Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012167.1 Corchorus olitorius cultivar O-4 contig12200, 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: 7341
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Found at i:484 original size:36 final size:35
Alignment explanation
Indices: 408--501 Score: 154
Period size: 36 Copynumber: 2.7 Consensus size: 35
398 GGCCTGCCTG
*
408 GCGCGGCCCAAACG-CTAGGCCAGGCGCCAGGCCA
1 GCGCGGCCCAAGCGCCTAGGCCAGGCGCCAGGCCA
*
442 GCGCGGCCCAAGCGCCTAGGCCAGGCGCGCGGGCCA
1 GCGCGGCCCAAGCGCCTAGGCCAGGCGC-CAGGCCA
478 GCGCGGCCCAAGCGCCTAGGCCAG
1 GCGCGGCCCAAGCGCCTAGGCCAG
502 CGCATGGCCC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
34 13 0.23
35 13 0.23
36 30 0.54
ACGTcount: A:0.17, C:0.41, G:0.38, T:0.03
Consensus pattern (35 bp):
GCGCGGCCCAAGCGCCTAGGCCAGGCGCCAGGCCA
Found at i:520 original size:24 final size:23
Alignment explanation
Indices: 473--522 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 23
463 CAGGCGCGCG
473 GGCCAGCGCGGCCCAAGCGCCTA
1 GGCCAGCGCGGCCCAAGCGCCTA
496 GGCCAGCGCATGGCCC-AGCGCCTA
1 GGCCAGCGC--GGCCCAAGCGCCTA
520 GGC
1 GGC
523 TAAGCTTAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 9 0.36
24 11 0.44
25 5 0.20
ACGTcount: A:0.16, C:0.42, G:0.36, T:0.06
Consensus pattern (23 bp):
GGCCAGCGCGGCCCAAGCGCCTA
Found at i:647 original size:24 final size:26
Alignment explanation
Indices: 606--653 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
596 GCCCAATGTG
606 AAATAAAAGAAAGAAATAA-AAATAA
1 AAATAAAAGAAAGAAATAAGAAATAA
631 AAAT-AAAGAAA-ATAATAAGAAAT
1 AAATAAAAGAAAGA-AATAAGAAAT
654 TTTAGAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 1 0.05
24 12 0.57
25 8 0.38
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (26 bp):
AAATAAAAGAAAGAAATAAGAAATAA
Found at i:3650 original size:18 final size:18
Alignment explanation
Indices: 3617--3652 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3607 CTGACCCGTG
*
3617 TGGCAGGCCACGCGGGCC
1 TGGCAGGCCACACGGGCC
*
3635 TGGCAGGCCGCACGGGCC
1 TGGCAGGCCACACGGGCC
3653 ACACGCGGGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.39, G:0.44, T:0.06
Consensus pattern (18 bp):
TGGCAGGCCACACGGGCC
Found at i:3720 original size:6 final size:6
Alignment explanation
Indices: 3688--3767 Score: 79
Period size: 6 Copynumber: 12.8 Consensus size: 6
3678 GCCCAAGTAA
* *
3688 AAAAAA AAAAAG AAGAAAG AAAGAAAG AGAAAG AAAAAG AAAAAG AAAAAG
1 AAAAAG AAAAAG AA-AAAG -AA-AAAG AAAAAG AAAAAG AAAAAG AAAAAG
* * * *
3739 GAAAAG GAAAAG AAAAGG AAAAAT AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
3768 TAAATAGGAA
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
6 52 0.81
7 5 0.08
8 7 0.11
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.01
Consensus pattern (6 bp):
AAAAAG
Found at i:3779 original size:30 final size:30
Alignment explanation
Indices: 3688--3767 Score: 88
Period size: 30 Copynumber: 2.6 Consensus size: 30
3678 GCCCAAGTAA
* * *
3688 AAAAAAAAAAAGAAGAAAGAAAGAAAGAGAAAG
1 AAAAAGAAAAAGAA-AAAGGAA-AAGGA-AAAG
3721 AAAAAGAAAAAGAAAAAGGAAAAGGAAAAG
1 AAAAAGAAAAAGAAAAAGGAAAAGGAAAAG
* *
3751 AAAAGGAAAAATAAAAA
1 AAAAAGAAAAAGAAAAA
3768 TAAATAGGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
30 19 0.45
31 4 0.10
32 6 0.14
33 13 0.31
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.01
Consensus pattern (30 bp):
AAAAAGAAAAAGAAAAAGGAAAAGGAAAAG
Found at i:3782 original size:18 final size:17
Alignment explanation
Indices: 3689--3779 Score: 69
Period size: 18 Copynumber: 5.2 Consensus size: 17
3679 CCCAAGTAAA
* *
3689 AAAAAAAAAAGAAGAAAG
1 AAAAGAAAAAGAA-AAGG
* *
3707 -AAAGAAAGAG-AAAGA
1 AAAAGAAAAAGAAAAGG
3722 AAAAGAAAAAGAAAAAGG
1 AAAAGAAAAAG-AAAAGG
*
3740 AAAAGGAAAAGAAAAGG
1 AAAAGAAAAAGAAAAGG
* *
3757 AAAAATAAAAATAAATAGG
1 -AAAAGAAAAAGAAA-AGG
3776 AAAA
1 AAAA
3780 TAAGAAAATC
Statistics
Matches: 58, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
15 2 0.03
16 10 0.17
17 14 0.24
18 29 0.50
19 3 0.05
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (17 bp):
AAAAGAAAAAGAAAAGG
Found at i:4020 original size:26 final size:26
Alignment explanation
Indices: 3965--4021 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
3955 TTGTAAGAAT
* *
3965 GTAAATTTCCGTTTTACCCATAAATG
1 GTAAATTACCGTTTTACCCATAAATA
* *
3991 GTAAATTACC-TTATTACCCCTAACTA
1 GTAAATTACCGTT-TTACCCATAAATA
4017 GTAAA
1 GTAAA
4022 AGTGTACTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 2 0.08
26 24 0.92
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (26 bp):
GTAAATTACCGTTTTACCCATAAATA
Found at i:6112 original size:82 final size:82
Alignment explanation
Indices: 5975--6133 Score: 300
Period size: 82 Copynumber: 1.9 Consensus size: 82
5965 TATAGGTATC
5975 ATAAAAGGAAATTGTTGTGATTATATCATTTATGCTAATTGATTTTGATTTACAATATTAAAATC
1 ATAAAAGGAAATTGTTGTGATTATATCATTTATGCTAATTGATTTTGATTTACAATATTAAAATC
6040 AAATCAAATCGGTAGAT
66 AAATCAAATCGGTAGAT
*
6057 ATAAAAGGAAATTGTTGTGATTATATCATTTATGCTAATTGATTTTGATTTACAATATTCAAATC
1 ATAAAAGGAAATTGTTGTGATTATATCATTTATGCTAATTGATTTTGATTTACAATATTAAAATC
*
6122 AAATTAAATCGG
66 AAATCAAATCGG
6134 AATATTTGAA
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
82 75 1.00
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.40
Consensus pattern (82 bp):
ATAAAAGGAAATTGTTGTGATTATATCATTTATGCTAATTGATTTTGATTTACAATATTAAAATC
AAATCAAATCGGTAGAT
Done.