Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01005086.1 Corchorus olitorius cultivar O-4 contig05107, 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, 622
Length: 1037
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Found at i:619 original size:8 final size:8
Alignment explanation
Indices: 606--693 Score: 54
Period size: 8 Copynumber: 9.8 Consensus size: 8
596 TCAAAATGAC
606 ATATAAAA
1 ATATAAAA
614 ATATAAAA
1 ATATAAAA
622 ATATAATGAA
1 ATATAA--AA
632 ATCA-AAATGA
1 AT-ATAAA--A
642 CATATAAAA
1 -ATATAAAA
651 ATATAATGAA
1 ATATAA--AA
661 ATCA-AAATGA
1 AT-ATAAA--A
671 CATATAAAA
1 -ATATAAAA
680 ATATAAAA
1 ATATAAAA
688 ATATAA
1 ATATAA
694 TGAATCAAAA
Statistics
Matches: 66, Mismatches: 0, Indels: 28
0.70 0.00 0.30
Matches are distributed among these distances:
8 36 0.55
9 2 0.03
10 16 0.24
11 12 0.18
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.25
Consensus pattern (8 bp):
ATATAAAA
Found at i:646 original size:37 final size:37
Alignment explanation
Indices: 596--721 Score: 189
Period size: 29 Copynumber: 3.6 Consensus size: 37
586 CAGAGTCAAT
596 TCAAAATGACATATAAAAATATAAAAATATAATGAAA
1 TCAAAATGACATATAAAAATATAAAAATATAATGAAA
633 TCAAAATGAC--------ATATAAAAATATAATGAAA
1 TCAAAATGACATATAAAAATATAAAAATATAATGAAA
662 TCAAAATGACATATAAAAATATAAAAATATAATG-AA
1 TCAAAATGACATATAAAAATATAAAAATATAATGAAA
698 TCAAAATGACATATAAAAATATAA
1 TCAAAATGACATATAAAAATATAA
722 TGAAATCAAA
Statistics
Matches: 81, Mismatches: 0, Indels: 17
0.83 0.00 0.17
Matches are distributed among these distances:
29 29 0.36
36 26 0.32
37 26 0.32
ACGTcount: A:0.63, C:0.06, G:0.06, T:0.25
Consensus pattern (37 bp):
TCAAAATGACATATAAAAATATAAAAATATAATGAAA
Found at i:647 original size:29 final size:29
Alignment explanation
Indices: 614--745 Score: 192
Period size: 29 Copynumber: 4.3 Consensus size: 29
604 ACATATAAAA
614 ATATAAAAATATAATGAAATCAAAATGAC
1 ATATAAAAATATAATGAAATCAAAATGAC
643 ATATAAAAATATAATGAAATCAAAATGAC
1 ATATAAAAATATAATGAAATCAAAATGAC
*
672 ATATAAAAATATAAAAATATAATGAATCAAAATGAC
1 ATATAAAAATAT----A-ATGA--AATCAAAATGAC
708 ATATAAAAATATAATGAAATCAAAATGAC
1 ATATAAAAATATAATGAAATCAAAATGAC
737 ATATAAAAA
1 ATATAAAAA
746 ATGACATATA
Statistics
Matches: 94, Mismatches: 2, Indels: 14
0.85 0.02 0.13
Matches are distributed among these distances:
29 62 0.66
31 3 0.03
32 1 0.01
33 1 0.01
34 3 0.03
36 24 0.26
ACGTcount: A:0.64, C:0.06, G:0.06, T:0.24
Consensus pattern (29 bp):
ATATAAAAATATAATGAAATCAAAATGAC
Found at i:707 original size:36 final size:37
Alignment explanation
Indices: 643--721 Score: 151
Period size: 36 Copynumber: 2.2 Consensus size: 37
633 TCAAAATGAC
643 ATATAAAAATATAATGAAATCAAAATGACATATAAAA
1 ATATAAAAATATAATGAAATCAAAATGACATATAAAA
680 ATATAAAAATATAATG-AATCAAAATGACATATAAAA
1 ATATAAAAATATAATGAAATCAAAATGACATATAAAA
716 ATATAA
1 ATATAA
722 TGAAATCAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
36 26 0.62
37 16 0.38
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.25
Consensus pattern (37 bp):
ATATAAAAATATAATGAAATCAAAATGACATATAAAA
Found at i:747 original size:66 final size:66
Alignment explanation
Indices: 596--745 Score: 293
Period size: 65 Copynumber: 2.3 Consensus size: 66
586 CAGAGTCAAT
596 TCAAAATGACATATAAAAATATAAAAATATAATGAAATCAAAATGACATATAAAAATATAATGAA
1 TCAAAATGACATATAAAAATATAAAAATATAATGAAATCAAAATGACATATAAAAATATAATGAA
661 A
66 A
662 TCAAAATGACATATAAAAATATAAAAATATAATG-AATCAAAATGACATATAAAAATATAATGAA
1 TCAAAATGACATATAAAAATATAAAAATATAATGAAATCAAAATGACATATAAAAATATAATGAA
726 A
66 A
727 TCAAAATGACATATAAAAA
1 TCAAAATGACATATAAAAA
746 ATGACATATA
Statistics
Matches: 84, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
65 50 0.60
66 34 0.40
ACGTcount: A:0.63, C:0.07, G:0.06, T:0.24
Consensus pattern (66 bp):
TCAAAATGACATATAAAAATATAAAAATATAATGAAATCAAAATGACATATAAAAATATAATGAA
A
Found at i:748 original size:14 final size:14
Alignment explanation
Indices: 700--756 Score: 57
Period size: 14 Copynumber: 4.0 Consensus size: 14
690 ATAATGAATC
700 AAAATGACATATAA
1 AAAATGACATATAA
714 AAATAT-A-ATGA-AA
1 AAA-ATGACAT-ATAA
727 TCAAAATGACATATAA
1 --AAAATGACATATAA
743 AAAATGACATATAA
1 AAAATGACATATAA
757 TTAAATATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 14
0.72 0.00 0.28
Matches are distributed among these distances:
13 4 0.11
14 21 0.58
15 7 0.19
16 4 0.11
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.23
Consensus pattern (14 bp):
AAAATGACATATAA
Done.