C:0.09, G:0.15, T:0.26
Consensus pattern (21 bp):
TAAGATAATGACTCGATATAA
Found at i:45119 original size:52 final size:52
Alignment explanation
Indices: 45041--45144 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
45031 ATACTAATAG
45041 TGCAGATTACATATTACACTCAAAAGCAGAGCTAATTAAATATAGCAACGGA
1 TGCAGATTACATATTACACTCAAAAGCAGAGCTAATTAAATATAGCAACGGA
45093 TGCAGATTACATATTACACTCAAAAGCAGAGCTAATTAAATATAGCAACGGA
1 TGCAGATTACATATTACACTCAAAAGCAGAGCTAATTAAATATAGCAACGGA
45145 AGTGGCAGAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.44, C:0.17, G:0.15, T:0.23
Consensus pattern (52 bp):
TGCAGATTACATATTACACTCAAAAGCAGAGCTAATTAAATATAGCAACGGA
Found at i:46448 original size:25 final size:25
Alignment explanation
Indices: 46400--46457 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
46390 CTCTAAATTT
* *
46400 AACTGAAAGTGGGAGTCGTAGGGGC
1 AACTAAAAGTGGGAGTCGAAGGGGC
* *
46425 AAGTAAAAGTGGGAGTC-AAGGGGGT
1 AACTAAAAGTGGGAGTCGAA-GGGGC
46450 AACTAAAA
1 AACTAAAA
46458 TAGGCACCAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 1 0.04
25 26 0.96
ACGTcount: A:0.38, C:0.09, G:0.38, T:0.16
Consensus pattern (25 bp):
AACTAAAAGTGGGAGTCGAAGGGGC
Found at i:53533 original size:14 final size:15
Alignment explanation
Indices: 53510--53542 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
53500 GGCCTAGCTT
*
53510 AAAGTTCTTCT-GAA
1 AAAGTGCTTCTGGAA
53524 AAAGTGCTTCTGGAA
1 AAAGTGCTTCTGGAA
53539 AAAG
1 AAAG
53543 CTTCAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.27
Consensus pattern (15 bp):
AAAGTGCTTCTGGAA
Found at i:53603 original size:13 final size:13
Alignment explanation
Indices: 53585--53611 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
53575 AAACAACTGA
53585 AAAGCACTTCTGG
1 AAAGCACTTCTGG
53598 AAAGCACTTCTGG
1 AAAGCACTTCTGG
53611 A
1 A
53612 TTTTCCGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (13 bp):
AAAGCACTTCTGG
Found at i:55748 original size:2 final size:2
Alignment explanation
Indices: 55741--55773 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
55731 AGTCTTATTG
55741 TA TA TA TA 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 TA TA TA TA T
55774 GAGTTCTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:69142 original size:211 final size:210
Alignment explanation
Indices: 68693--69238 Score: 607
Period size: 211 Copynumber: 2.6 Consensus size: 210
68683 GACAATGGGG
* * * * * *
68693 CTTGAACAAACACCAACATGAACATCAACCAGGTCAGCCAAAGAACCGCCAGGTATGACATCGCT
1 CTTGAACAAAAACCAACACGAACATCAACCAGGTCAACCAAAGAACCTCCAGGTATTAAATCGCT
* * ** * * *
68758 CTGCAGATAAGGTTGTGGCAGTGAAGAACACACTCGATCAGGACATGATCCAACATAATGGAAAG
66 CTGCAGATAAGGTTGTGGCAGAGAAGAACACCCAAGATCAGGACATAACCCAACAGAATGGAAAG
* * * * *
68823 GAGTAGGCGGCACCAAAGGTGATCCATCAAGAGAGTGACCCAAGGTAGATGATCACCCTTCAACG
131 GAGCACGCGGAACCAAAGGTAATCCATCAAGAGAGTCACCCAAGGTAGATGATCACCCTTCAACG
* *
68888 TCCTGGAGAGTGGGA
196 TCCTCGAGAGTAGGA
* * * **
68903 CTTGAACAAATACCGACACGAACATCAACCAGGTCAACCAAATAACCTCC-GGATATTATGTCGC
1 CTTGAACAAAAACCAACACGAACATCAACCAGGTCAACCAAAGAACCTCCAGG-TATTAAATCGC
* * * *
68967 TCTGCAAATACGGTTGTGGCAAAGAAGCAA-ACCCAAGCTCAGGACATAACCCAACCAGAATGGC
65 TCTGCAGATAAGGTTGTGGCAGAGAAG-AACACCCAAGATCAGGACATAACCCAA-CAGAATGG-
** * * * *
69031 AAA-GAGCACGCGGAACCACGGGTAATCCATTATGAGAGTCAGCCAAGGTAGATGATCCCCCTTC
127 AAAGGAGCACGCGGAACCAAAGGTAATCCATCAAGAGAGTCACCCAAGGTAGATGATCACCCTTC
*
69095 AATGTCCTCGAGAGTAGGA
192 AACGTCCTCGAGAGTAGGA
* * * *
69114 CTTGAACAAAAAACAACAGGAACATCAACCAGGTCAACCGAAGCACCTCCAGGTATTAAATCGC-
1 CTTGAACAAAAACCAACACGAACATCAACCAGGTCAACCAAAGAACCTCCAGGTATTAAATCGCT
** * *
69178 CTTGCAGATAAGGTTGTGGCAGAGAAGAACACCCACCATCA-GAGCATGATCCAACAGAATG
66 C-TGCAGATAAGGTTGTGGCAGAGAAGAACACCCAAGATCAGGA-CATAACCCAACAGAATG
69239 ACAAAGAGCA
Statistics
Matches: 277, Mismatches: 51, Indels: 16
0.81 0.15 0.05
Matches are distributed among these distances:
209 2 0.01
210 105 0.38
211 165 0.60
212 5 0.02
ACGTcount: A:0.36, C:0.25, G:0.23, T:0.16
Consensus pattern (210 bp):
CTTGAACAAAAACCAACACGAACATCAACCAGGTCAACCAAAGAACCTCCAGGTATTAAATCGCT
CTGCAGATAAGGTTGTGGCAGAGAAGAACACCCAAGATCAGGACATAACCCAACAGAATGGAAAG
GAGCACGCGGAACCAAAGGTAATCCATCAAGAGAGTCACCCAAGGTAGATGATCACCCTTCAACG
TCCTCGAGAGTAGGA
Found at i:72737 original size:43 final size:43
Alignment explanation
Indices: 72671--72753 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
72661 AAGAATAGAC
* * *
72671 GTTAGATGGGCCAGAAGTGGACCATGGCTT-TAAATCAATAAAA
1 GTTAAATGGGCCAAAAGTAGACCATGG-TTGTAAATCAATAAAA
* *
72714 GTTAAATGGGCTAAAAGTAGACCATGGTTGTAACTCAATA
1 GTTAAATGGGCCAAAAGTAGACCATGGTTGTAAATCAATA
72754 TAATCAATTG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 2 0.06
43 32 0.94
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.25
Consensus pattern (43 bp):
GTTAAATGGGCCAAAAGTAGACCATGGTTGTAAATCAATAAAA
Found at i:80434 original size:16 final size:17
Alignment explanation
Indices: 80413--80446 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
80403 GTATGTATAA
*
80413 ATTATAT-TTAATAAAT
1 ATTATATATTAACAAAT
80429 ATTATATATTAACAAAT
1 ATTATATATTAACAAAT
80446 A
1 A
80447 AAAATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTATATATTAACAAAT
Found at i:81890 original size:27 final size:27
Alignment explanation
Indices: 81866--81937 Score: 144
Period size: 27 Copynumber: 2.7 Consensus size: 27
81856 TGTGAACTTA
81866 AAATGACTAAAATGCCCCTGAAACTGC
1 AAATGACTAAAATGCCCCTGAAACTGC
81893 AAATGACTAAAATGCCCCTGAAACTGC
1 AAATGACTAAAATGCCCCTGAAACTGC
81920 AAATGACTAAAATGCCCC
1 AAATGACTAAAATGCCCC
81938 CCAGATTCTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.42, C:0.26, G:0.14, T:0.18
Consensus pattern (27 bp):
AAATGACTAAAATGCCCCTGAAACTGC
Found at i:96275 original size:14 final size:13
Alignment explanation
Indices: 96252--96298 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
96242 TTCTTTCTAA
*
96252 AAAAAAAAAAGAAC
1 AAAAAACAAA-AAC
96266 -AAAAACAAAAAC
1 AAAAAACAAAAAC
96278 AAAAAACAAAAAAC
1 AAAAAAC-AAAAAC
96292 AAAAAAC
1 AAAAAAC
96299 TTGAAACTCG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 3 0.10
13 14 0.47
14 13 0.43
ACGTcount: A:0.85, C:0.13, G:0.02, T:0.00
Consensus pattern (13 bp):
AAAAAACAAAAAC
Found at i:96276 original size:7 final size:7
Alignment explanation
Indices: 96251--96298 Score: 64
Period size: 7 Copynumber: 7.0 Consensus size: 7
96241 ATTCTTTCTA
*
96251 AAAAAAA
1 AAAAAAC
96258 AAAAGAAC
1 AAAA-AAC
96266 -AAAAAC
1 AAAAAAC
96272 -AAAAAC
1 AAAAAAC
96278 AAAAAAC
1 AAAAAAC
96285 AAAAAAC
1 AAAAAAC
96292 AAAAAAC
1 AAAAAAC
96299 TTGAAACTCG
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
6 9 0.24
7 27 0.71
8 2 0.05
ACGTcount: A:0.85, C:0.12, G:0.02, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:97958 original size:68 final size:69
Alignment explanation
Indices: 97857--97994 Score: 206
Period size: 68 Copynumber: 2.0 Consensus size: 69
97847 TCCAGTTGAA
* * *
97857 TTGGTCTCACCTTCCGACGTGTAGGTCAGGTGGCTGCCTTCACGTGCAACCTCACAAACCTACTC
1 TTGGTCTCACCTTCCGACGTGAAAGTCAGGTGGCCGCCTTCACGTGCAACCTCACAAACCTACTC
97922 GTGG
66 GTGG
* * * *
97926 TTGGTCTCACCTTCC-ATGTGAAAGTCAGGTGGCCGCCTTCATGTGCAACTTCACAAACCTCCTC
1 TTGGTCTCACCTTCCGACGTGAAAGTCAGGTGGCCGCCTTCACGTGCAACCTCACAAACCTACTC
97990 GTGG
66 GTGG
97994 T
1 T
97995 CTCCTTTCAC
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
68 47 0.76
69 15 0.24
ACGTcount: A:0.18, C:0.31, G:0.23, T:0.28
Consensus pattern (69 bp):
TTGGTCTCACCTTCCGACGTGAAAGTCAGGTGGCCGCCTTCACGTGCAACCTCACAAACCTACTC
GTGG
Found at i:101073 original size:20 final size:21
Alignment explanation
Indices: 101048--101095 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
101038 TAAAAATAAC
* *
101048 AATTAAAAAGAAAGC-AATTA
1 AATTAAAAACAAAGCAAAGTA
101068 AATTAAAAACAAAGCAAAGTA
1 AATTAAAAACAAAGCAAAGTA
101089 AATTAAA
1 AATTAAA
101096 TCTAATTCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.67, C:0.06, G:0.08, T:0.19
Consensus pattern (21 bp):
AATTAAAAACAAAGCAAAGTA
Found at i:105807 original size:29 final size:31
Alignment explanation
Indices: 105755--105814 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 31
105745 GAAGTTCGTG
*
105755 TTTGAAGACCATTTGAAGACTTATTTGAAGA
1 TTTGAAGACCATTTGAAGACTTATTTCAAGA
*
105786 TTTGAAGA-C-TTTGAAGATTTATTTCAAGA
1 TTTGAAGACCATTTGAAGACTTATTTCAAGA
105815 GCAAGAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 18 0.67
30 1 0.04
31 8 0.30
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.38
Consensus pattern (31 bp):
TTTGAAGACCATTTGAAGACTTATTTCAAGA
Done.