Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga08g01649.C1
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: 5436
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.27
Found at i:4141 original size:45 final size:45
Alignment explanation
Indices: 4087--4397 Score: 300
Period size: 45 Copynumber: 7.5 Consensus size: 45
4077 AAGAGGAAGT
** * *
4087 GCAGCCCGAGACCTTAACAGACAAGGAAGAGCAAGAGAAGGCGCA
1 GCAGCCCGAGAGTTTACCAGACAAGGAAGAGAAAGAGAAGGCGCA
4132 GCAGCCCGAGAGTTTACCAGACAAGGAAG-G---GA-AA---G-A
1 GCAGCCCGAGAGTTTACCAGACAAGGAAGAGAAAGAGAAGGCGCA
* * *
4168 TGC-GCCCAAGAGTTTACCGGACAAGGAAGAGAAAGAGGAGGCGCA
1 -GCAGCCCGAGAGTTTACCAGACAAGGAAGAGAAAGAGAAGGCGCA
*
4213 GCAGCCCGAGAGTTTACCAGACAAGGAAGAG-AA-AG-A-----T
1 GCAGCCCGAGAGTTTACCAGACAAGGAAGAGAAAGAGAAGGCGCA
* *
4250 GC-GCCCAAGAGTTTACCAGACAAGGAAGAGAAAGAGGAGGCGCA
1 GCAGCCCGAGAGTTTACCAGACAAGGAAGAGAAAGAGAAGGCGCA
4294 GCAGCCCGAGAGTTTACCAGACAAGGAAGAG-AA-AG-A-----A
1 GCAGCCCGAGAGTTTACCAGACAAGGAAGAGAAAGAGAAGGCGCA
* * *
4331 GC-GCCCAAGAGTTTACCAGACAAGGAAGAGAACGAGGAGGCGCA
1 GCAGCCCGAGAGTTTACCAGACAAGGAAGAGAAAGAGAAGGCGCA
4375 GCAGCCCGAGAGTTTACCAGACA
1 GCAGCCCGAGAGTTTACCAGACA
4398 GGGCTGCAAA
Statistics
Matches: 222, Mismatches: 15, Indels: 58
0.75 0.05 0.20
Matches are distributed among these distances:
36 79 0.36
37 12 0.05
38 4 0.02
39 2 0.01
40 4 0.02
41 3 0.01
42 2 0.01
43 4 0.02
44 13 0.06
45 99 0.45
ACGTcount: A:0.38, C:0.22, G:0.32, T:0.08
Consensus pattern (45 bp):
GCAGCCCGAGAGTTTACCAGACAAGGAAGAGAAAGAGAAGGCGCA
Found at i:4180 original size:36 final size:36
Alignment explanation
Indices: 4135--4358 Score: 196
Period size: 36 Copynumber: 5.7 Consensus size: 36
4125 AGGCGCAGCA
* *
4135 GCCCGAGAGTTTACCAGACAAGGAAGGGAAAGATGC
1 GCCCAAGAGTTTACCAGACAAGGAAGGGAAAGAAGC
* *
4171 GCCCAAGAGTTTACCGGACAAGGAAGAGAAAGAGGAGGCGCAGC
1 GCCCAAGAGTTTACCAGACAAGGAAG-GGAA-A-GA-----AGC
* * *
4215 AGCCCGAGAGTTTACCAGACAAGGAAGAGAAAGATGC
1 -GCCCAAGAGTTTACCAGACAAGGAAGGGAAAGAAGC
*
4252 GCCCAAGAGTTTACCAGACAAGGAAGAGAAAGAGGAGGCGCAGC
1 GCCCAAGAGTTTACCAGACAAGGAAG-GGAA-A-GA-----AGC
* *
4296 AGCCCGAGAGTTTACCAGACAAGGAAGAGAAAGAAGC
1 -GCCCAAGAGTTTACCAGACAAGGAAGGGAAAGAAGC
4333 GCCCAAGAGTTTACCAGACAAGGAAG
1 GCCCAAGAGTTTACCAGACAAGGAAG
4359 AGAACGAGGA
Statistics
Matches: 153, Mismatches: 17, Indels: 36
0.74 0.08 0.17
Matches are distributed among these distances:
36 74 0.48
37 10 0.07
38 2 0.01
39 4 0.03
42 4 0.03
43 2 0.01
44 8 0.05
45 49 0.32
ACGTcount: A:0.39, C:0.20, G:0.32, T:0.09
Consensus pattern (36 bp):
GCCCAAGAGTTTACCAGACAAGGAAGGGAAAGAAGC
Found at i:4193 original size:81 final size:81
Alignment explanation
Indices: 4104--4397 Score: 534
Period size: 81 Copynumber: 3.6 Consensus size: 81
4094 GAGACCTTAA
* * *
4104 CAGACAAGGAAGAGCAAGAGAAGGCGCAGCAGCCCGAGAGTTTACCAGACAAGGAAGGGAAAGAT
1 CAGACAAGGAAGAGAAAGAGGAGGCGCAGCAGCCCGAGAGTTTACCAGACAAGGAAGAGAAAGAT
4169 GCGCCCAAGAGTTTAC
66 GCGCCCAAGAGTTTAC
*
4185 CGGACAAGGAAGAGAAAGAGGAGGCGCAGCAGCCCGAGAGTTTACCAGACAAGGAAGAGAAAGAT
1 CAGACAAGGAAGAGAAAGAGGAGGCGCAGCAGCCCGAGAGTTTACCAGACAAGGAAGAGAAAGAT
4250 GCGCCCAAGAGTTTAC
66 GCGCCCAAGAGTTTAC
*
4266 CAGACAAGGAAGAGAAAGAGGAGGCGCAGCAGCCCGAGAGTTTACCAGACAAGGAAGAGAAAGAA
1 CAGACAAGGAAGAGAAAGAGGAGGCGCAGCAGCCCGAGAGTTTACCAGACAAGGAAGAGAAAGAT
4331 GCGCCCAAGAGTTTAC
66 GCGCCCAAGAGTTTAC
*
4347 CAGACAAGGAAGAGAACGAGGAGGCGCAGCAGCCCGAGAGTTTACCAGACA
1 CAGACAAGGAAGAGAAAGAGGAGGCGCAGCAGCCCGAGAGTTTACCAGACA
4398 GGGCTGCAAA
Statistics
Matches: 206, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
81 206 1.00
ACGTcount: A:0.39, C:0.21, G:0.33, T:0.08
Consensus pattern (81 bp):
CAGACAAGGAAGAGAAAGAGGAGGCGCAGCAGCCCGAGAGTTTACCAGACAAGGAAGAGAAAGAT
GCGCCCAAGAGTTTAC
Done.