Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01000872.1 Corchorus capsularis cultivar CVL-1 contig00872, 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: 3112
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Found at i:90 original size:15 final size:14
Alignment explanation
Indices: 40--131 Score: 56
Period size: 11 Copynumber: 7.0 Consensus size: 14
30 TTATGATTAG
*
40 TTTAATTAGTTAAT
1 TTTAATTAGTTTAT
** * *
54 TAAAATTA-CTTAG
1 TTTAATTAGTTTAT
67 TTT-ATTAGTTTAT
1 TTTAATTAGTTTAT
80 GTTTAATTAG--TA-
1 -TTTAATTAGTTTAT
*
92 TCTAATTAGTTTAT
1 TTTAATTAGTTTAT
106 TATTAATTAG--TA-
1 T-TTAATTAGTTTAT
118 TTTAATTAGTTTAT
1 TTTAATTAGTTTAT
132 GATTAAAATG
Statistics
Matches: 57, Mismatches: 11, Indels: 20
0.65 0.12 0.23
Matches are distributed among these distances:
11 16 0.28
12 5 0.09
13 14 0.25
14 10 0.18
15 12 0.21
ACGTcount: A:0.34, C:0.02, G:0.09, T:0.55
Consensus pattern (14 bp):
TTTAATTAGTTTAT
Found at i:99 original size:26 final size:26
Alignment explanation
Indices: 70--137 Score: 102
Period size: 26 Copynumber: 2.6 Consensus size: 26
60 TACTTAGTTT
70 ATTAGTTTATGTTTAATTAGTATCTA
1 ATTAGTTTATGTTTAATTAGTATCTA
*
96 ATTAGTTTAT-TATTAATTAGTATTTA
1 ATTAGTTTATGT-TTAATTAGTATCTA
*
122 ATTAGTTTATGATTAA
1 ATTAGTTTATGTTTAA
138 AATGAAGGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
25 1 0.03
26 37 0.97
ACGTcount: A:0.34, C:0.01, G:0.10, T:0.54
Consensus pattern (26 bp):
ATTAGTTTATGTTTAATTAGTATCTA
Found at i:99 original size:52 final size:50
Alignment explanation
Indices: 21--137 Score: 120
Period size: 52 Copynumber: 2.4 Consensus size: 50
11 TTTTTTAATA
*
21 TTAATTAGTTTATG----ATTAGTTTAATTAGTTAATTA-AAATTACTTAGT
1 TTAATTAGTTTATGATTAATTAGTTTAATTAGTTAATTATAAATTA-GTA-T
* * *
68 TT-ATTAGTTTATGTTTAATTAGTATCTAATTAGTTTATTATTAATTAGTAT
1 TTAATTAGTTTATGATTAATTAGT-T-TAATTAGTTAATTATAAATTAGTAT
119 TTAATTAGTTTATGATTAA
1 TTAATTAGTTTATGATTAA
138 AATGAAGGAA
Statistics
Matches: 58, Mismatches: 4, Indels: 11
0.79 0.05 0.15
Matches are distributed among these distances:
46 11 0.19
47 2 0.03
50 6 0.10
51 4 0.07
52 30 0.52
53 5 0.09
ACGTcount: A:0.34, C:0.02, G:0.10, T:0.54
Consensus pattern (50 bp):
TTAATTAGTTTATGATTAATTAGTTTAATTAGTTAATTATAAATTAGTAT
Found at i:185 original size:24 final size:25
Alignment explanation
Indices: 146--205 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 25
136 AAAATGAAGG
*
146 AAAATGAA-TTTGAAG-ATTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
169 AAAATGAAGTTTGAAGAAGTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
*
194 GAAATGAAGTTT
1 AAAATGAAGTTT
206 AGGGTTTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
23 8 0.24
24 7 0.21
25 18 0.55
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (25 bp):
AAAATGAAGTTTGAAGAAGTTGTTA
Found at i:631 original size:20 final size:21
Alignment explanation
Indices: 594--636 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
584 CAAAATAATT
594 ATATATATATATTTTTTA-AA
1 ATATATATATATTTTTTACAA
*
614 ATATATATGT-TTTATTTACAA
1 ATATATATATATTT-TTTACAA
635 AT
1 AT
637 TTCCCAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 3 0.15
20 13 0.65
21 4 0.20
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (21 bp):
ATATATATATATTTTTTACAA
Done.