Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023028.1 Corchorus olitorius cultivar O-4 contig23061, 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: 69055
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:410 original size:18 final size:18
Alignment explanation
Indices: 384--432 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
374 GGCTGTTTGA
*
384 TAAACCATTGAAATTTTT
1 TAAATCATTGAAATTTTT
402 TAAATCATTGAAATTTTT
1 TAAATCATTGAAATTTTT
420 TAAATCATTGAAA
1 TAAATCATTGAAA
433 ATGAAAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (18 bp):
TAAATCATTGAAATTTTT
Found at i:1349 original size:17 final size:17
Alignment explanation
Indices: 1327--1360 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1317 TCACGAGTTG
*
1327 ACTCGGATACAAACTCA
1 ACTCGGACACAAACTCA
1344 ACTCGGACACAAACTCA
1 ACTCGGACACAAACTCA
1361 GTTTTTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.41, C:0.32, G:0.12, T:0.15
Consensus pattern (17 bp):
ACTCGGACACAAACTCA
Found at i:4892 original size:77 final size:77
Alignment explanation
Indices: 4810--4962 Score: 252
Period size: 77 Copynumber: 2.0 Consensus size: 77
4800 AATTAGAATA
* *
4810 GTAAAATGGTAAAATAAAAAAGTTATAAGGATATTAGATTTAATTAAATGAAAATAGAATTTTTA
1 GTAAAATGGTAAAATAAAAAAGTTATAAGGATATTAAATTTAATTAAATAAAAATAGAATTTTTA
*
4875 GTTGAGTAAAAT
66 GTAGAGTAAAAT
* * *
4887 GTAAAATGGTAAAATAAAATAGTTATAAGGATATTAAATTTTATTAAATAAAAATAGAGTTTTTA
1 GTAAAATGGTAAAATAAAAAAGTTATAAGGATATTAAATTTAATTAAATAAAAATAGAATTTTTA
4952 GTAGAGTAAAA
66 GTAGAGTAAAA
4963 CTATAAAAAT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
77 70 1.00
ACGTcount: A:0.51, C:0.00, G:0.15, T:0.34
Consensus pattern (77 bp):
GTAAAATGGTAAAATAAAAAAGTTATAAGGATATTAAATTTAATTAAATAAAAATAGAATTTTTA
GTAGAGTAAAAT
Found at i:5478 original size:16 final size:15
Alignment explanation
Indices: 5459--5492 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
5449 TTTTTTTTTA
*
5459 AAATGATTTTTTCAAT
1 AAATAATTTTTT-AAT
5475 AAATAATTTTTTAAT
1 AAATAATTTTTTAAT
5490 AAA
1 AAA
5493 AAATCTGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (15 bp):
AAATAATTTTTTAAT
Found at i:6312 original size:31 final size:31
Alignment explanation
Indices: 6271--6349 Score: 106
Period size: 31 Copynumber: 2.5 Consensus size: 31
6261 CGTTTCTATT
6271 TTTAGACTCAAATTGGTCAACTTTTGAAAGG
1 TTTAGACTCAAATTGGTCAACTTTTGAAAGG
* *
6302 TTTAGGCTCAAATCGAG-CAACTTTTGAAAGG
1 TTTAGACTCAAATTG-GTCAACTTTTGAAAGG
* *
6333 TTTTGCCTCAAATTGGT
1 TTTAGACTCAAATTGGT
6350 GATTAAAGAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
30 1 0.02
31 39 0.95
32 1 0.02
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.35
Consensus pattern (31 bp):
TTTAGACTCAAATTGGTCAACTTTTGAAAGG
Found at i:10728 original size:2 final size:2
Alignment explanation
Indices: 10721--10749 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
10711 CATGTGCATA
10721 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
10750 AGATAAACTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:23258 original size:29 final size:30
Alignment explanation
Indices: 23216--23284 Score: 131
Period size: 30 Copynumber: 2.3 Consensus size: 30
23206 TTACTTCATT
23216 TTCTCTCAACTCTTTT-TTTCCCAAACAAA
1 TTCTCTCAACTCTTTTCTTTCCCAAACAAA
23245 TTCTCTCAACTCTTTTCTTTCCCAAACAAA
1 TTCTCTCAACTCTTTTCTTTCCCAAACAAA
23275 TTCTCTCAAC
1 TTCTCTCAAC
23285 CTTAATCAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
29 16 0.41
30 23 0.59
ACGTcount: A:0.26, C:0.33, G:0.00, T:0.41
Consensus pattern (30 bp):
TTCTCTCAACTCTTTTCTTTCCCAAACAAA
Found at i:23313 original size:22 final size:21
Alignment explanation
Indices: 23288--23335 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
23278 TCTCAACCTT
23288 AATCAATCAAAACAACATCAAA
1 AATCAA-CAAAACAACATCAAA
** *
23310 AATCAACCCAACAACATCTAA
1 AATCAACAAAACAACATCAAA
23331 AATCA
1 AATCA
23336 TGGAGGGGCG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.58, C:0.27, G:0.00, T:0.15
Consensus pattern (21 bp):
AATCAACAAAACAACATCAAA
Found at i:23644 original size:17 final size:17
Alignment explanation
Indices: 23622--23654 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
23612 AATTAATTTA
23622 ATTATTTATTAG-TTATT
1 ATTATTT-TTAGATTATT
23639 ATTATTTTTAGATTAT
1 ATTATTTTTAGATTAT
23655 CTAATTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (17 bp):
ATTATTTTTAGATTATT
Found at i:23836 original size:20 final size:22
Alignment explanation
Indices: 23811--23859 Score: 75
Period size: 20 Copynumber: 2.3 Consensus size: 22
23801 AGAATTAGGA
23811 TTATTAAGTATTAA-TATG-TT
1 TTATTAAGTATTAATTATGATT
*
23831 TTATTAATTATTAATTATGATT
1 TTATTAAGTATTAATTATGATT
23853 TTATTAA
1 TTATTAA
23860 AATATGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 13 0.50
21 4 0.15
22 9 0.35
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (22 bp):
TTATTAAGTATTAATTATGATT
Found at i:25733 original size:24 final size:24
Alignment explanation
Indices: 25677--25751 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
25667 ATAATTATAA
* *
25677 TTCTTTCAAATATTCTCTCTAAATT
1 TTCTTTAAAATATTCTCTCT-ATTT
*
25702 TTCATTAAAATATTCTCTCTATTT
1 TTCTTTAAAATATTCTCTCTATTT
25726 TTCTTTAAAATA-TCTTCTCTATTT
1 TTCTTTAAAATATTC-TCTCTATTT
25750 TT
1 TT
25752 AATTGCTCAA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
23 2 0.04
24 25 0.56
25 18 0.40
ACGTcount: A:0.27, C:0.17, G:0.00, T:0.56
Consensus pattern (24 bp):
TTCTTTAAAATATTCTCTCTATTT
Found at i:29043 original size:20 final size:20
Alignment explanation
Indices: 29005--29043 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
28995 AATAAATATT
* **
29005 AAAATTAATTTAATTAAAAC
1 AAAATAAATTTAAAAAAAAC
29025 AAAATAAATTTAAAAAAAA
1 AAAATAAATTTAAAAAAAA
29044 AAATCGGACC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAATAAATTTAAAAAAAAC
Found at i:29225 original size:21 final size:21
Alignment explanation
Indices: 29199--29242 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
29189 TTTTACCCCG
*
29199 TCTGGCATCGATGGCTCGTTA
1 TCTGGCATCGATGGATCGTTA
*
29220 TCTGGCGTCGATGGATCGTTA
1 TCTGGCATCGATGGATCGTTA
29241 TC
1 TC
29243 GCCCATATCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.23, G:0.30, T:0.34
Consensus pattern (21 bp):
TCTGGCATCGATGGATCGTTA
Found at i:31475 original size:44 final size:44
Alignment explanation
Indices: 31412--31500 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
31402 CTAGCTCTCC
*
31412 AACTTTTCTTTGCCGTTTGTTTGCATACTTTATATTGTAGAACT
1 AACTTTCCTTTGCCGTTTGTTTGCATACTTTATATTGTAGAACT
31456 AACTTTCCTTTGCCGTTTGTTTGCATACTTTATATTGTAGAACT
1 AACTTTCCTTTGCCGTTTGTTTGCATACTTTATATTGTAGAACT
31500 A
1 A
31501 TTTAGAAATA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.21, C:0.17, G:0.13, T:0.48
Consensus pattern (44 bp):
AACTTTCCTTTGCCGTTTGTTTGCATACTTTATATTGTAGAACT
Found at i:31840 original size:16 final size:16
Alignment explanation
Indices: 31819--31850 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
31809 GATCCGCGTC
31819 GCGCACCTGGTTATGG
1 GCGCACCTGGTTATGG
31835 GCGCACCTGGTTATGG
1 GCGCACCTGGTTATGG
31851 TGGGTGAGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.25, G:0.38, T:0.25
Consensus pattern (16 bp):
GCGCACCTGGTTATGG
Found at i:57026 original size:26 final size:26
Alignment explanation
Indices: 56992--57046 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
56982 TTAACTGAAT
56992 TTCTTTACCATTGTGCTTCTTGTAAA
1 TTCTTTACCATTGTGCTTCTTGTAAA
57018 TTCTTTACCATTGTGCTTCTTGTAAA
1 TTCTTTACCATTGTGCTTCTTGTAAA
57044 TTC
1 TTC
57047 GATCTGCATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.18, C:0.20, G:0.11, T:0.51
Consensus pattern (26 bp):
TTCTTTACCATTGTGCTTCTTGTAAA
Found at i:65867 original size:30 final size:29
Alignment explanation
Indices: 65818--65874 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 29
65808 GAATACCCCC
65818 CCCCCAAAAAAAAAGAAGAAGAAGAAGGA
1 CCCCCAAAAAAAAAGAAGAAGAAGAAGGA
65847 CCCCCAAAAAGCAAAA-AAGAAGAAGAAG
1 CCCCCAAAAA--AAAAGAAGAAGAAGAAG
65875 AAGTTCCCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 10 0.38
30 12 0.46
31 4 0.15
ACGTcount: A:0.61, C:0.19, G:0.19, T:0.00
Consensus pattern (29 bp):
CCCCCAAAAAAAAAGAAGAAGAAGAAGGA
Found at i:66732 original size:6 final size:6
Alignment explanation
Indices: 66723--66761 Score: 51
Period size: 6 Copynumber: 6.0 Consensus size: 6
66713 CTTTTAAGAA
66723 ATCTAT ATCTATCT ATCTAT ATCTAT ATCTAT ACTCTAT
1 ATCTAT ATCTA--T ATCTAT ATCTAT ATCTAT A-TCTAT
66762 TAAAAAGTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 19 0.63
7 5 0.17
8 6 0.20
ACGTcount: A:0.31, C:0.21, G:0.00, T:0.49
Consensus pattern (6 bp):
ATCTAT
Found at i:66941 original size:78 final size:78
Alignment explanation
Indices: 66849--67022 Score: 244
Period size: 78 Copynumber: 2.2 Consensus size: 78
66839 TTGTTTAAAT
* * *
66849 TTTTA-TACTTTTACTTAACTAAAAACTCTGTTCTTATTTAATTTAA-TCTAATATCTTTATAAC
1 TTTTACTA-TTTTACTTAACTAAAAACTCTATTCTTATTTAA-TTAAGTATAATATCCTTATAAC
* *
66912 TATTTTATTTTATCA
64 TATTTTACTTTACCA
* *
66927 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAGTATAATATCCTTATAACTA
1 TTTTACTATTTTACTTAACTAAAAACTCTATTCTTATTTAATTAAGTATAATATCCTTATAACTA
66992 TTTTACTTTACCA
66 TTTTACTTTACCA
*
67005 TTTTACTATTTTAATTAA
1 TTTTACTATTTTACTTAA
67023 AAAAATTGAT
Statistics
Matches: 85, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
77 4 0.05
78 79 0.93
79 2 0.02
ACGTcount: A:0.33, C:0.13, G:0.01, T:0.52
Consensus pattern (78 bp):
TTTTACTATTTTACTTAACTAAAAACTCTATTCTTATTTAATTAAGTATAATATCCTTATAACTA
TTTTACTTTACCA
Found at i:67593 original size:31 final size:32
Alignment explanation
Indices: 67548--67620 Score: 94
Period size: 31 Copynumber: 2.3 Consensus size: 32
67538 TAGGTAATTT
* * *
67548 TCTCGGATCATTCGGGTTTCGACTCATCTGGG
1 TCTCGGGTCATTCGGGTCTCGACTCAGCTGGG
* *
67580 T-TCTGGTCATTCGGGTCTCGAGTCAGCTGGG
1 TCTCGGGTCATTCGGGTCTCGACTCAGCTGGG
67611 TCTCGGGTCA
1 TCTCGGGTCA
67621 GGAGGGTTCG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
31 26 0.76
32 8 0.24
ACGTcount: A:0.11, C:0.25, G:0.32, T:0.33
Consensus pattern (32 bp):
TCTCGGGTCATTCGGGTCTCGACTCAGCTGGG
Found at i:67954 original size:15 final size:16
Alignment explanation
Indices: 67934--67968 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
67924 CATCAATTTA
67934 AAATTATAAATAA-AT
1 AAATTATAAATAATAT
*
67949 AAATTATTAATAATAT
1 AAATTATAAATAATAT
67965 AAAT
1 AAAT
67969 ATCCATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AAATTATAAATAATAT
Found at i:68797 original size:19 final size:19
Alignment explanation
Indices: 68773--68809 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
68763 GTACAGTACC
68773 TAATTTAATCTGTACAGTG
1 TAATTTAATCTGTACAGTG
*
68792 TAATTTCATCTGTACAGT
1 TAATTTAATCTGTACAGT
68810 TGCTAAACAG
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:0.30, C:0.14, G:0.14, T:0.43
Consensus pattern (19 bp):
TAATTTAATCTGTACAGTG
Done.