Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023061.1 Corchorus olitorius cultivar O-4 contig23094, 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: 17590
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:4670 original size:20 final size:20
Alignment explanation
Indices: 4647--4686 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
4637 TGATATGAAC
4647 TTGTTAAATGGGATAAATTA
1 TTGTTAAATGGGATAAATTA
4667 TTGTTAAATGGGATAAATTA
1 TTGTTAAATGGGATAAATTA
4687 ATCCTTTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (20 bp):
TTGTTAAATGGGATAAATTA
Found at i:4851 original size:14 final size:15
Alignment explanation
Indices: 4821--4856 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
4811 TTTTAAAAAG
*
4821 TTTAAAACTTAACTT
1 TTTAAAACATAACTT
4836 TTTAAAACAT-ACTT
1 TTTAAAACATAACTT
4850 TTTAAAA
1 TTTAAAA
4857 TTTTAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 11 0.55
15 9 0.45
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (15 bp):
TTTAAAACATAACTT
Found at i:6525 original size:75 final size:75
Alignment explanation
Indices: 6359--6527 Score: 196
Period size: 75 Copynumber: 2.3 Consensus size: 75
6349 ATTTAATTAA
* * * * **
6359 TTAAAAGTTGATGGGAACTATTAATAAATTTCAGAATGAGAAAGGATCAAAACGGGGTGAAAAGG
1 TTAAAAGTTGATGGGAGCTATTAATAAATTTCAGAATAAGAAAAGACCAAAACGGGGCAAAAAGG
* *
6424 CTCTCCTACG
66 CTCCCCCACG
* ** * *
6434 TTAAAAGTTGAAGGGAGCTATTGGTGAA-TTCAAGAGTAAGAAAAGACCAAAACGGGGCAAAAAG
1 TTAAAAGTTGATGGGAGCTATTAATAAATTTC-AGAATAAGAAAAGACCAAAACGGGGCAAAAAG
*
6498 GTTCCCCCACG
65 GCTCCCCCACG
6509 TTAAAAGTTGATGGGAGCT
1 TTAAAAGTTGATGGGAGCT
6528 TTTAGTAATT
Statistics
Matches: 78, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
74 3 0.04
75 75 0.96
ACGTcount: A:0.39, C:0.13, G:0.26, T:0.22
Consensus pattern (75 bp):
TTAAAAGTTGATGGGAGCTATTAATAAATTTCAGAATAAGAAAAGACCAAAACGGGGCAAAAAGG
CTCCCCCACG
Found at i:6849 original size:75 final size:75
Alignment explanation
Indices: 6746--6890 Score: 211
Period size: 75 Copynumber: 1.9 Consensus size: 75
6736 AGCTATATCA
* * *
6746 GTAAATTCTAGAGTGAGAAAAGATCAAAAC-GGCACGAAAAGGCTCTCCCACGTTAAAAGCTGAA
1 GTAAATTCCAGAGTGAGAAAAGACCAAAACAGG-ACGAAAAGGCTCTCACACGTTAAAAGCTGAA
6810 GGGAGCTATTG
65 GGGAGCTATTG
* * * *
6821 GTAAATTCCAGAGTGAGAAAAGACCAAAACAGGGCGAAAAGGTTCTCACACGTTAAAAGTTGATG
1 GTAAATTCCAGAGTGAGAAAAGACCAAAACAGGACGAAAAGGCTCTCACACGTTAAAAGCTGAAG
6886 GGAGC
66 GGAGC
6891 CTTTAGTAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
75 60 0.97
76 2 0.03
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.18
Consensus pattern (75 bp):
GTAAATTCCAGAGTGAGAAAAGACCAAAACAGGACGAAAAGGCTCTCACACGTTAAAAGCTGAAG
GGAGCTATTG
Found at i:14940 original size:76 final size:76
Alignment explanation
Indices: 14803--14954 Score: 184
Period size: 76 Copynumber: 2.0 Consensus size: 76
14793 ATAAGGACCC
* *
14803 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGT
1 CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
14868 GGGCAGTGTCA
66 GGGCAGTGTCA
* * * **
14879 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAG-ACCCATGT-GTTTCGCCTGATCACCCA
1 CGACTCCACCTGGGCGCCCACATGG-TTGCCTTG-AGCACCCATGTGGTTT-GCCTGAGAACCCA
*
14941 GATGGGCTGTGTCA
63 GATGGGCAGTGTCA
14955 TAGCTCATCA
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
75 4 0.06
76 55 0.85
77 6 0.09
ACGTcount: A:0.17, C:0.30, G:0.29, T:0.24
Consensus pattern (76 bp):
CGACTCCACCTGGGCGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCCTGAGAACCCAGAT
GGGCAGTGTCA
Found at i:15926 original size:26 final size:26
Alignment explanation
Indices: 15884--15933 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
15874 ATGATTTAGG
*
15884 GGTTACTAACTCCCTTTTTCTTTTGA
1 GGTTACTAACGCCCTTTTTCTTTTGA
* *
15910 GGTTACTAACGCTCTTTTTTTTTT
1 GGTTACTAACGCCCTTTTTCTTTT
15934 TTTTTTCAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.14, C:0.20, G:0.12, T:0.54
Consensus pattern (26 bp):
GGTTACTAACGCCCTTTTTCTTTTGA
Done.