Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012842.1 Corchorus olitorius cultivar O-4 contig12875, 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: 13873
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.30
Found at i:10197 original size:27 final size:27
Alignment explanation
Indices: 10145--10210 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
10135 AACGGAGTGA
*
10145 ATAACAGATC-ACGGACATCGGAATCAG
1 ATAACAGA-CAACGGACAACGGAATCAG
10172 ATAACAGACAACGGACAACAGG-ATCAG
1 ATAACAGACAACGGACAAC-GGAATCAG
* *
10199 ACAACGGACAAC
1 ATAACAGACAAC
10211 ATAATCATCA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
26 1 0.03
27 31 0.91
28 2 0.06
ACGTcount: A:0.45, C:0.24, G:0.21, T:0.09
Consensus pattern (27 bp):
ATAACAGACAACGGACAACGGAATCAG
Found at i:10217 original size:20 final size:20
Alignment explanation
Indices: 10172--10217 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
10162 TCGGAATCAG
10172 ATAA-CAGACAACGGACAAC
1 ATAATCAGACAACGGACAAC
**
10191 AGGATCAGACAACGGACAAC
1 ATAATCAGACAACGGACAAC
10211 ATAATCA
1 ATAATCA
10218 TCAAGAATAC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 2 0.09
20 20 0.91
ACGTcount: A:0.50, C:0.24, G:0.17, T:0.09
Consensus pattern (20 bp):
ATAATCAGACAACGGACAAC
Found at i:10253 original size:27 final size:28
Alignment explanation
Indices: 10221--10280 Score: 95
Period size: 28 Copynumber: 2.2 Consensus size: 28
10211 ATAATCATCA
* *
10221 AGAATACGGGA-CAATTAGGTCAAGGGC
1 AGAATACGGGACCAAATAGGTCAAGGAC
10248 AGAATACGGGACCAAATAGGTCAAGGAC
1 AGAATACGGGACCAAATAGGTCAAGGAC
10276 AGAAT
1 AGAAT
10281 TCAGAATCAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 11 0.37
28 19 0.63
ACGTcount: A:0.42, C:0.15, G:0.30, T:0.13
Consensus pattern (28 bp):
AGAATACGGGACCAAATAGGTCAAGGAC
Found at i:10458 original size:13 final size:13
Alignment explanation
Indices: 10440--10483 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
10430 ACTCGCGGAG
10440 GTCAAAGTCAACA
1 GTCAAAGTCAACA
*
10453 GTCAAAGTTAACA
1 GTCAAAGTCAACA
*
10466 GTCAACAATCAA-A
1 GTCAA-AGTCAACA
10479 GTCAA
1 GTCAA
10484 TGCTGACGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 23 0.85
14 4 0.15
ACGTcount: A:0.48, C:0.20, G:0.14, T:0.18
Consensus pattern (13 bp):
GTCAAAGTCAACA
Found at i:12373 original size:106 final size:104
Alignment explanation
Indices: 12161--12402 Score: 396
Period size: 106 Copynumber: 2.3 Consensus size: 104
12151 TATAAATTTT
*
12161 AATTTTAATTTGGGCTAAACTTAGTG-AATTAGTTATATATTTTATTTCTAAATCCCTATAACAA
1 AATTTTAATTTGGGCTAAACTTAGTGAAATTAGTTATATATTTTATTTCTAAAACCCTATAACAA
* *
12225 TATTATTAATTATGGAATTTACCCTTAAAATAAAAATAA
66 TAATATTAATTATGAAATTTACCCTTAAAATAAAAATAA
* *
12264 AATTTTAATTTGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTATTTCTAAAACCCTATAACAA
1 AATTTTAATTTGGGCTAAACTTAGTGAAATTAGTTATATATTTTATTTCTAAAACCCTATAACAA
*
12329 TAAAATATTAATTTTGAAATTTACCCTTAAAATAAAAATAA
66 T--AATATTAATTATGAAATTTACCCTTAAAATAAAAATAA
12370 AATTTTAATTTGGGGCTAAACTTAGTGAAATTA
1 AATTTTAATTT-GGGCTAAACTTAGTGAAATTA
12403 AGGCTAAACT
Statistics
Matches: 129, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
103 26 0.20
104 36 0.28
106 46 0.36
107 21 0.16
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (104 bp):
AATTTTAATTTGGGCTAAACTTAGTGAAATTAGTTATATATTTTATTTCTAAAACCCTATAACAA
TAATATTAATTATGAAATTTACCCTTAAAATAAAAATAA
Done.