Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020678.1 Corchorus olitorius cultivar O-4 contig20711, 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: 51383
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:7111 original size:29 final size:30
Alignment explanation
Indices: 7051--7130 Score: 99
Period size: 29 Copynumber: 2.7 Consensus size: 30
7041 GGCTAAATAC
* *
7051 CAAAAAAATCCCTTATGTTTTCCTTTTGGGA
1 CAAAATAATCCCTTATGTTTT-CTTTGGGGA
7082 CAAAATAATCCCTTATGTTTT-TTTGGGGA
1 CAAAATAATCCCTTATGTTTTCTTTGGGGA
* * *
7111 CAAATTTATCCCTTACGTTT
1 CAAAATAATCCCTTATGTTT
7131 CAAAAATGAG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
29 24 0.55
31 20 0.45
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (30 bp):
CAAAATAATCCCTTATGTTTTCTTTGGGGA
Found at i:7289 original size:31 final size:31
Alignment explanation
Indices: 7254--7350 Score: 158
Period size: 31 Copynumber: 3.1 Consensus size: 31
7244 AAGGGACTGA
7254 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
1 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
7285 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
1 TTTGTCCCAAAAGAAAAACATAAGGGATTTT
* * *
7316 TTTGTCCCAGAAGAAAAATATAAGAGAATTTT
1 TTTGTCCCAAAAGAAAAACATAAG-GGATTTT
7348 TTT
1 TTT
7351 AGTATTTAGT
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
31 53 0.85
32 9 0.15
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.32
Consensus pattern (31 bp):
TTTGTCCCAAAAGAAAAACATAAGGGATTTT
Found at i:7956 original size:126 final size:126
Alignment explanation
Indices: 7788--8027 Score: 313
Period size: 126 Copynumber: 1.9 Consensus size: 126
7778 CTTATTTTTC
* * **
7788 AAATATATTTCTTAAGTGCCATTTTTAAACTTTTACAATTTTACTCAATTAAAAACTCTATTTTT
1 AAATATATTTCTTAAATGACATTTTTAAACTTTTACAATTTTACTCAACCAAAAACTCTATTTTT
* *
7853 ATTTAA-TCAAATCTAATATATTT-ATAACTATTTTATTTTTACTATTTTACTATTTTAATT
66 ATTTAATTCAAATC-AATATATTTAATAACTATTTTATCTTTACCATTTTACTATTTTAATT
* * * ** *
7913 AAATATATTTCTTAAATGACATTATTTAAACTTTTATAGTTTTATTTTACCAAAAATTCTATTTT
1 AAATATATTTCTTAAATGACATT-TTTAAACTTTTACAATTTTACTCAACCAAAAACTCTATTTT
* * *
7978 TATTTAATTCAATTCAATTTTTTTAATAACTATTTTATCTTTACCATTTT
65 TATTTAATTCAAATCAATATATTTAATAACTATTTTATCTTTACCATTTT
8028 TTAGGGAATT
Statistics
Matches: 97, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
125 21 0.22
126 47 0.48
127 29 0.30
ACGTcount: A:0.35, C:0.11, G:0.02, T:0.53
Consensus pattern (126 bp):
AAATATATTTCTTAAATGACATTTTTAAACTTTTACAATTTTACTCAACCAAAAACTCTATTTTT
ATTTAATTCAAATCAATATATTTAATAACTATTTTATCTTTACCATTTTACTATTTTAATT
Found at i:8129 original size:102 final size:105
Alignment explanation
Indices: 7960--8167 Score: 386
Period size: 103 Copynumber: 2.0 Consensus size: 105
7950 AGTTTTATTT
*
7960 TACCAAAAATTCTATTTTTATTTAATTCAATTCAATTTTTTTAATAACTATTTTATCTTTACCA-
1 TACCAAAAATTCTATTTTTATTTAATTAAATTCAATTTTTTTAATAACTATTTTATCTTTACCAT
8024 TTTTTTAGGGAATTATCTTTACCATTTTAATTTTAAAAGA
66 TTTTTTAGGGAATTATCTTTACCATTTTAATTTTAAAAGA
8064 TACCAAAAATTCTATTTTTATTTAATTAAATTCAA-TTTTTT-ATAACTATTTTATCTTTACCAT
1 TACCAAAAATTCTATTTTTATTTAATTAAATTCAATTTTTTTAATAACTATTTTATCTTTACCAT
8127 TTTTTTAGGGAATTATCTTTACCATTTTAATTTTAAAAGA
66 TTTTTTAGGGAATTATCTTTACCATTTTAATTTTAAAAGA
8167 T
1 T
8168 GAGTTATTAT
Statistics
Matches: 102, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
102 21 0.21
103 47 0.46
104 34 0.33
ACGTcount: A:0.34, C:0.11, G:0.04, T:0.51
Consensus pattern (105 bp):
TACCAAAAATTCTATTTTTATTTAATTAAATTCAATTTTTTTAATAACTATTTTATCTTTACCAT
TTTTTTAGGGAATTATCTTTACCATTTTAATTTTAAAAGA
Found at i:8303 original size:15 final size:15
Alignment explanation
Indices: 8283--8312 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
8273 TAAATACTAA
8283 AAAAATCCCTAATGT
1 AAAAATCCCTAATGT
*
8298 AAAAATCCCTTATGT
1 AAAAATCCCTAATGT
8313 TTTTCTTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.20, G:0.07, T:0.30
Consensus pattern (15 bp):
AAAAATCCCTAATGT
Found at i:8540 original size:29 final size:30
Alignment explanation
Indices: 8503--8576 Score: 105
Period size: 29 Copynumber: 2.5 Consensus size: 30
8493 CTCATTTTTG
* *
8503 AAACGTAAGGGATTAATTTGTCCCGAAA-A
1 AAACATAAGGGATTAATTTGTCCCAAAACA
*
8532 AAACATAAGGGATTATTTTGTCCCAAAAGCA
1 AAACATAAGGGATTAATTTGTCCCAAAA-CA
8563 AAACATAAGGGATT
1 AAACATAAGGGATT
8577 TTTCTGGGTA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 25 0.62
31 15 0.38
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24
Consensus pattern (30 bp):
AAACATAAGGGATTAATTTGTCCCAAAACA
Found at i:18359 original size:18 final size:18
Alignment explanation
Indices: 18332--18366 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
18322 GTCACAAGGT
* *
18332 TAAGATTAGATGATTTGG
1 TAAGAGTAGATAATTTGG
18350 TAAGAGTAGATAATTTG
1 TAAGAGTAGATAATTTG
18367 AGATGTTTTT
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:0.37, C:0.00, G:0.26, T:0.37
Consensus pattern (18 bp):
TAAGAGTAGATAATTTGG
Found at i:18718 original size:16 final size:18
Alignment explanation
Indices: 18693--18729 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
18683 AACGTGATAA
18693 TTTTGTTTTCA-TATTGT
1 TTTTGTTTTCACTATTGT
*
18710 TTTTG-TTTCACTCTTGT
1 TTTTGTTTTCACTATTGT
18727 TTT
1 TTT
18730 CATGAGTTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.08, C:0.11, G:0.11, T:0.70
Consensus pattern (18 bp):
TTTTGTTTTCACTATTGT
Found at i:19160 original size:113 final size:114
Alignment explanation
Indices: 18923--19171 Score: 301
Period size: 113 Copynumber: 2.2 Consensus size: 114
18913 AAGTTTATTC
* * *
18923 ACGCCACTAATTTTAGTCTTTATTTTTACCAAATTTGCATTTCTAGTAAAAAAATTATATATTAT
1 ACGCCACTAATTTTAGTCTTTATTCTTACCAAATTTGCATTTCTAGTAAAAAAATTATATAATAG
* * * *
18988 GGCGTTTTTATCTTGAAACGCCCCAATTTAGTGGCGATTTGAGTAAGAA
66 GGCGTTTTTATCCTGAAACACCCCAATTTAATGGCGATTTCAGTAAGAA
* * * * *
19037 ATGCCACTAATTTTAGTCTTTATTCTTACCAAATTTGTATTTGTAG-GAAAAGATTATA-AATAG
1 ACGCCACTAATTTTAGTCTTTATTCTTACCAAATTTGCATTTCTAGTAAAAAAATTATATAATA-
*
19100 GGGCGTTTTTATCCTGAAACACCCC-ATTTAATGGCGTTTTTCTCA-TAA-AA
65 GGGCGTTTTTATCCTGAAACACCCCAATTTAATGGCG--ATT-TCAGTAAGAA
*
19150 ACGCCGCTAATTTTAGTCTTTA
1 ACGCCACTAATTTTAGTCTTTA
19172 GGGTATTTTA
Statistics
Matches: 116, Mismatches: 15, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
112 13 0.11
113 54 0.47
114 47 0.41
115 2 0.02
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (114 bp):
ACGCCACTAATTTTAGTCTTTATTCTTACCAAATTTGCATTTCTAGTAAAAAAATTATATAATAG
GGCGTTTTTATCCTGAAACACCCCAATTTAATGGCGATTTCAGTAAGAA
Found at i:33009 original size:100 final size:100
Alignment explanation
Indices: 32843--33040 Score: 315
Period size: 100 Copynumber: 2.0 Consensus size: 100
32833 CCTATGAAAA
* * * *
32843 TTGGAAACTCTGCTTCTTTTCGGTTTTCTTCACTCGCTCCAATTCTCATCTCTCGCCGCCTATTG
1 TTGGAAACTCTGCTTCTTTTCGGCTTTCTCCACTCGCTCCAATTCCCATCTCTCGCCACCTATTG
* *
32908 CCGCAGCCAAGGGACAGTCCCTTACCATTCCCTAT
66 CCACAGCCAAGGCACAGTCCCTTACCATTCCCTAT
* *
32943 TTGGAAACTCTGCTTCTTTTCGGCTTTCTCCACTCGCTCCAATTCCCATCTCTTGCCACCTGTTG
1 TTGGAAACTCTGCTTCTTTTCGGCTTTCTCCACTCGCTCCAATTCCCATCTCTCGCCACCTATTG
*
33008 CCACAGCCAAGGCACAGTCCCTTATCATTCCCT
66 CCACAGCCAAGGCACAGTCCCTTACCATTCCCT
33041 CTCAAGTAAG
Statistics
Matches: 89, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
100 89 1.00
ACGTcount: A:0.16, C:0.36, G:0.14, T:0.33
Consensus pattern (100 bp):
TTGGAAACTCTGCTTCTTTTCGGCTTTCTCCACTCGCTCCAATTCCCATCTCTCGCCACCTATTG
CCACAGCCAAGGCACAGTCCCTTACCATTCCCTAT
Found at i:34826 original size:3 final size:3
Alignment explanation
Indices: 34818--34885 Score: 118
Period size: 3 Copynumber: 22.7 Consensus size: 3
34808 AACATTTTTC
34818 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
34866 TAG TAA TAA TAG TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA
34886 TAAGCCAAAT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:37929 original size:100 final size:100
Alignment explanation
Indices: 37755--37954 Score: 310
Period size: 100 Copynumber: 2.0 Consensus size: 100
37745 AGCCTATGAA
* * *
37755 ATTTGGAAACTCTACTTCTTTTCGGTTTTCTTCACTCGCTCCAATTCCCATCTCTCGCCGCCTGT
1 ATTTGGAAACTCTACTTATTTTCGGCTTTCTCCACTCGCTCCAATTCCCATCTCTCGCCGCCTGT
* * * *
37820 TGCCGCAGCCAAGGGATAGTCTCTTACCATTCCCT
66 TGCCACAGCCAAGGCACAGTCCCTTACCATTCCCT
* *
37855 ATTTGGAAACTTTGCTTATTTTCGGCTTTCTCCACTCGCTCCAATTCCCATCTCTCGCCGCCTGT
1 ATTTGGAAACTCTACTTATTTTCGGCTTTCTCCACTCGCTCCAATTCCCATCTCTCGCCGCCTGT
*
37920 TGCCACAGCCAAGGCACAGTCCCTTATCATTCCCT
66 TGCCACAGCCAAGGCACAGTCCCTTACCATTCCCT
37955 CTCAAGTAAG
Statistics
Matches: 90, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
100 90 1.00
ACGTcount: A:0.17, C:0.35, G:0.14, T:0.34
Consensus pattern (100 bp):
ATTTGGAAACTCTACTTATTTTCGGCTTTCTCCACTCGCTCCAATTCCCATCTCTCGCCGCCTGT
TGCCACAGCCAAGGCACAGTCCCTTACCATTCCCT
Found at i:40184 original size:21 final size:20
Alignment explanation
Indices: 40160--40211 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
40150 CCTTTTTCTA
** *
40160 ATAATGATAATTATTATAATT
1 ATAAT-ATAATTACAATAATG
40181 ATAATAATAATTACAATAATG
1 ATAAT-ATAATTACAATAATG
40202 ATAATATAAT
1 ATAATATAAT
40212 CTAAGTCAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 5 0.19
21 22 0.81
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (20 bp):
ATAATATAATTACAATAATG
Found at i:42076 original size:100 final size:100
Alignment explanation
Indices: 41894--42095 Score: 298
Period size: 100 Copynumber: 2.0 Consensus size: 100
41884 GCATATGAAA
* * * * *
41894 TTTGGAAACTCTGCTTCTTTTCAGCTTTCTGCACTTGCTCCAATTCCCATCTCTCGCCGCTTGTT
1 TTTGGAAACTCTGCTTCATTTCAGCTTTCTCCACTCGCTCCAATTCACATCTCTCGCCGCCTGTT
* *
41959 GCTGTAGCAAAGGCACAGTCCCTTATCATTCCCTC
66 GCCGTAGCAAAGACACAGTCCCTTATCATTCCCTC
* *
41994 TTTGGAAACTCTGCTTCATTTC-GACTTTTTCCACTCGCTTCAATTCACATCTCTCGCCGCCTGT
1 TTTGGAAACTCTGCTTCATTTCAG-CTTTCTCCACTCGCTCCAATTCACATCTCTCGCCGCCTGT
*
42058 TGCCGTAGCCAAGACACAGTCCCTTATCATTCCCTC
65 TGCCGTAGCAAAGACACAGTCCCTTATCATTCCCTC
42094 TT
1 TT
42096 AAGTAAGTGA
Statistics
Matches: 91, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
99 1 0.01
100 90 0.99
ACGTcount: A:0.17, C:0.34, G:0.14, T:0.36
Consensus pattern (100 bp):
TTTGGAAACTCTGCTTCATTTCAGCTTTCTCCACTCGCTCCAATTCACATCTCTCGCCGCCTGTT
GCCGTAGCAAAGACACAGTCCCTTATCATTCCCTC
Found at i:43058 original size:23 final size:23
Alignment explanation
Indices: 43032--43085 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
43022 CTTGGTGTCA
*
43032 AAAAAAAAGAAA-GATATTTGGAT
1 AAAAAAAAGAAACGAAATTT-GAT
*
43055 AAAAAAAAGAAACTAAATTTGAT
1 AAAAAAAAGAAACGAAATTTGAT
43078 AAAAAAAA
1 AAAAAAAA
43086 AACGAATCTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 23 0.82
24 5 0.18
ACGTcount: A:0.69, C:0.02, G:0.11, T:0.19
Consensus pattern (23 bp):
AAAAAAAAGAAACGAAATTTGAT
Found at i:43430 original size:3 final size:3
Alignment explanation
Indices: 43422--43447 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
43412 TAATGCATAT
43422 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
43448 TAACTAGCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:44537 original size:16 final size:16
Alignment explanation
Indices: 44500--44555 Score: 78
Period size: 16 Copynumber: 3.6 Consensus size: 16
44490 GGCAAATGGG
*
44500 CGGGTTCGGGTA-CTT
1 CGGGTTCGGGTATTTT
44515 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
* *
44531 TGGGTTCGGGTATTCT
1 CGGGTTCGGGTATTTT
44547 CGGGTTCGG
1 CGGGTTCGG
44556 TCTCGGGTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
15 12 0.33
16 24 0.67
ACGTcount: A:0.05, C:0.16, G:0.41, T:0.38
Consensus pattern (16 bp):
CGGGTTCGGGTATTTT
Found at i:44555 original size:6 final size:6
Alignment explanation
Indices: 44546--44609 Score: 71
Period size: 6 Copynumber: 11.0 Consensus size: 6
44536 TCGGGTATTC
* *
44546 TCGGGT TC-GGT CTCGGGT T-GGGT TCGGGC TCAGG- TCGGGT TCGGGT
1 TCGGGT TCGGGT -TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT
*
44592 TCGGGT TCGGGC TCGGGT
1 TCGGGT TCGGGT TCGGGT
44610 CGAGTACGTT
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
5 12 0.24
6 34 0.69
7 3 0.06
ACGTcount: A:0.02, C:0.20, G:0.48, T:0.30
Consensus pattern (6 bp):
TCGGGT
Found at i:44570 original size:17 final size:17
Alignment explanation
Indices: 44548--44598 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
44538 GGGTATTCTC
44548 GGGTTCGGTCTCGGGTT
1 GGGTTCGGTCTCGGGTT
* * *
44565 GGGTTCGGGCTCAGGTC
1 GGGTTCGGTCTCGGGTT
44582 GGGTTCGGGT-TCGGGTT
1 GGGTTC-GGTCTCGGGTT
44599 CGGGCTCGGG
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
17 25 0.93
18 2 0.07
ACGTcount: A:0.02, C:0.18, G:0.49, T:0.31
Consensus pattern (17 bp):
GGGTTCGGTCTCGGGTT
Found at i:44839 original size:15 final size:16
Alignment explanation
Indices: 44819--44859 Score: 52
Period size: 14 Copynumber: 2.7 Consensus size: 16
44809 TGCATATGAA
44819 AATTATTCTAAA-TCT
1 AATTATTCTAAAGTCT
44834 AATTA-T-TAAAGTCT
1 AATTATTCTAAAGTCT
44848 AATTAATTCTAA
1 AATT-ATTCTAA
44860 TTTCACAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 4 0.18
14 8 0.36
15 6 0.27
16 1 0.05
17 3 0.14
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (16 bp):
AATTATTCTAAAGTCT
Done.