Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013414.1 Corchorus olitorius cultivar O-4 contig13447, 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: 27096
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Found at i:7246 original size:15 final size:15
Alignment explanation
Indices: 7222--7277 Score: 85
Period size: 15 Copynumber: 3.7 Consensus size: 15
7212 TGCACCATTT
* *
7222 CCATTATTGTTCACA
1 CCATTGTTGTTCGCA
7237 CCATTGTTGTTCGCA
1 CCATTGTTGTTCGCA
*
7252 CCATTGTTGTTTGCA
1 CCATTGTTGTTCGCA
7267 CCATTGTTGTT
1 CCATTGTTGTT
7278 TGCGCCATTC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.16, C:0.23, G:0.16, T:0.45
Consensus pattern (15 bp):
CCATTGTTGTTCGCA
Found at i:7256 original size:30 final size:30
Alignment explanation
Indices: 7222--7286 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
7212 TGCACCATTT
7222 CCATTATTGTTCACACCATTGTTGTTCGCA
1 CCATTATTGTTCACACCATTGTTGTTCGCA
* ** * *
7252 CCATTGTTGTTTGCACCATTGTTGTTTGCG
1 CCATTATTGTTCACACCATTGTTGTTCGCA
7282 CCATT
1 CCATT
7287 CACCCTAGCA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.15, C:0.25, G:0.17, T:0.43
Consensus pattern (30 bp):
CCATTATTGTTCACACCATTGTTGTTCGCA
Found at i:7278 original size:15 final size:15
Alignment explanation
Indices: 7235--7286 Score: 86
Period size: 15 Copynumber: 3.5 Consensus size: 15
7225 TTATTGTTCA
*
7235 CACCATTGTTGTTCG
1 CACCATTGTTGTTTG
7250 CACCATTGTTGTTTG
1 CACCATTGTTGTTTG
7265 CACCATTGTTGTTTG
1 CACCATTGTTGTTTG
*
7280 CGCCATT
1 CACCATT
7287 CACCCTAGCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.13, C:0.25, G:0.19, T:0.42
Consensus pattern (15 bp):
CACCATTGTTGTTTG
Found at i:8211 original size:49 final size:47
Alignment explanation
Indices: 8110--8251 Score: 160
Period size: 49 Copynumber: 3.0 Consensus size: 47
8100 GAGCGTGCCA
* ** *
8110 ATCAATTTTGTCAAAAAATTGATAAAAAGTGTGATGAAAATTAAAAG
1 ATCAATTTTGTCTAAAAATTGATAAAAAGTGCAATGAAAAATAAAAG
*
8157 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAA-GTAAAAATAAAAG
1 ATCAATTTTGTC-TAAAAATTGATAAAAAG-TGCAATG-AAAAATAAAAG
* * * *
8206 TTCAATTTTGTAGTAAAAATTGATAAAAAGTGCAGTGAAAAGTAAA
1 ATCAATTTTGT-CTAAAAATTGATAAAAAGTGCAATGAAAAATAAA
8252 GGATTGCTTG
Statistics
Matches: 80, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
47 12 0.15
48 28 0.35
49 40 0.50
ACGTcount: A:0.51, C:0.05, G:0.15, T:0.29
Consensus pattern (47 bp):
ATCAATTTTGTCTAAAAATTGATAAAAAGTGCAATGAAAAATAAAAG
Found at i:9548 original size:9 final size:9
Alignment explanation
Indices: 9530--9558 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
9520 TTAATTCATT
9530 TAATTT-CA
1 TAATTTCCA
9538 TAATTTCCA
1 TAATTTCCA
9547 TAATTTCCA
1 TAATTTCCA
9556 TAA
1 TAA
9559 GTAATTTGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 6 0.30
9 14 0.70
ACGTcount: A:0.38, C:0.17, G:0.00, T:0.45
Consensus pattern (9 bp):
TAATTTCCA
Found at i:11076 original size:39 final size:39
Alignment explanation
Indices: 11032--11109 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
11022 CATGTCAAAT
11032 TTCAAGTTAATTGAAGATATTTAACTATATGTTTGATAC
1 TTCAAGTTAATTGAAGATATTTAACTATATGTTTGATAC
11071 TTCAAGTTAATTGAAGATATTTAACTATATGTTTGATAC
1 TTCAAGTTAATTGAAGATATTTAACTATATGTTTGATAC
11110 ATGATATTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.44
Consensus pattern (39 bp):
TTCAAGTTAATTGAAGATATTTAACTATATGTTTGATAC
Found at i:15571 original size:2 final size:2
Alignment explanation
Indices: 15564--15591 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
15554 TTCACTATTC
15564 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
15592 GAATAAAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17316 original size:3 final size:3
Alignment explanation
Indices: 17308--17349 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
17298 ATATTTATTG
17308 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
17350 TTTGTAATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:18498 original size:25 final size:25
Alignment explanation
Indices: 18444--18507 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
18434 ATTCTTTCTC
*
18444 CAGGCCCTGCGCCACTTCCTTTATT
1 CAGGCCCTGCGCCACTTCCTTCATT
*
18469 CAGGCCCTGCGCCACTTTTCTCTCA-T
1 CAGGCCCTGCGCCAC-TTCCT-TCATT
18495 -AGGCCCTGCGCCA
1 CAGGCCCTGCGCCA
18508 TCCTCTGCAG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 28 0.80
26 5 0.14
27 2 0.06
ACGTcount: A:0.12, C:0.42, G:0.19, T:0.27
Consensus pattern (25 bp):
CAGGCCCTGCGCCACTTCCTTCATT
Found at i:18597 original size:18 final size:18
Alignment explanation
Indices: 18574--18618 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
18564 TCTCAAATTT
18574 GCTCCGTGCAACAACTAA
1 GCTCCGTGCAACAACTAA
18592 GCTCCGTGCAACAACTAA
1 GCTCCGTGCAACAACTAA
*
18610 GCCCCGTGC
1 GCTCCGTGC
18619 TTATCTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.27, C:0.38, G:0.20, T:0.16
Consensus pattern (18 bp):
GCTCCGTGCAACAACTAA
Found at i:25753 original size:19 final size:18
Alignment explanation
Indices: 25720--25755 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
25710 TTGAGATAAT
25720 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
25738 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
25756 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Done.