Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023073.1 Corchorus olitorius cultivar O-4 contig23106, 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: 12450
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Found at i:62 original size:32 final size:33
Alignment explanation
Indices: 25--97 Score: 103
Period size: 32 Copynumber: 2.2 Consensus size: 33
15 GCCCTCCCTT
* *
25 GGGCGGCATGACCATGGCCACG-CGCCCACTGA
1 GGGCGGCATCACCATGGCCACGCCGCCCACCGA
* *
57 GGGCGGCATCCCCATGGCCATGCCGCCCACCGA
1 GGGCGGCATCACCATGGCCACGCCGCCCACCGA
90 GGGCGGCA
1 GGGCGGCA
98 CCGACCATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
32 19 0.53
33 17 0.47
ACGTcount: A:0.16, C:0.40, G:0.36, T:0.08
Consensus pattern (33 bp):
GGGCGGCATCACCATGGCCACGCCGCCCACCGA
Found at i:965 original size:15 final size:15
Alignment explanation
Indices: 937--969 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
927 GGAATAAAAA
937 TTAAATATTATTATT
1 TTAAATATTATTATT
952 TTAATATATT-TTATT
1 TTAA-ATATTATTATT
967 TTA
1 TTA
970 TTGAAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TTAAATATTATTATT
Found at i:2194 original size:15 final size:15
Alignment explanation
Indices: 2162--2191 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2152 TAAATTTCAA
2162 TAAAATAAAATATAT
1 TAAAATAAAATATAT
2177 TAAAATAAAA-ATAT
1 TAAAATAAAATATAT
2191 T
1 T
2192 TAATTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
TAAAATAAAATATAT
Found at i:6926 original size:19 final size:19
Alignment explanation
Indices: 6902--6940 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
6892 TTTCTAAAAA
6902 GGGAGGAGGGGGGG-GGGGG
1 GGGAGG-GGGGGGGTGGGGG
6921 GGGAGGGGGGGGGTGGGGG
1 GGGAGGGGGGGGGTGGGGG
6940 G
1 G
6941 TGCATTTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.08, C:0.00, G:0.90, T:0.03
Consensus pattern (19 bp):
GGGAGGGGGGGGGTGGGGG
Found at i:6927 original size:16 final size:17
Alignment explanation
Indices: 6906--6940 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
6896 TAAAAAGGGA
6906 GGAGGGGGGGGG-GGGG
1 GGAGGGGGGGGGTGGGG
6922 GGAGGGGGGGGGTGGGG
1 GGAGGGGGGGGGTGGGG
6939 GG
1 GG
6941 TGCATTTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.06, C:0.00, G:0.91, T:0.03
Consensus pattern (17 bp):
GGAGGGGGGGGGTGGGG
Found at i:6928 original size:10 final size:10
Alignment explanation
Indices: 6902--6940 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
6892 TTTCTAAAAA
*
6902 GGGAGGAGGG
1 GGGAGGGGGG
6912 GGG-GGGGGG
1 GGGAGGGGGG
6921 GGGAGGGGGG
1 GGGAGGGGGG
*
6931 GGGTGGGGGG
1 GGGAGGGGGG
6941 TGCATTTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
9 8 0.31
10 18 0.69
ACGTcount: A:0.08, C:0.00, G:0.90, T:0.03
Consensus pattern (10 bp):
GGGAGGGGGG
Found at i:10676 original size:28 final size:27
Alignment explanation
Indices: 10645--10703 Score: 95
Period size: 25 Copynumber: 2.2 Consensus size: 27
10635 CATCTTTATG
10645 TAATTGTCTACTTTTTTGTTGATTACTA
1 TAATT-TCTACTTTTTTGTTGATTACTA
10673 TAA--TCTACTTTTTTGTTGATTACTA
1 TAATTTCTACTTTTTTGTTGATTACTA
10698 TAATTT
1 TAATTT
10704 ACTTACTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
25 25 0.86
27 1 0.03
28 3 0.10
ACGTcount: A:0.24, C:0.10, G:0.08, T:0.58
Consensus pattern (27 bp):
TAATTTCTACTTTTTTGTTGATTACTA
Found at i:10679 original size:25 final size:25
Alignment explanation
Indices: 10651--10707 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
10641 TATGTAATTG
10651 TCTACTTTTTTGTTGATTACTATAA
1 TCTACTTTTTTGTTGATTACTATAA
10676 TCTACTTTTTTGTTGATTACTATAA
1 TCTACTTTTTTGTTGATTACTATAA
*
10701 TTTACTT
1 TCTACTT
10708 ACTATTGAGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.23, C:0.12, G:0.07, T:0.58
Consensus pattern (25 bp):
TCTACTTTTTTGTTGATTACTATAA
Done.