Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016511.1 Corchorus olitorius cultivar O-4 contig16544, 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: 55730
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:236 original size:31 final size:32
Alignment explanation
Indices: 183--247 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 32
173 TTCTCAGATT
*
183 ATTCGGGTTTCGGCTCATCTGGATTCA-GGTC
1 ATTCGGGTCTCGGCTCATCTGGATTCAGGGTC
* *
214 ATTCGGGTCTCGGGTC-TGCTGGATTTAGGGTC
1 ATTCGGGTCTCGGCTCAT-CTGGATTCAGGGTC
246 AT
1 AT
248 GCAGGTTCGG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 1 0.03
31 22 0.76
32 6 0.21
ACGTcount: A:0.12, C:0.20, G:0.32, T:0.35
Consensus pattern (32 bp):
ATTCGGGTCTCGGCTCATCTGGATTCAGGGTC
Found at i:258 original size:31 final size:31
Alignment explanation
Indices: 201--259 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
191 TTCGGCTCAT
* *
201 CTGGATTCAGGTCATTCGGGTCTCGGGTCTG
1 CTGGATTCAGGTCATGCAGGTCTCGGGTCTG
*
232 CTGGATTTAGGGTCATGCAGGT-TCGGGT
1 CTGGATTCA-GGTCATGCAGGTCTCGGGT
260 TTTGGCCTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 14 0.58
32 10 0.42
ACGTcount: A:0.12, C:0.19, G:0.37, T:0.32
Consensus pattern (31 bp):
CTGGATTCAGGTCATGCAGGTCTCGGGTCTG
Found at i:3014 original size:31 final size:31
Alignment explanation
Indices: 2979--3116 Score: 161
Period size: 31 Copynumber: 4.4 Consensus size: 31
2969 TTTGTGCACG
* **
2979 TGGCATGCTACGTGTCACTTTTTGAAACACA
1 TGGCATGCCACGTGTCACTTTTTGGTACACA
3010 TGGCATGCCACGTGTCACTTTTTTGGTACACA
1 TGGCATGCCACGTGTCAC-TTTTTGGTACACA
** **
3042 TGGTGTGATACGTGTCACTTTTTGGTACA-A
1 TGGCATGCCACGTGTCACTTTTTGGTACACA
* * *
3072 GTGGCGTGCCACATGTCGCTTTTTGGTACACA
1 -TGGCATGCCACGTGTCACTTTTTGGTACACA
3104 TGGCATGCCACGT
1 TGGCATGCCACGT
3117 CGGACACCGT
Statistics
Matches: 90, Mismatches: 14, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
30 1 0.01
31 63 0.70
32 26 0.29
ACGTcount: A:0.20, C:0.22, G:0.25, T:0.33
Consensus pattern (31 bp):
TGGCATGCCACGTGTCACTTTTTGGTACACA
Found at i:3055 original size:63 final size:62
Alignment explanation
Indices: 2987--3106 Score: 170
Period size: 63 Copynumber: 1.9 Consensus size: 62
2977 CGTGGCATGC
*
2987 TACGTGTCACTTTTTGAAACACA-TGGCATGCCACGTGTCACTTTTTTGGTACACATGGTGTGA
1 TACGTGTCACTTTTTGAAACA-AGTGGCATGCCACATGTCAC-TTTTTGGTACACATGGTGTGA
** * *
3050 TACGTGTCACTTTTTGGTACAAGTGGCGTGCCACATGTCGCTTTTTGGTACACATGG
1 TACGTGTCACTTTTTGAAACAAGTGGCATGCCACATGTCACTTTTTGGTACACATGG
3107 CATGCCACGT
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
62 17 0.33
63 34 0.67
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.35
Consensus pattern (62 bp):
TACGTGTCACTTTTTGAAACAAGTGGCATGCCACATGTCACTTTTTGGTACACATGGTGTGA
Found at i:7577 original size:12 final size:12
Alignment explanation
Indices: 7568--7594 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
7558 ACATAAATGT
7568 TATAATAAATCA
1 TATAATAAATCA
7580 TATAATAAATCA
1 TATAATAAATCA
7592 TAT
1 TAT
7595 CCCATTAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (12 bp):
TATAATAAATCA
Found at i:8654 original size:4 final size:4
Alignment explanation
Indices: 8647--8672 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
8637 TTTTTCTTCC
8647 TTCT TTCT TTCT TTCT TTCT TTCT TT
1 TTCT TTCT TTCT TTCT TTCT TTCT TT
8673 TTTTTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:8789 original size:18 final size:18
Alignment explanation
Indices: 8766--8803 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
8756 AACAATGGAT
8766 CAGAACCAAAATCAAAAC
1 CAGAACCAAAATCAAAAC
8784 CAGAACCAAAATCAAAAC
1 CAGAACCAAAATCAAAAC
8802 CA
1 CA
8804 ACAGAAGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.61, C:0.29, G:0.05, T:0.05
Consensus pattern (18 bp):
CAGAACCAAAATCAAAAC
Found at i:22230 original size:109 final size:109
Alignment explanation
Indices: 22039--22248 Score: 312
Period size: 109 Copynumber: 1.9 Consensus size: 109
22029 CGAGAATTTC
** * *
22039 TTTCTAATTAAAGTCTGGTGTAGTTTAACTCCAAACTAGTCGAGACCCGATATAACTTACGGATA
1 TTTCTAATTAAAGTCAAGTGTAGTTTAACTCCAAACTAATCGAGACCCGATATAACTGACGGATA
** * **
22104 TGGATACTTGTACCGAAATTACTTGAAAAGTTGTGAAGAACTTA
66 TAAAGACTCATACCGAAATTACTTGAAAAGTTGTGAAGAACTTA
* *
22148 TTTCTAATTAAGGTCAAGTGTAGTTTAACTCCAAACTAATCGAGATCCGATATAACTGACGGATA
1 TTTCTAATTAAAGTCAAGTGTAGTTTAACTCCAAACTAATCGAGACCCGATATAACTGACGGATA
*
22213 TAAAGACTCATACCGAAATTACTTGAAGAGTTGTGA
66 TAAAGACTCATACCGAAATTACTTGAAAAGTTGTGA
22249 TTAGGAAAAA
Statistics
Matches: 89, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
109 89 1.00
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (109 bp):
TTTCTAATTAAAGTCAAGTGTAGTTTAACTCCAAACTAATCGAGACCCGATATAACTGACGGATA
TAAAGACTCATACCGAAATTACTTGAAAAGTTGTGAAGAACTTA
Found at i:28097 original size:11 final size:11
Alignment explanation
Indices: 28073--28107 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
28063 TTCACAACGT
28073 AACAAAAACAA
1 AACAAAAACAA
* *
28084 AACGAAAACGA
1 AACAAAAACAA
28095 AACAAAAACAA
1 AACAAAAACAA
28106 AA
1 AA
28108 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:40647 original size:15 final size:15
Alignment explanation
Indices: 40627--40658 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
40617 ATCACATGTC
40627 TAACAGGTTCCACAT
1 TAACAGGTTCCACAT
*
40642 TAACAGTTTCCACAT
1 TAACAGGTTCCACAT
40657 TA
1 TA
40659 TTCATAGAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.25, G:0.09, T:0.31
Consensus pattern (15 bp):
TAACAGGTTCCACAT
Found at i:41677 original size:25 final size:25
Alignment explanation
Indices: 41649--41700 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
41639 CAATGATCAG
41649 AACGCAGAGATAGAATGCAAAACCC
1 AACGCAGAGATAGAATGCAAAACCC
**
41674 AACGCAGAGATAGAATGCTCAACCC
1 AACGCAGAGATAGAATGCAAAACCC
41699 AA
1 AA
41701 AGGAACAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.46, C:0.25, G:0.19, T:0.10
Consensus pattern (25 bp):
AACGCAGAGATAGAATGCAAAACCC
Found at i:46731 original size:48 final size:47
Alignment explanation
Indices: 46656--46796 Score: 178
Period size: 49 Copynumber: 3.0 Consensus size: 47
46646 GAGCGTGCCA
* * *
46656 ATCAATTTTGTCAAAAAATTGATAAAAAGTGCGA-TGAAAATTAAAAG
1 ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAAGT-AAAATTAAAAG
46703 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAAGTAAAATTAAAAG
1 ATCAATTTTGTC-TAAAAATTGAGAAAAAG-TGCAAGTAAAATTAAAAG
* * *
46752 TTCAATTTTGTAGTAAAAATTGAGAAAAAGTGC-AGTAAAAGTAAA
1 ATCAATTTTGT-CTAAAAATTGAGAAAAAGTGCAAGTAAAATTAAA
46797 GGATTGCTTG
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
47 23 0.27
48 18 0.21
49 42 0.50
50 1 0.01
ACGTcount: A:0.50, C:0.06, G:0.16, T:0.28
Consensus pattern (47 bp):
ATCAATTTTGTCTAAAAATTGAGAAAAAGTGCAAGTAAAATTAAAAG
Found at i:48716 original size:60 final size:59
Alignment explanation
Indices: 48644--48806 Score: 182
Period size: 60 Copynumber: 2.7 Consensus size: 59
48634 ACAATTAGGG
* * * *
48644 TTAATTGTTCAAATAGGACCCTAACGTATTCGAAAATGCTCAATTTAGGCTTCATGTTT
1 TTAATTGATCAAATAGGGCCCTAACGTATGCGAAAATGCTCAATTTAGGCCTCATGTTT
* * * * * *
48703 TTAATTTGGTCAAATAGGGTCTTAACGCATGCGGAAATGCTTAATTTAGGCCTCATGTTT
1 TTAA-TTGATCAAATAGGGCCCTAACGTATGCGAAAATGCTCAATTTAGGCCTCATGTTT
* * * *
48763 TTAACGTGATCAAATAGGGCTCTAATGTATGAGAAAATGCTCAA
1 TTAA-TTGATCAAATAGGGCCCTAACGTATGCGAAAATGCTCAA
48807 ATAAGTCCCC
Statistics
Matches: 83, Mismatches: 20, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
59 4 0.05
60 79 0.95
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.34
Consensus pattern (59 bp):
TTAATTGATCAAATAGGGCCCTAACGTATGCGAAAATGCTCAATTTAGGCCTCATGTTT
Found at i:53907 original size:30 final size:28
Alignment explanation
Indices: 53837--53898 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 28
53827 GGCCATAAAC
53837 GCTTTTAAGCCAACCTTGTACATAATTA
1 GCTTTTAAGCCAACCTTGTACATAATTA
53865 GCTTTTAAGCCAACCTTGTACATAATTA
1 GCTTTTAAGCCAACCTTGTACATAATTA
53893 G-TTTTA
1 GCTTTTA
53899 TCAAGCCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 5 0.15
28 29 0.85
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (28 bp):
GCTTTTAAGCCAACCTTGTACATAATTA
Done.