Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012103.1 Corchorus olitorius cultivar O-4 contig12136, 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: 6722
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.28
Found at i:1079 original size:69 final size:70
Alignment explanation
Indices: 995--1130 Score: 238
Period size: 69 Copynumber: 2.0 Consensus size: 70
985 ACTAACAACT
* **
995 AAGGAAAAAATGGTAGGAGCACCATTAATTACATCTTAATGCTAAAATTACATATAAAGACAATG
1 AAGGAAAAAATGGTAGGAACACCATTAATTACATCCAAATGCTAAAATTACATATAAAGACAATG
1060 CACCA
66 CACCA
1065 AAGG-AAAAATGGTAGGAACACCATTAATTACATCCAAATGCTAAAATTACATATAAAGACAATG
1 AAGGAAAAAATGGTAGGAACACCATTAATTACATCCAAATGCTAAAATTACATATAAAGACAATG
1129 CA
66 CA
1131 TTTCAAGCAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
69 59 0.94
70 4 0.06
ACGTcount: A:0.49, C:0.15, G:0.14, T:0.22
Consensus pattern (70 bp):
AAGGAAAAAATGGTAGGAACACCATTAATTACATCCAAATGCTAAAATTACATATAAAGACAATG
CACCA
Found at i:4557 original size:216 final size:216
Alignment explanation
Indices: 4177--4828 Score: 1295
Period size: 216 Copynumber: 3.0 Consensus size: 216
4167 CCCGACCCGG
*
4177 AAGTCGGACGTGAACAACCGCCGCGTCTCCTTGAACTACGTGCCGCGCGTCACACGTATCCAAGG
1 AAGTCAGACGTGAACAACCGCCGCGTCTCCTTGAACTACGTGCCGCGCGTCACACGTATCCAAGG
4242 TATCGCGAAGCGTCGATACCAGATCAAAAACAATAAAACGAGAACACAATATAAATTTTAAATAC
66 TATCGCGAAGCGTCGATACCAGATCAAAAACAATAAAACGAGAACACAATATAAATTTTAAATAC
4307 GACAGTTTCAAATCAGAGTAAAAGCGGAATCGTCAAAAATCGAAGTAGTAAAAGTATTCTAATAA
131 GACAGTTTCAAATCAGAGTAAAAGCGGAATCGTCAAAAATCGAAGTAGTAAAAGTATTCTAATAA
4372 ATCAAACACCAAGTCAAATCC
196 ATCAAACACCAAGTCAAATCC
4393 AAGTCAGACGTGAACAACCGCCGCGTCTCCTTGAACTACGTGCCGCGCGTCACACGTATCCAAGG
1 AAGTCAGACGTGAACAACCGCCGCGTCTCCTTGAACTACGTGCCGCGCGTCACACGTATCCAAGG
4458 TATCGCGAAGCGTCGATACCAGATCAAAAACAATAAAACGAGAACACAATATAAATTTTAAATAC
66 TATCGCGAAGCGTCGATACCAGATCAAAAACAATAAAACGAGAACACAATATAAATTTTAAATAC
4523 GACAGTTTCAAATCAGAGTAAAAGCGGAATCGTCAAAAATCGAAGTAGTAAAAGTATTCTAATAA
131 GACAGTTTCAAATCAGAGTAAAAGCGGAATCGTCAAAAATCGAAGTAGTAAAAGTATTCTAATAA
4588 ATCAAACACCAAGTCAAATCC
196 ATCAAACACCAAGTCAAATCC
4609 AAGTCAGACGTGAACAACCGCCGCGTCTCCTTGAACTACGTGCCGCGCGTCACACGTATCCAAGG
1 AAGTCAGACGTGAACAACCGCCGCGTCTCCTTGAACTACGTGCCGCGCGTCACACGTATCCAAGG
4674 TATCGCGAAGCGTCGATACCAGATCAAAAACAATAAAACGAGAACACAATATAAATTTTAAATAC
66 TATCGCGAAGCGTCGATACCAGATCAAAAACAATAAAACGAGAACACAATATAAATTTTAAATAC
4739 GACAGTTTCAAATCAGAGTAAAAGCGGAATCGTCAAAAATCGAAGTAGTAAAAGTATTCTAATAA
131 GACAGTTTCAAATCAGAGTAAAAGCGGAATCGTCAAAAATCGAAGTAGTAAAAGTATTCTAATAA
4804 ATCAAACACCAAGTCAAATCC
196 ATCAAACACCAAGTCAAATCC
4825 AAGT
1 AAGT
4829 AGTCAGTTAG
Statistics
Matches: 435, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
216 435 1.00
ACGTcount: A:0.41, C:0.23, G:0.17, T:0.19
Consensus pattern (216 bp):
AAGTCAGACGTGAACAACCGCCGCGTCTCCTTGAACTACGTGCCGCGCGTCACACGTATCCAAGG
TATCGCGAAGCGTCGATACCAGATCAAAAACAATAAAACGAGAACACAATATAAATTTTAAATAC
GACAGTTTCAAATCAGAGTAAAAGCGGAATCGTCAAAAATCGAAGTAGTAAAAGTATTCTAATAA
ATCAAACACCAAGTCAAATCC
Found at i:6099 original size:28 final size:27
Alignment explanation
Indices: 6035--6100 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 27
6025 TCTGGCATTT
*
6035 AAGGGCAAAACTGTAATTTAGTTAACC
1 AAGGGCAAAACTGTAATTTAGCTAACC
* * *
6062 AGGGGTAAAA-TGGTAATTTTAGCTGACC
1 AAGGGCAAAACT-GTAA-TTTAGCTAACC
6090 AAGGGCAAAAC
1 AAGGGCAAAAC
6101 AATAATTTGA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
26 1 0.03
27 12 0.40
28 17 0.57
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.23
Consensus pattern (27 bp):
AAGGGCAAAACTGTAATTTAGCTAACC
Done.