Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013479.1 Corchorus olitorius cultivar O-4 contig13512, 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: 13562
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Found at i:3937 original size:20 final size:21
Alignment explanation
Indices: 3912--3971 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 21
3902 AAGGGAATCT
3912 TTCAATAATGCTCTGCAAAG-
1 TTCAATAATGCTCTGCAAAGC
***
3932 TTCAATAATG-GAAG-ACAAGC
1 TTCAATAATGCTCTGCA-AAGC
3952 TTCAATAATGCTCTGCAAAG
1 TTCAATAATGCTCTGCAAAG
3972 ATAGTTCAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
18 1 0.03
19 4 0.13
20 20 0.67
21 4 0.13
22 1 0.03
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (21 bp):
TTCAATAATGCTCTGCAAAGC
Found at i:7932 original size:16 final size:15
Alignment explanation
Indices: 7913--7961 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
7903 TATTTTAACC
7913 AAAACTTATTTTTTAT
1 AAAA-TTATTTTTTAT
*
7929 AAAATTAATTTTCTAT
1 AAAATT-ATTTTTTAT
*
7945 AAAATTAATTTTTAT
1 AAAATTATTTTTTAT
7960 AA
1 AA
7962 CTAAACAGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
15 11 0.38
16 18 0.62
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (15 bp):
AAAATTATTTTTTAT
Found at i:8885 original size:6 final size:6
Alignment explanation
Indices: 8870--8899 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
8860 ATGAGGCTTG
*
8870 AAAAAA AAAAAC AAAAAC AAAAAC AAAAAC
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC
8900 TTAATTAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:10171 original size:15 final size:15
Alignment explanation
Indices: 10151--10180 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
10141 GTTGCACGTA
10151 TGCTGGAATTAACTC
1 TGCTGGAATTAACTC
10166 TGCTGGAATTAACTC
1 TGCTGGAATTAACTC
10181 AGTTCTCTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (15 bp):
TGCTGGAATTAACTC
Found at i:10737 original size:19 final size:19
Alignment explanation
Indices: 10713--10753 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
10703 AAATAACTAA
10713 ATAAAAAGT-AATAAATCGC
1 ATAAAAA-TAAATAAATCGC
10732 ATAAAAATAAATAAATCGC
1 ATAAAAATAAATAAATCGC
10751 ATA
1 ATA
10754 TTAATCTGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 1 0.05
19 20 0.95
ACGTcount: A:0.61, C:0.10, G:0.07, T:0.22
Consensus pattern (19 bp):
ATAAAAATAAATAAATCGC
Found at i:11503 original size:273 final size:271
Alignment explanation
Indices: 10995--11538 Score: 971
Period size: 273 Copynumber: 2.0 Consensus size: 271
10985 CTAACTTGGC
* *
10995 TTTTCTTGGAACTCTTTTTTCTTTTGGTTTTTCATATGCTTGTCTTGGCAAATCATCCATCGAGC
1 TTTTCTTGCAACTCTTTTTTCTTTTGGTTTTTCATATGCTTATCTTGGCAAATCATCCATCGAGC
*
11060 ATAATTAAGTCTGCATCTACATTTCCATCTTTACTTCCATCAACCTTTTGCCTCTTCTTGAGCTT
66 ATAATTAAGTATGCATCTACATTTCCATCTTTACTTCCATCAACCTTTTGCCTCTTCTTGAGCTT
11125 TCTCTTTTCCACGAAAATGTTGAGATGTGTCAACATTTTCTTCATCTTCAAATTTGTAATTTTGC
131 TCTCTTTTCCACGAAAATGTTGAGATGTGTCAACATTTTCTTCATCTTCAAATTTGTAATTTTGC
* *
11190 AACTTCTTTGATTAACTCGGCATTTTAACCAAAATTATTAACTTTAAGAGAACAAAATTTTGTTG
196 AACTTCTTTGATTAACTCGGCATCTTAACCAAAATTATTAACTTTAAGAGAACAAAATTTTGTTA
11255 CAGATATCAGT
261 CAGATATCAGT
11266 TTTTCTTGCAACTCCTTTTTTCGTTTTGGTTTTTCATATGCTTATCTTGGCAAATCATCCATCGA
1 TTTTCTTGCAACT-CTTTTTTC-TTTTGGTTTTTCATATGCTTATCTTGGCAAATCATCCATCGA
* * * *
11331 GCATAATTGAGTATGCATCTACATTTCCATCTTTATTTCCATCAACCTTTTGGCTCTTCTTGAGT
64 GCATAATTAAGTATGCATCTACATTTCCATCTTTACTTCCATCAACCTTTTGCCTCTTCTTGAGC
11396 TTTCTCTTTTCCACGAAAATGTTGAGATGTGTCAACATTTTCTTCATCTTCAAATTTGTAATTTT
129 TTTCTCTTTTCCACGAAAATGTTGAGATGTGTCAACATTTTCTTCATCTTCAAATTTGTAATTTT
*
11461 GCAATTTCTTTGATTAACTCGGCATCTTAACCAAAATTATTAACTTTAAGAGAACAAAATTTTGT
194 GCAACTTCTTTGATTAACTCGGCATCTTAACCAAAATTATTAACTTTAAGAGAACAAAATTTTGT
*
11526 TATAGATATCAGT
259 TACAGATATCAGT
11539 GCTAGTTCCA
Statistics
Matches: 260, Mismatches: 11, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
271 12 0.05
272 8 0.03
273 240 0.92
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.44
Consensus pattern (271 bp):
TTTTCTTGCAACTCTTTTTTCTTTTGGTTTTTCATATGCTTATCTTGGCAAATCATCCATCGAGC
ATAATTAAGTATGCATCTACATTTCCATCTTTACTTCCATCAACCTTTTGCCTCTTCTTGAGCTT
TCTCTTTTCCACGAAAATGTTGAGATGTGTCAACATTTTCTTCATCTTCAAATTTGTAATTTTGC
AACTTCTTTGATTAACTCGGCATCTTAACCAAAATTATTAACTTTAAGAGAACAAAATTTTGTTA
CAGATATCAGT
Done.