Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012790.1 Corchorus capsularis cultivar CVL-1 contig12811, 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: 25643
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:1097 original size:78 final size:79
Alignment explanation
Indices: 1009--1174 Score: 282
Period size: 81 Copynumber: 2.1 Consensus size: 79
999 TTTTTTTAAT
1009 TAAAATAGTAAAATGGTAAAATATAATAG-TAATAAGG-ATATTAGATTTAATTATATAAAAATA
1 TAAAATAGTAAAATGGTAAAATATAATAGCT-ATAAGGAATATTAGATTTAATTATATAAAAATA
*
1072 GAGTTTTTAGTTGAG
65 GAGTTTTTAGTTGAA
1087 TAAAATAGTAAAATGGTAAAATATAATAGCTATAAGGATAATATTAGATTTAATTATATAAAAAT
1 TAAAATAGTAAAATGGTAAAATATAATAGCTATAAGG--AATATTAGATTTAATTATATAAAAAT
1152 AGAGTTTTTAGTTGAA
64 AGAGTTTTTAGTTGAA
1168 TAAAATA
1 TAAAATA
1175 AAATAGTTAT
Statistics
Matches: 83, Mismatches: 1, Indels: 5
0.93 0.01 0.06
Matches are distributed among these distances:
78 35 0.42
79 1 0.01
81 47 0.57
ACGTcount: A:0.50, C:0.01, G:0.14, T:0.36
Consensus pattern (79 bp):
TAAAATAGTAAAATGGTAAAATATAATAGCTATAAGGAATATTAGATTTAATTATATAAAAATAG
AGTTTTTAGTTGAA
Found at i:1213 original size:62 final size:63
Alignment explanation
Indices: 1103--1234 Score: 187
Period size: 62 Copynumber: 2.1 Consensus size: 63
1093 AGTAAAATGG
*
1103 TAAAATATAATAGCTATAAGGATAATATTAGATTTAATTATATAAAAATAGAGTTTTTAGTTGAA
1 TAAAATAAAATAGCTATAAGG--AATATTAGATTTAATTATATAAAAATAGAGTTTTTAGTTGAA
* * *
1168 TAAAATAAAATAGTTATAAGG-ATATTATATTTAATTGA-ATAAAAATAGAGTTTTTAGTTGAG
1 TAAAATAAAATAGCTATAAGGAATATTAGATTTAATT-ATATAAAAATAGAGTTTTTAGTTGAA
1230 TAAAA
1 TAAAA
1235 CTATAAAAAC
Statistics
Matches: 62, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
62 42 0.68
63 1 0.02
65 19 0.31
ACGTcount: A:0.48, C:0.01, G:0.13, T:0.38
Consensus pattern (63 bp):
TAAAATAAAATAGCTATAAGGAATATTAGATTTAATTATATAAAAATAGAGTTTTTAGTTGAA
Found at i:1568 original size:29 final size:29
Alignment explanation
Indices: 1534--1591 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
1524 TAACTATCAA
*
1534 TTTTGGGACAAATTGGCCCATTGACTTTT
1 TTTTGGGACAAATTGGCCCATTAACTTTT
*
1563 TTTTGGGACAAATTGGCCCCTTAACTTTT
1 TTTTGGGACAAATTGGCCCATTAACTTTT
1592 AAAAAACGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.41
Consensus pattern (29 bp):
TTTTGGGACAAATTGGCCCATTAACTTTT
Found at i:2339 original size:27 final size:28
Alignment explanation
Indices: 2283--2339 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
2273 TCTCGTTTTT
*
2283 AAAAGTTAAGGGGTCAATTTGTCCCAAA
1 AAAAGTTAAGGGGGCAATTTGTCCCAAA
*
2311 AAAAGTTAAGGGGGCAATTTGTCCTAAA
1 AAAAGTTAAGGGGGCAATTTGTCCCAAA
2339 A
1 A
2340 TGGATAGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.40, C:0.12, G:0.23, T:0.25
Consensus pattern (28 bp):
AAAAGTTAAGGGGGCAATTTGTCCCAAA
Found at i:11375 original size:20 final size:19
Alignment explanation
Indices: 11350--11412 Score: 81
Period size: 20 Copynumber: 3.2 Consensus size: 19
11340 GCCTTGGTTA
11350 TTTATTGTGTTAGCAGCAAG
1 TTTATT-TGTTAGCAGCAAG
*
11370 TTTATTACGTTAGCAGCAAG
1 TTTATT-TGTTAGCAGCAAG
*
11390 TTTATTTCGTTAGGAGCAAG
1 TTTATTT-GTTAGCAGCAAG
11410 TTT
1 TTT
11413 GTGATTTCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.25, C:0.11, G:0.22, T:0.41
Consensus pattern (19 bp):
TTTATTTGTTAGCAGCAAG
Found at i:11420 original size:23 final size:20
Alignment explanation
Indices: 11358--11412 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
11348 TATTTATTGT
*
11358 GTTAGCAGCAAGTTTATTAC
1 GTTAGCAGCAAGTTTATTTC
11378 GTTAGCAGCAAGTTTATTTC
1 GTTAGCAGCAAGTTTATTTC
*
11398 GTTAGGAGCAAGTTT
1 GTTAGCAGCAAGTTT
11413 GTGATTTCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.36
Consensus pattern (20 bp):
GTTAGCAGCAAGTTTATTTC
Found at i:23738 original size:30 final size:29
Alignment explanation
Indices: 23682--23738 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 29
23672 ATTGCAAATA
* * *
23682 TTTTAAGTACATGGTAAAAGTGTAAATCT
1 TTTTAAGGACATGGCAAAAGTATAAATCT
*
23711 TTTTAGAGGACATGGCAAAATTATAAAT
1 TTTTA-AGGACATGGCAAAAGTATAAAT
23739 TTTCACCTAC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 5 0.22
30 18 0.78
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.35
Consensus pattern (29 bp):
TTTTAAGGACATGGCAAAAGTATAAATCT
Done.