Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021522.1 Corchorus olitorius cultivar O-4 contig21555, 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: 4346
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.33
Found at i:613 original size:9 final size:9
Alignment explanation
Indices: 599--638 Score: 50
Period size: 8 Copynumber: 4.8 Consensus size: 9
589 CTATTCCGGC
599 AAAGAAGAA
1 AAAGAAGAA
608 AAAGAAGAA
1 AAAGAAGAA
*
617 GAA-AA-AA
1 AAAGAAGAA
624 AAAGAA-AA
1 AAAGAAGAA
632 AAAGAAG
1 AAAGAAG
639 GAAGAGGGCC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
7 4 0.15
8 12 0.44
9 11 0.41
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (9 bp):
AAAGAAGAA
Found at i:617 original size:12 final size:11
Alignment explanation
Indices: 599--638 Score: 64
Period size: 12 Copynumber: 3.6 Consensus size: 11
589 CTATTCCGGC
599 AAAGAAGAAAA
1 AAAGAAGAAAA
610 AGAAGAAGAAAA
1 A-AAGAAGAAAA
622 AAA-AAGAAAA
1 AAAGAAGAAAA
632 AAAGAAG
1 AAAGAAG
639 GAAGAGGGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.37
11 6 0.22
12 11 0.41
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAGAAGAAAA
Found at i:738 original size:6 final size:6
Alignment explanation
Indices: 716--804 Score: 110
Period size: 6 Copynumber: 14.7 Consensus size: 6
706 CCAAGCCAAG
* *
716 AAAAGA AAGAGA AAAAAA GAAAAG- AAAA-A AAAAGA AAAAGA AAAAGA
1 AAAAGA AAAAGA AAAAGA -AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
*
763 AAAAGA AAAAGA AAAAGA AAAAGGA AAAGGA AAAAGGA AAAA
1 AAAAGA AAAAGA AAAAGA AAAA-GA AAAAGA AAAA-GA AAAA
805 ATAAAATGAA
Statistics
Matches: 72, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
5 8 0.11
6 49 0.68
7 15 0.21
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:741 original size:13 final size:12
Alignment explanation
Indices: 725--820 Score: 79
Period size: 13 Copynumber: 7.8 Consensus size: 12
715 GAAAAGAAAG
725 AGAAAAAAAGAAA
1 AGAAAAAAA-AAA
738 AG--AAAAAAAA
1 AGAAAAAAAAAA
*
748 AGAAAAAGAAAA
1 AGAAAAAAAAAA
*
760 AGAAAAAGAAAA
1 AGAAAAAAAAAA
772 AGAAAAAGAAAAA
1 AGAAAAA-AAAAA
* *
785 GGAAAAGGAAAAA
1 AGAAAA-AAAAAA
*
798 GGAAAAAATAAAA
1 AGAAAAAA-AAAA
*
811 TGAAATAAAA
1 AGAAA-AAAA
821 TAATAAATAA
Statistics
Matches: 71, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
10 5 0.07
11 5 0.07
12 27 0.38
13 31 0.44
14 3 0.04
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (12 bp):
AGAAAAAAAAAA
Found at i:743 original size:12 final size:11
Alignment explanation
Indices: 713--820 Score: 83
Period size: 12 Copynumber: 8.9 Consensus size: 11
703 GGCCCAAGCC
*
713 AAGAAAAGAAA
1 AAGAAAAAAAA
*
724 GAGAAAAAAAGA
1 AAGAAAAAAA-A
736 AA-AGAAAAAAA
1 AAGA-AAAAAAA
747 AAGAAAAAGAAA
1 AAGAAAAA-AAA
759 AAGAAAAAGAAA
1 AAGAAAAA-AAA
771 AAGAAAAAGAAA
1 AAGAAAAA-AAA
783 AAGGAAAAGGAAAA
1 AA-GAAAA--AAAA
*
797 AGGAAAAAATAA
1 AAGAAAAAA-AA
809 AATGAAATAAAA
1 AA-GAAA-AAAA
821 TAATAAATAA
Statistics
Matches: 82, Mismatches: 5, Indels: 18
0.78 0.05 0.17
Matches are distributed among these distances:
11 18 0.22
12 41 0.50
13 15 0.18
14 7 0.09
15 1 0.01
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.03
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:1658 original size:28 final size:27
Alignment explanation
Indices: 1617--1690 Score: 71
Period size: 28 Copynumber: 2.7 Consensus size: 27
1607 TTAAAATATC
** *
1617 AAAATTACTGTTTTGCCCTTGTTTGGCT
1 AAAATTACCATTTTGCCCTTG-TTGACT
* *
1645 AAAATTACCATTTTACCCCTGTTGACT
1 AAAATTACCATTTTGCCCTTGTTGACT
1672 -AAATTA-CAGTTTTGCCCTT
1 AAAATTACCA-TTTTGCCCTT
1691 AAACGCCAGA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
25 2 0.05
26 14 0.37
27 5 0.13
28 17 0.45
ACGTcount: A:0.24, C:0.22, G:0.12, T:0.42
Consensus pattern (27 bp):
AAAATTACCATTTTGCCCTTGTTGACT
Done.