Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01004580.1 Corchorus olitorius cultivar O-4 contig04596, 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, 886
Length: 1477
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:759 original size:29 final size:29
Alignment explanation
Indices: 727--795 Score: 138
Period size: 29 Copynumber: 2.4 Consensus size: 29
717 ATTATATGTC
727 TATTTTTATATGTCATTTTGATTTCATTA
1 TATTTTTATATGTCATTTTGATTTCATTA
756 TATTTTTATATGTCATTTTGATTTCATTA
1 TATTTTTATATGTCATTTTGATTTCATTA
785 TATTTTTATAT
1 TATTTTTATAT
796 TTTTATATGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.64
Consensus pattern (29 bp):
TATTTTTATATGTCATTTTGATTTCATTA
Found at i:786 original size:21 final size:21
Alignment explanation
Indices: 761--824 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
751 CATTATATTT
761 TTATATGTCATTTTGATTTCA
1 TTATATGTCATTTTGATTTCA
782 TTATAT-T--TTTAT-ATTT--
1 TTATATGTCATTT-TGATTTCA
798 TTATATGTCATTTTGATTTCA
1 TTATATGTCATTTTGATTTCA
819 TTATAT
1 TTATAT
825 TTTTTATATG
Statistics
Matches: 36, Mismatches: 0, Indels: 14
0.72 0.00 0.28
Matches are distributed among these distances:
16 6 0.17
17 1 0.03
18 8 0.22
19 8 0.22
20 1 0.03
21 12 0.33
ACGTcount: A:0.25, C:0.06, G:0.06, T:0.62
Consensus pattern (21 bp):
TTATATGTCATTTTGATTTCA
Found at i:794 original size:37 final size:37
Alignment explanation
Indices: 708--881 Score: 182
Period size: 37 Copynumber: 4.6 Consensus size: 37
698 TTTCCTTTAA
* *
708 TTATATTTAATTATATGTCTATTTTTATATGTCATTTTGATTT
1 TTATATTT--TTATATGTC-ATTTTGAT-T-TCATTAT-ATTT
751 CATTATATTTTTATATGTCATTTTGATTTCATTATATTT
1 --TTATATTTTTATATGTCATTTTGATTTCATTATATTT
790 TTATATTTTTATATGTCATTTTGATTTCA-T-TA---
1 TTATATTTTTATATGTCATTTTGATTTCATTATATTT
822 -TAT-TTTTTATATGTCATTTTTGATTTCATTATATTTT
1 TTATATTTTTATATGTCA-TTTTGATTTCATTATA-TTT
859 TTATATTTTTTATATGTCATTTT
1 TTATA-TTTTTATATGTCATTTT
882 TGAATTGACT
Statistics
Matches: 117, Mismatches: 2, Indels: 26
0.81 0.01 0.18
Matches are distributed among these distances:
30 13 0.11
31 14 0.12
32 1 0.01
33 2 0.02
35 2 0.02
36 1 0.01
37 29 0.25
38 3 0.03
39 8 0.07
40 19 0.16
41 1 0.01
42 7 0.06
43 9 0.08
45 8 0.07
ACGTcount: A:0.24, C:0.06, G:0.06, T:0.64
Consensus pattern (37 bp):
TTATATTTTTATATGTCATTTTGATTTCATTATATTT
Found at i:799 original size:66 final size:69
Alignment explanation
Indices: 727--881 Score: 280
Period size: 66 Copynumber: 2.3 Consensus size: 69
717 ATTATATGTC
727 TATTTTTATATGTCATTTTGATTTCATTATA-TTTTTATATGTCA-TTTTGATTTCATTATA-TT
1 TATTTTTATATGTCATTTTGATTTCATTATATTTTTTATATGTCATTTTTGATTTCATTATATTT
789 TTTA
66 TTTA
793 TATTTTTATATGTCATTTTGATTTCATTATATTTTTTATATGTCATTTTTGATTTCATTATATTT
1 TATTTTTATATGTCATTTTGATTTCATTATATTTTTTATATGTCATTTTTGATTTCATTATATTT
858 TTTA
66 TTTA
862 TATTTTTTATATGTCATTTT
1 TA-TTTTTATATGTCATTTT
882 TGAATTGACT
Statistics
Matches: 85, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
66 31 0.36
67 13 0.15
68 16 0.19
69 8 0.09
70 17 0.20
ACGTcount: A:0.23, C:0.06, G:0.06, T:0.65
Consensus pattern (69 bp):
TATTTTTATATGTCATTTTGATTTCATTATATTTTTTATATGTCATTTTTGATTTCATTATATTT
TTTA
Found at i:831 original size:30 final size:31
Alignment explanation
Indices: 790--864 Score: 136
Period size: 31 Copynumber: 2.5 Consensus size: 31
780 CATTATATTT
790 TTATA-TTTTTATATGTCA-TTTTGATTTCA
1 TTATATTTTTTATATGTCATTTTTGATTTCA
819 TTATATTTTTTATATGTCATTTTTGATTTCA
1 TTATATTTTTTATATGTCATTTTTGATTTCA
850 TTATATTTTTTATAT
1 TTATATTTTTTATAT
865 TTTTTATATG
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
29 5 0.11
30 13 0.30
31 26 0.59
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.65
Consensus pattern (31 bp):
TTATATTTTTTATATGTCATTTTTGATTTCA
Done.