Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005251.1 Corchorus capsularis cultivar CVL-1 contig05269, 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: 8217
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.30
Found at i:5148 original size:73 final size:73
Alignment explanation
Indices: 5025--5176 Score: 288
Period size: 73 Copynumber: 2.1 Consensus size: 73
5015 CGAGCATGAC
*
5025 AGAT-TAGGAGATAGCCAGTTGGTCCCAAGAAATGTATCAAAGTATGAATGTTGTTTTACTTCAG
1 AGATGTAGGAGATAGCCAGTTGGTCCCAAGAAATGTATCAAAGTATGAATGTCGTTTTACTTCAG
5089 CAGTAAGG
66 CAGTAAGG
5097 AGATGTAGGAGATAGCCAGTTGGTCCCAAGAAATGTATCAAAGTATGAATGTCGTTTTACTTCAG
1 AGATGTAGGAGATAGCCAGTTGGTCCCAAGAAATGTATCAAAGTATGAATGTCGTTTTACTTCAG
5162 CAGTAAGG
66 CAGTAAGG
5170 AGATGTA
1 AGATGTA
5177 ATAACTTTTA
Statistics
Matches: 78, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
72 4 0.05
73 74 0.95
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.28
Consensus pattern (73 bp):
AGATGTAGGAGATAGCCAGTTGGTCCCAAGAAATGTATCAAAGTATGAATGTCGTTTTACTTCAG
CAGTAAGG
Found at i:5752 original size:10 final size:10
Alignment explanation
Indices: 5737--5780 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
5727 GGATAAGTGG
*
5737 AAAAAATAAA
1 AAAAAAGAAA
5747 AAAAAAGAAA
1 AAAAAAGAAA
5757 AAAGAAAGAAA
1 AAA-AAAGAAA
* *
5768 AAGAGAGAAA
1 AAAAAAGAAA
5778 AAA
1 AAA
5781 GCAACGATGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
10 20 0.69
11 9 0.31
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:5756 original size:17 final size:17
Alignment explanation
Indices: 5736--5771 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5726 AGGATAAGTG
*
5736 GAAAAAATAAAAAAAAA
1 GAAAAAAGAAAAAAAAA
*
5753 GAAAAAAGAAAGAAAAA
1 GAAAAAAGAAAAAAAAA
5770 GA
1 GA
5772 GAGAAAAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (17 bp):
GAAAAAAGAAAAAAAAA
Found at i:5779 original size:11 final size:11
Alignment explanation
Indices: 5744--5781 Score: 53
Period size: 10 Copynumber: 3.6 Consensus size: 11
5734 TGGAAAAAAT
5744 AAAAAA-AAAG
1 AAAAAAGAAAG
5754 AAAAAAGAAAG
1 AAAAAAGAAAG
*
5765 -AAAAAGAGAG
1 AAAAAAGAAAG
5775 AAAAAAG
1 AAAAAAG
5782 CAACGATGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
10 15 0.60
11 10 0.40
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAG
Found at i:5813 original size:19 final size:19
Alignment explanation
Indices: 5791--5849 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
5781 GCAACGATGA
5791 TTTTCAAAAAGAGTCATGG
1 TTTTCAAAAAGAGTCATGG
5810 TTTTC--AAA-A---A-GG
1 TTTTCAAAAAGAGTCATGG
5822 TTTTCAAAAAGAGTCATGG
1 TTTTCAAAAAGAGTCATGG
5841 TTTTCAAAA
1 TTTTCAAAA
5850 GGTTTTGATA
Statistics
Matches: 33, Mismatches: 0, Indels: 14
0.70 0.00 0.30
Matches are distributed among these distances:
12 7 0.21
13 1 0.03
14 3 0.09
15 1 0.03
16 1 0.03
17 3 0.09
18 1 0.03
19 16 0.48
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (19 bp):
TTTTCAAAAAGAGTCATGG
Found at i:5825 original size:12 final size:12
Alignment explanation
Indices: 5808--5832 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5798 AAAGAGTCAT
5808 GGTTTTCAAAAA
1 GGTTTTCAAAAA
5820 GGTTTTCAAAAA
1 GGTTTTCAAAAA
5832 G
1 G
5833 AGTCATGGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (12 bp):
GGTTTTCAAAAA
Found at i:5826 original size:31 final size:30
Alignment explanation
Indices: 5791--5855 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 30
5781 GCAACGATGA
5791 TTTTCAAAAAGAGTCATGGTTTTCAAAAAGG
1 TTTTCAAAAAGAGTCATGGTTTTC-AAAAGG
5822 TTTTCAAAAAGAGTCATGGTTTTCAAAAGG
1 TTTTCAAAAAGAGTCATGGTTTTCAAAAGG
5852 TTTT
1 TTTT
5856 GATAAAAAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 10 0.29
31 24 0.71
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.37
Consensus pattern (30 bp):
TTTTCAAAAAGAGTCATGGTTTTCAAAAGG
Found at i:5869 original size:44 final size:44
Alignment explanation
Indices: 5815--5970 Score: 188
Period size: 44 Copynumber: 3.4 Consensus size: 44
5805 CATGGTTTTC
5815 AAAAAGGTTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGAT
1 AAAAAGGTTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGAT
*
5859 AAAAAGGTTTTCAAAAAGAGTC-TCAGTTTTCAAAAGGTTTTGAT
1 AAAAAGGTTTTCAAAAAGAGTCAT-GGTTTTCAAAAGGTTTTGAT
* * *
5903 AAAATGGTTTTTTTTTCAAAAAAAAGTCATGGTTTTCAAAAGGTTTTGAC
1 AAAAAGG-----TTTTC-AAAAAGAGTCATGGTTTTCAAAAGGTTTTGAT
*
5953 AAAATGGTTTTCCAAAAA
1 AAAAAGGTTTT-CAAAAA
5971 TGATTTCAAA
Statistics
Matches: 98, Mismatches: 5, Indels: 17
0.82 0.04 0.14
Matches are distributed among these distances:
43 1 0.01
44 47 0.48
45 9 0.09
46 1 0.01
49 5 0.05
50 34 0.35
51 1 0.01
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.35
Consensus pattern (44 bp):
AAAAAGGTTTTCAAAAAGAGTCATGGTTTTCAAAAGGTTTTGAT
Found at i:6689 original size:4 final size:4
Alignment explanation
Indices: 6662--6705 Score: 54
Period size: 4 Copynumber: 10.8 Consensus size: 4
6652 AAAAAAAATA
*
6662 AAAG AAAAG AAAAG AAAA AAAG AAAG AAAG AAAG AAA- AAAG AAA
1 AAAG -AAAG -AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA
6706 AATGAATGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
3 3 0.08
4 24 0.67
5 9 0.25
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:6725 original size:5 final size:5
Alignment explanation
Indices: 6650--6706 Score: 50
Period size: 5 Copynumber: 12.0 Consensus size: 5
6640 CGAGTGCACT
* *
6650 GAAAA AAAAA TAAAA GAAAA GAAAA G-AAA -AAAA G-AAA G-AAA GAAAGA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAA-A
*
6697 AAAAA GAAAA
1 GAAAA GAAAA
6707 ATGAATGATG
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
4 14 0.33
5 25 0.58
6 4 0.09
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (5 bp):
GAAAA
Found at i:7872 original size:36 final size:36
Alignment explanation
Indices: 7831--7936 Score: 110
Period size: 36 Copynumber: 3.0 Consensus size: 36
7821 GTTGACCCAG
7831 GGTGGTTTTTCTTCAGTTTATGTCGGAATGATCGAA
1 GGTGGTTTTTCTTCAGTTTATGTCGGAATGATCGAA
* * * * **
7867 GGTGGTCTTTCTTTAGTTTATTTCGG-TTGA-CCCA
1 GGTGGTTTTTCTTCAGTTTATGTCGGAATGATCGAA
*
7901 GG-GCGTTCTTTCTTCAGTTTATGTCAGAATGATCGA
1 GGTG-GTT-TTTCTTCAGTTTATGTCGGAATGATCGA
7937 TTCAGTCGAC
Statistics
Matches: 53, Mismatches: 13, Indels: 7
0.73 0.18 0.10
Matches are distributed among these distances:
33 1 0.02
34 6 0.11
35 19 0.36
36 26 0.49
37 1 0.02
ACGTcount: A:0.17, C:0.15, G:0.25, T:0.42
Consensus pattern (36 bp):
GGTGGTTTTTCTTCAGTTTATGTCGGAATGATCGAA
Found at i:7920 original size:35 final size:35
Alignment explanation
Indices: 7816--7922 Score: 99
Period size: 35 Copynumber: 3.0 Consensus size: 35
7806 CTTCAATGCG
* *
7816 TTTCAGTTGACCCAGGGTGGTT-TTTCTTCAGTTTA
1 TTTCGGTTGACCCAGGG-CGTTCTTTCTTCAGTTTA
* * * * * * * *
7851 TGTCGGAATGATCGAAGGTGGTCTTTCTTTAGTTTA
1 TTTCGG-TTGACCCAGGGCGTTCTTTCTTCAGTTTA
7887 TTTCGGTTGACCCAGGGCGTTCTTTCTTCAGTTTA
1 TTTCGGTTGACCCAGGGCGTTCTTTCTTCAGTTTA
7922 T
1 T
7923 GTCAGAATGA
Statistics
Matches: 53, Mismatches: 17, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
35 29 0.55
36 24 0.45
ACGTcount: A:0.15, C:0.17, G:0.24, T:0.44
Consensus pattern (35 bp):
TTTCGGTTGACCCAGGGCGTTCTTTCTTCAGTTTA
Found at i:7967 original size:49 final size:48
Alignment explanation
Indices: 7895--8014 Score: 204
Period size: 49 Copynumber: 2.4 Consensus size: 48
7885 TATTTCGGTT
7895 GACCCAGGGCGTTCTTTCTTCAGTTTATGTCAGAATGATCGATTCAGTC
1 GACCCAGGGCG-TCTTTCTTCAGTTTATGTCAGAATGATCGATTCAGTC
7944 GACCCAGGGCAGTCTTTCTTCAGTTTATGTCAGAATGATCGATTCAGTC
1 GACCCAGGGC-GTCTTTCTTCAGTTTATGTCAGAATGATCGATTCAGTC
*
7993 GACCCAGGGTGGTCTTTCTTCA
1 GACCCAGGG-CGTCTTTCTTCA
8015 ATTGTTTTCA
Statistics
Matches: 68, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
49 67 0.99
50 1 0.01
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.33
Consensus pattern (48 bp):
GACCCAGGGCGTCTTTCTTCAGTTTATGTCAGAATGATCGATTCAGTC
Found at i:8053 original size:71 final size:69
Alignment explanation
Indices: 7965--8154 Score: 290
Period size: 71 Copynumber: 2.7 Consensus size: 69
7955 GTCTTTCTTC
* *
7965 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGTGGTCTTTCTTCAATTGTTTTCAAGTTT
1 AGTTTATGTCAGAATGATAGATTCAGTCGACCCAGGGCGGTCTTTCTTCAATTG-TTTCAAGTTT
*
8030 ATTCGA
65 A-TCCA
* *
8036 AGTTTATGTCAGAATGATTGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCAAGTTTA
1 AGTTTATGTCAGAATGATAGATTCAGTCGACCCAGGGCGGTCTTTCTTCAATTGTTTCAAGTTTA
8101 TCCA
66 TCCA
* * *
8105 AGTTTAGGTTAGAATGATAGATTCAGTTGACCCAGGGCGGTCTTTCTTCA
1 AGTTTATGTCAGAATGATAGATTCAGTCGACCCAGGGCGGTCTTTCTTCA
8155 GTTTATGTCA
Statistics
Matches: 111, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
69 49 0.44
70 11 0.10
71 51 0.46
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (69 bp):
AGTTTATGTCAGAATGATAGATTCAGTCGACCCAGGGCGGTCTTTCTTCAATTGTTTCAAGTTTA
TCCA
Found at i:8143 original size:69 final size:71
Alignment explanation
Indices: 7965--8157 Score: 300
Period size: 69 Copynumber: 2.7 Consensus size: 71
7955 GTCTTTCTTC
* * *
7965 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGTGGTCTTTCTTCAATTGTTTTCAAGTTT
1 AGTTTATGTCAGAATGATAGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTTCAAGTTT
*
8030 ATTCGA
66 ATTCCA
*
8036 AGTTTATGTCAGAATGATTGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTG-TTTCAAGTTT
1 AGTTTATGTCAGAATGATAGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTTCAAGTTT
8100 A-TCCA
66 ATTCCA
* * *
8105 AGTTTAGGTTAGAATGATAGATTCAGTTGACCCAGGGCGGTCTTTCTTCAGTT
1 AGTTTATGTCAGAATGATAGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTT
8158 TATGTCAGAA
Statistics
Matches: 114, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
69 52 0.46
70 11 0.10
71 51 0.45
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.38
Consensus pattern (71 bp):
AGTTTATGTCAGAATGATAGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTTCAAGTTT
ATTCCA
Found at i:8168 original size:49 final size:50
Alignment explanation
Indices: 8105--8207 Score: 136
Period size: 49 Copynumber: 2.1 Consensus size: 50
8095 AGTTTATCCA
* *
8105 AGTTTAGGTTAGAATGATAGATTCAGTTGACCCAGGGCGGTC-TTTCTTC
1 AGTTTAGGTCAGAATGATAGATTCAGTCGACCCAGGGCGGTCTTTTCTTC
* * * * *
8154 AGTTTATGTCAGAATGATCGATTCAGTCGACCCATGGCGTTCTTTTTTTC
1 AGTTTAGGTCAGAATGATAGATTCAGTCGACCCAGGGCGGTCTTTTCTTC
8204 AGTT
1 AGTT
8208 GTTTTCAAGT
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
49 36 0.78
50 10 0.22
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.38
Consensus pattern (50 bp):
AGTTTAGGTCAGAATGATAGATTCAGTCGACCCAGGGCGGTCTTTTCTTC
Done.