Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023834.1 Corchorus olitorius cultivar O-4 contig23867, 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: 29215
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:7317 original size:21 final size:21
Alignment explanation
Indices: 7293--7336 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
7283 GTCACTCAAA
7293 TCCATTTTCTCCTTTTCGCTT
1 TCCATTTTCTCCTTTTCGCTT
* *
7314 TCCATTTTCTGCTTTTCGGTT
1 TCCATTTTCTCCTTTTCGCTT
7335 TC
1 TC
7337 TTCCTTTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.05, C:0.30, G:0.09, T:0.57
Consensus pattern (21 bp):
TCCATTTTCTCCTTTTCGCTT
Found at i:7826 original size:36 final size:36
Alignment explanation
Indices: 7786--7905 Score: 116
Period size: 36 Copynumber: 3.2 Consensus size: 36
7776 GATCTCTTGG
*
7786 TCTTGGGTTTTGCCTTGATCGTCTTCTTCGTTGATC
1 TCTTGGGTTTTGCCTTGATCGTCTTCTTCCTTGATC
* * *
7822 TCTTGGGAATTT-CCTTCATCGTCTTCTTCCTTCATC
1 TCTTGGG-TTTTGCCTTGATCGTCTTCTTCCTTGATC
* * * * *
7858 TCCTGGGTATTGTCTTGGTCGTTTTCTTCACTTATGATC
1 TCTTGGGTTTTGCCTTGATCGTCTTCTTC-C-T-TGATC
7897 TCTTGGGTT
1 TCTTGGGTT
7906 GAACTGTCTG
Statistics
Matches: 65, Mismatches: 14, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
35 2 0.03
36 47 0.72
37 4 0.06
38 1 0.02
39 11 0.17
ACGTcount: A:0.08, C:0.23, G:0.19, T:0.49
Consensus pattern (36 bp):
TCTTGGGTTTTGCCTTGATCGTCTTCTTCCTTGATC
Found at i:12886 original size:28 final size:28
Alignment explanation
Indices: 12849--12920 Score: 103
Period size: 26 Copynumber: 2.6 Consensus size: 28
12839 CTAACCAATT
12849 AAAATATTATAAAAATATTACCTCAAAA
1 AAAATATTATAAAAATATTACCTCAAAA
**
12877 AAAATATTAT-AAAAT-TTATTTCAAAA
1 AAAATATTATAAAAATATTACCTCAAAA
*
12903 AAAATCTTATAAAAATAT
1 AAAATATTATAAAAATAT
12921 AAGTAAACAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
26 18 0.46
27 10 0.26
28 11 0.28
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (28 bp):
AAAATATTATAAAAATATTACCTCAAAA
Found at i:13021 original size:53 final size:53
Alignment explanation
Indices: 12963--13070 Score: 207
Period size: 53 Copynumber: 2.0 Consensus size: 53
12953 TTTCATTTCT
*
12963 TGAAGAGATTAGGATTACAAATCCCCATGTAAAAAGGAATACCCGTACAATGC
1 TGAAGAGATTAGGATTACAAATCCCCATGTAAAAAGGAATACCCGTACAACGC
13016 TGAAGAGATTAGGATTACAAATCCCCATGTAAAAAGGAATACCCGTACAACGC
1 TGAAGAGATTAGGATTACAAATCCCCATGTAAAAAGGAATACCCGTACAACGC
13069 TG
1 TG
13071 CATGATTAGC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.20
Consensus pattern (53 bp):
TGAAGAGATTAGGATTACAAATCCCCATGTAAAAAGGAATACCCGTACAACGC
Found at i:13149 original size:41 final size:41
Alignment explanation
Indices: 13092--13175 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
13082 GCATTATCGA
13092 AACGCTAATCTATGAGCCAACAAACCCCTTCCCCAACAAAC
1 AACGCTAATCTATGAGCCAACAAACCCCTTCCCCAACAAAC
13133 AACGCTAATCTATGAGCCAACAAACCCCTTCCCCAACAAAC
1 AACGCTAATCTATGAGCCAACAAACCCCTTCCCCAACAAAC
13174 AA
1 AA
13176 ACCCATTTCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.40, C:0.38, G:0.07, T:0.14
Consensus pattern (41 bp):
AACGCTAATCTATGAGCCAACAAACCCCTTCCCCAACAAAC
Found at i:13586 original size:26 final size:27
Alignment explanation
Indices: 13555--13606 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 27
13545 TTATAGTAGT
13555 AATTGATTAATAAAT-AAAACAAAAAA
1 AATTGATTAATAAATAAAAACAAAAAA
13581 AATTGATTAATAAATAAAAACAAAAA
1 AATTGATTAATAAATAAAAACAAAAA
13607 TCTGAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 15 0.60
27 10 0.40
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.23
Consensus pattern (27 bp):
AATTGATTAATAAATAAAAACAAAAAA
Found at i:16032 original size:24 final size:24
Alignment explanation
Indices: 15962--16032 Score: 97
Period size: 24 Copynumber: 3.0 Consensus size: 24
15952 TACAACCATC
*
15962 AAAAAAGAAAATTGAAGAAACCAG
1 AAAAAAGAAAATTGAAGAAACCGG
* *
15986 AAACACGAAAATTGAAGAAACCGG
1 AAAAAAGAAAATTGAAGAAACCGG
* *
16010 AAAAATGAAACTTGAAGAAACCG
1 AAAAAAGAAAATTGAAGAAACCG
16033 ATACTATTGA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (24 bp):
AAAAAAGAAAATTGAAGAAACCGG
Done.