Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga10g01858.F1
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: 3280
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.23
Found at i:1566 original size:24 final size:24
Alignment explanation
Indices: 1529--1580 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
1519 TTCCCCGGTA
*
1529 GAAGTCAAAACCGAAAAAGGGTCT
1 GAAGTCAAAACCGAAAAAAGGTCT
* *
1553 GAAGTCGAATCCGAAAAAAGGTCT
1 GAAGTCAAAACCGAAAAAAGGTCT
1577 GAAG
1 GAAG
1581 AACACGTCCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.44, C:0.15, G:0.27, T:0.13
Consensus pattern (24 bp):
GAAGTCAAAACCGAAAAAAGGTCT
Found at i:1690 original size:48 final size:48
Alignment explanation
Indices: 1623--1806 Score: 271
Period size: 48 Copynumber: 3.8 Consensus size: 48
1613 GCCATGGCCG
* * * * *
1623 ATGAATCGAAAGCAATAAGTTCTGTTCCAAAATCTGTAGAGAAAGCCG
1 ATGAACCGAAAGCAGTAAGTTCTGTTCCGAAATCTGCAGAGAAAGCCA
1671 ATGAACCGAAAGCAGTAAGTTCTGTTCCGAAATCTGCAGA-AGAAGCCA
1 ATGAACCGAAAGCAGTAAGTTCTGTTCCGAAATCTGCAGAGA-AAGCCA
* * *
1719 ATGAATCGAAAGCAGTAAGTTCTGTTCCGAAATCTGCAAAGGAAGCCA
1 ATGAACCGAAAGCAGTAAGTTCTGTTCCGAAATCTGCAGAGAAAGCCA
*
1767 ATGAACCAAAAGCAGTAAGTTCTGTTCCGAAATCTGCAGA
1 ATGAACCGAAAGCAGTAAGTTCTGTTCCGAAATCTGCAGA
1807 AGAAGGAAGC
Statistics
Matches: 123, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
47 1 0.01
48 122 0.99
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.21
Consensus pattern (48 bp):
ATGAACCGAAAGCAGTAAGTTCTGTTCCGAAATCTGCAGAGAAAGCCA
Found at i:1787 original size:96 final size:96
Alignment explanation
Indices: 1623--1811 Score: 315
Period size: 96 Copynumber: 2.0 Consensus size: 96
1613 GCCATGGCCG
* * * *
1623 ATGAATCGAAAGCAATAAGTTCTGTTCCAAAATCTGTAGAGAAAGCCGATGAACCGAAAGCAGTA
1 ATGAATCGAAAGCAATAAGTTCTGTTCCAAAATCTGCAAAGAAAGCCAATGAACCAAAAGCAGTA
1688 AGTTCTGTTCCGAAATCTGCAGAAGAAGCCA
66 AGTTCTGTTCCGAAATCTGCAGAAGAAGCCA
* * *
1719 ATGAATCGAAAGCAGTAAGTTCTGTTCCGAAATCTGCAAAGGAAGCCAATGAACCAAAAGCAGTA
1 ATGAATCGAAAGCAATAAGTTCTGTTCCAAAATCTGCAAAGAAAGCCAATGAACCAAAAGCAGTA
1784 AGTTCTGTTCCGAAATCTGCAGAAGAAG
66 AGTTCTGTTCCGAAATCTGCAGAAGAAG
1812 GAAGCGTTAG
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
96 86 1.00
ACGTcount: A:0.39, C:0.19, G:0.22, T:0.21
Consensus pattern (96 bp):
ATGAATCGAAAGCAATAAGTTCTGTTCCAAAATCTGCAAAGAAAGCCAATGAACCAAAAGCAGTA
AGTTCTGTTCCGAAATCTGCAGAAGAAGCCA
Found at i:2215 original size:9 final size:9
Alignment explanation
Indices: 2203--2261 Score: 57
Period size: 9 Copynumber: 6.6 Consensus size: 9
2193 CAATTCCAGC
2203 AGAAGAGAA
1 AGAAGAGAA
*
2212 AGAAGTGAA
1 AGAAGAGAA
*
2221 GGAAGTA-AA
1 AGAAG-AGAA
*
2230 AGAAGTGAA
1 AGAAGAGAA
*
2239 ACAAGAGAA
1 AGAAGAGAA
*
2248 AGAAAAGAA
1 AGAAGAGAA
2257 AGAAG
1 AGAAG
2262 TAGCTCTGGG
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
9 38 1.00
ACGTcount: A:0.63, C:0.02, G:0.31, T:0.05
Consensus pattern (9 bp):
AGAAGAGAA
Done.