Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013382.1 Corchorus olitorius cultivar O-4 contig13415, 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: 57959
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:3120 original size:21 final size:19
Alignment explanation
Indices: 3095--3152 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 19
3085 GCTGCTCTAA
3095 TAATCTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGT--C
* * *
3116 TAATCTAATCTGTATAGTG
1 TAATCTCATCTGTACAGTC
*
3135 TAATCCCATCTGTACAGT
1 TAATCTCATCTGTACAGT
3153 TGCTAAATAG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
19 15 0.48
21 16 0.52
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.36
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTC
Found at i:11061 original size:13 final size:13
Alignment explanation
Indices: 11043--11067 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11033 TCCCTCTCAA
11043 GAATGCAGCACAT
1 GAATGCAGCACAT
11056 GAATGCAGCACA
1 GAATGCAGCACA
11068 AGGATTTAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.24, T:0.12
Consensus pattern (13 bp):
GAATGCAGCACAT
Found at i:12485 original size:210 final size:209
Alignment explanation
Indices: 12122--12539 Score: 811
Period size: 210 Copynumber: 2.0 Consensus size: 209
12112 CCATAAGAAA
12122 ATCAAAACAATTCGAAAAAGTGTATAAAATGGCACATGTTAATATGTTATGCCAAGAGGATAGAT
1 ATCAAAACAATTCGAAAAAGTGTATAAAATGGCACATGTTAATATGTTATGCCAAGAGGATAGAT
12187 GCTAAATCTACACCTAGCATAGCAAAAGCAAACCATATCTAATTGCCTGATACTTCCGGAGGAAA
66 GCTAAATCTACACCTAGCATAGCAAAAGCAAACCATATCTAATTGCCTGATACTTCCGGAGGAAA
12252 TTACACTAGTAACTAGTAACTAGTAACCTATTTTGTCAAGCCAAAATATATGACTTGACAGAGCA
131 TTACACTAGTAACTAGTAACTAGTAACCTATTTTGTCAAGCC-AAA-ATATGACTTGACAGAGCA
12317 CATAAAAGCCTAAAAG
194 CATAAAAGCCTAAAAG
12333 ATCAAAACAATTCGAAAAAGTGTAT-AAATGGCACATGTTAATATGTTATGCCAAGAGGATAGAT
1 ATCAAAACAATTCGAAAAAGTGTATAAAATGGCACATGTTAATATGTTATGCCAAGAGGATAGAT
12397 GCTAAATCTACACCTAGCATAGCAAAAGCAAACCATATCTAATTGCCTGATACTTCCGGAGGAAA
66 GCTAAATCTACACCTAGCATAGCAAAAGCAAACCATATCTAATTGCCTGATACTTCCGGAGGAAA
12462 TTACACTAGTAACTAGTAACTAGTAACCTATTTTGTCAAGCCAAAATATGACTTGACAGAGCACA
131 TTACACTAGTAACTAGTAACTAGTAACCTATTTTGTCAAGCCAAAATATGACTTGACAGAGCACA
12527 TAAAAGCCTAAAA
196 TAAAAGCCTAAAA
12540 TAAACCATAA
Statistics
Matches: 207, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
208 33 0.16
209 3 0.01
210 146 0.71
211 25 0.12
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.25
Consensus pattern (209 bp):
ATCAAAACAATTCGAAAAAGTGTATAAAATGGCACATGTTAATATGTTATGCCAAGAGGATAGAT
GCTAAATCTACACCTAGCATAGCAAAAGCAAACCATATCTAATTGCCTGATACTTCCGGAGGAAA
TTACACTAGTAACTAGTAACTAGTAACCTATTTTGTCAAGCCAAAATATGACTTGACAGAGCACA
TAAAAGCCTAAAAG
Found at i:19756 original size:144 final size:139
Alignment explanation
Indices: 19501--19786 Score: 500
Period size: 144 Copynumber: 2.0 Consensus size: 139
19491 CGTTAAGTTC
*
19501 ATCGGAGTCTGAATCTGCCTCTTGGGATAGGGTGCCTCTCCTTGCCCACATATTCTGTCGTTGGT
1 ATCGGAGTCTGAATCTGCCTCCTGGGATAGGGTGCCTCTCCTTGCCCACATATTCTGTCGTTGGT
19566 GGTTTCGGCGCTTCATTTCTATCAACAAAGGTCTCTCCAGTAGGAAAAACAAAGGGAAGGTGCTT
66 GGTTTCGGCGCTTCATTTCTATCAACAAAGGTCTCTCCAGTAGGAAAAACAAAGGGAAGGTGCTT
19631 GGGTGAAAA
131 GGGTGAAAA
* *
19640 ATCGGGGTCTGAATCTGCCTCCTGGGATGGGGTGCCCTGCCTCTCCTTGCCCACATATTCTGTCG
1 ATCGGAGTCTGAATCTGCCTCCTGGGAT-AGG-G---TGCCTCTCCTTGCCCACATATTCTGTCG
19705 TTGGTGGTTTCGGCGCTTCATTTCTATCAACAAAGGTCTCTCCAGTAGGAAAAACAAAGGGAAGG
61 TTGGTGGTTTCGGCGCTTCATTTCTATCAACAAAGGTCTCTCCAGTAGGAAAAACAAAGGGAAGG
19770 TGCTTGGGTGAAAA
126 TGCTTGGGTGAAAA
19784 ATC
1 ATC
19787 AGGACTCGGC
Statistics
Matches: 139, Mismatches: 3, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
139 26 0.19
140 2 0.01
141 1 0.01
144 110 0.79
ACGTcount: A:0.22, C:0.23, G:0.27, T:0.28
Consensus pattern (139 bp):
ATCGGAGTCTGAATCTGCCTCCTGGGATAGGGTGCCTCTCCTTGCCCACATATTCTGTCGTTGGT
GGTTTCGGCGCTTCATTTCTATCAACAAAGGTCTCTCCAGTAGGAAAAACAAAGGGAAGGTGCTT
GGGTGAAAA
Found at i:31115 original size:1 final size:1
Alignment explanation
Indices: 31111--31145 Score: 61
Period size: 1 Copynumber: 35.0 Consensus size: 1
31101 TTTGTTTATT
*
31111 AAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
31146 CCCAAGAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.97, C:0.03, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:50717 original size:2 final size:2
Alignment explanation
Indices: 50710--50743 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
50700 AACACTTCAC
50710 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
50744 TTTAAAGTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52362 original size:14 final size:14
Alignment explanation
Indices: 52343--52381 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
52333 GAACAAAAGG
52343 AAATAACTGAAACA
1 AAATAACTGAAACA
* *
52357 AAATAACTTAAAGA
1 AAATAACTGAAACA
52371 AAATTAACTGA
1 AAA-TAACTGA
52382 TTATTAAGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.62, C:0.10, G:0.08, T:0.21
Consensus pattern (14 bp):
AAATAACTGAAACA
Found at i:55779 original size:35 final size:35
Alignment explanation
Indices: 55739--55810 Score: 99
Period size: 35 Copynumber: 2.1 Consensus size: 35
55729 GATCTTGTTT
* *
55739 GATATTGGAGTTAGTAGGATATTAAGGTGTTTGGA
1 GATATTGAAGTTAGTAGGATATTAAGGTGTTTAGA
* * *
55774 GATATTGAAGTTAGTGGGGTCTTAAGGTGTTTAGA
1 GATATTGAAGTTAGTAGGATATTAAGGTGTTTAGA
55809 GA
1 GA
55811 GTTTAAGATC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.28, C:0.01, G:0.35, T:0.36
Consensus pattern (35 bp):
GATATTGAAGTTAGTAGGATATTAAGGTGTTTAGA
Found at i:56687 original size:22 final size:22
Alignment explanation
Indices: 56563--56699 Score: 88
Period size: 22 Copynumber: 6.3 Consensus size: 22
56553 ATTATAAAAA
56563 TCATAG-GAAGGTTA-CAAAATT
1 TCATAGTGAA-GTTATCAAAATT
*
56584 TCATAG-GAATGTTTAT-AATATT
1 TCATAGTGAA-G-TTATCAAAATT
* * * *
56606 TCATAATTAGGTTATCAAAGTT
1 TCATAGTGAAGTTATCAAAATT
* *
56628 TCATA-TGGAGTTCATCACAATT
1 TCATAGTGAAGTT-ATCAAAATT
**
56650 TCATAAGT-AAAATATCAAAATT
1 TCAT-AGTGAAGTTATCAAAATT
*
56672 TCATAGTGTAGTTATCAAAATT
1 TCATAGTGAAGTTATCAAAATT
*
56694 TAATAG
1 TCATAG
56700 GACAGTAATT
Statistics
Matches: 88, Mismatches: 20, Indels: 15
0.72 0.16 0.12
Matches are distributed among these distances:
21 21 0.24
22 62 0.70
23 4 0.05
24 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.37
Consensus pattern (22 bp):
TCATAGTGAAGTTATCAAAATT
Found at i:57918 original size:2 final size:2
Alignment explanation
Indices: 57911--57944 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
57901 ATTTATGACT
57911 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
57945 CGTACGGTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.