Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018657.1 Corchorus olitorius cultivar O-4 contig18690, 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: 18202
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:6680 original size:17 final size:18
Alignment explanation
Indices: 6639--6680 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
6629 TAAAAAGGTT
6639 TTCAAAAATCCAAAAAAA
1 TTCAAAAATCCAAAAAAA
* *
6657 TTC-AAAATTCAAGAAAA
1 TTCAAAAATCCAAAAAAA
6674 -TCAAAAA
1 TTCAAAAA
6681 GAATTTCACT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 2 0.10
17 16 0.76
18 3 0.14
ACGTcount: A:0.64, C:0.14, G:0.02, T:0.19
Consensus pattern (18 bp):
TTCAAAAATCCAAAAAAA
Found at i:6776 original size:52 final size:53
Alignment explanation
Indices: 6698--6807 Score: 177
Period size: 52 Copynumber: 2.1 Consensus size: 53
6688 ACTCAAGACA
*
6698 TCAAAGTATTCAATTTAGCACTTTTTCAAGTCGGGAAAGTTCCCAT-CAGTTT
1 TCAAAGTATTCAATTTAGCACTTTTTCAAATCGGGAAAGTTCCCATCCAGTTT
* * *
6750 TCAAAGTATTTAATTTAGCTCTTTTTCAAATTGGGAAAGTTCCCATCCAGTTT
1 TCAAAGTATTCAATTTAGCACTTTTTCAAATCGGGAAAGTTCCCATCCAGTTT
6803 TCAAA
1 TCAAA
6808 ATTGTCAGAT
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
52 42 0.79
53 11 0.21
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (53 bp):
TCAAAGTATTCAATTTAGCACTTTTTCAAATCGGGAAAGTTCCCATCCAGTTT
Found at i:6862 original size:35 final size:37
Alignment explanation
Indices: 6772--6878 Score: 148
Period size: 35 Copynumber: 3.0 Consensus size: 37
6762 ATTTAGCTCT
6772 TTTTCAAATTGGGAAAGTTCCCATCCAGTTTTCAAAA
1 TTTTCAAATTGGGAAAGTTCCCATCCAGTTTTCAAAA
* * * *
6809 TTGTCAGATTGGGAAAGTTCCCA-CCAGTTTT-TAAG
1 TTTTCAAATTGGGAAAGTTCCCATCCAGTTTTCAAAA
*
6844 TTTTCAAATTGGGAAAGTTCCCAT-CAATTTTCAAA
1 TTTTCAAATTGGGAAAGTTCCCATCCAGTTTTCAAA
6879 GTATTCAATT
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
35 29 0.48
36 10 0.17
37 21 0.35
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.36
Consensus pattern (37 bp):
TTTTCAAATTGGGAAAGTTCCCATCCAGTTTTCAAAA
Found at i:6943 original size:123 final size:124
Alignment explanation
Indices: 6720--6989 Score: 436
Period size: 123 Copynumber: 2.2 Consensus size: 124
6710 ATTTAGCACT
* * * * * *
6720 TTTTCAAGTCGGGAAAGTTCCCATCAGTTTTCAAAGTATTTAATTTAGCTCTTTTTCAAATTGGG
1 TTTTCAAATTGGGAAAGTTCCCATCAATTTTCAAAGTATTCAATTTAGCTCGTCTTCAAATTGGG
*
6785 AAAGTTCCCATCCAGTTTTCAAAATTGTCAGATTGGGAAAGTTCCCACCAGTTTTTAAG
66 AAAGTTCCCATCCAGTTTTCAAAATTGTCAAATTGGGAAAGTTCCCACCAGTTTTTAAG
6844 TTTTCAAATTGGGAAAGTTCCCATCAATTTTCAAAGTATTCAA-TTAGC-CAGTCTTCAAATTGG
1 TTTTCAAATTGGGAAAGTTCCCATCAATTTTCAAAGTATTCAATTTAGCTC-GTCTTCAAATTGG
6907 GAAAGTTCCCATCCAGTTTTCAAAATTGTCAAATTGGGAAAGTTCCCACCAGTTTTTAAG
65 GAAAGTTCCCATCCAGTTTTCAAAATTGTCAAATTGGGAAAGTTCCCACCAGTTTTTAAG
* *
6967 TTTTTAAAATGGGAAAGTTCCCA
1 TTTTCAAATTGGGAAAGTTCCCA
6990 CCAGTTTTTA
Statistics
Matches: 136, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
122 1 0.01
123 96 0.71
124 39 0.29
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (124 bp):
TTTTCAAATTGGGAAAGTTCCCATCAATTTTCAAAGTATTCAATTTAGCTCGTCTTCAAATTGGG
AAAGTTCCCATCCAGTTTTCAAAATTGTCAAATTGGGAAAGTTCCCACCAGTTTTTAAG
Found at i:6987 original size:35 final size:36
Alignment explanation
Indices: 6897--7033 Score: 197
Period size: 35 Copynumber: 3.8 Consensus size: 36
6887 TTAGCCAGTC
* *
6897 TTCAAATTGGGAAAGTTCCCATCCAGTTTTCAAAATT
1 TTCAAATTGGGAAAGTTCCCATCCAGTTTT-TAAGTT
*
6934 GTCAAATTGGGAAAGTTCCCA-CCAGTTTTTAAGTT
1 TTCAAATTGGGAAAGTTCCCATCCAGTTTTTAAGTT
* *
6969 TTTAAAATGGGAAAGTTCCCA-CCAGTTTTTAAGTT
1 TTCAAATTGGGAAAGTTCCCATCCAGTTTTTAAGTT
*
7004 TTCAAATTGGGAAAGTTCCCATTCAGTTTT
1 TTCAAATTGGGAAAGTTCCCATCCAGTTTT
7034 CAAAATGGCA
Statistics
Matches: 90, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
35 55 0.61
36 15 0.17
37 20 0.22
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (36 bp):
TTCAAATTGGGAAAGTTCCCATCCAGTTTTTAAGTT
Found at i:7732 original size:26 final size:25
Alignment explanation
Indices: 7703--7751 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
7693 AATGTAATGC
*
7703 ATGCAAACTTAAGAAAAGAAAAAAAA
1 ATGCAAACATAA-AAAAGAAAAAAAA
*
7729 ATGCAAACATAAAAAGGAAAAAA
1 ATGCAAACATAAAAAAGAAAAAA
7752 TGCAAATTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.69, C:0.08, G:0.12, T:0.10
Consensus pattern (25 bp):
ATGCAAACATAAAAAAGAAAAAAAA
Found at i:13103 original size:22 final size:22
Alignment explanation
Indices: 13054--13104 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
13044 AAATATTATC
* **
13054 ATAATTATTTTTGGCAGCCATA
1 ATAATTATTTTTGCCAGAAATA
13076 ATAATTATTTTTGCCAAGAAATA
1 ATAATTATTTTTGCC-AGAAATA
13099 A-AATTA
1 ATAATTA
13105 AGGAATAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 19 0.76
23 6 0.24
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (22 bp):
ATAATTATTTTTGCCAGAAATA
Done.