Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga03g00622.F3
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: 4835
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.28
Found at i:2265 original size:217 final size:217
Alignment explanation
Indices: 1890--2322 Score: 769
Period size: 217 Copynumber: 2.0 Consensus size: 217
1880 CTGCTGAAGA
*
1890 GGAAGGGGGTTGGATAAATATCAATTTTTGAAAATCTATTGCTTTGCGCCTTGTTCTTTTTAATT
1 GGAAGGGGGTTGGACAAATATCAATTTTTGAAAATCTATTGCTTTGCGCCTTGTTCTTTTTAATT
*
1955 CTCACTTAAGTGTTCTTCCATTACAATATTTGAAGAGTTTTCTTTGTTTTAATGGTGAAGAAATG
66 CTCACTTAAGTGTTCTTCCATTACAATATTTGAAGAGTTGTCTTTGTTTTAATGGTGAAGAAATG
2020 ATTCATTTTGCCAATTTAAGATTATTCATGACTTTGATTGTTTATTAAATTGCATAGGGAGACAA
131 ATTCATTTTGCCAATTTAAGATTATTCATGACTTTGATTGTTTATTAAATTGCATAGGGAGACAA
2085 CATTCCAGCACCATTCATAAGG
196 CATTCCAGCACCATTCATAAGG
* * *
2107 GGAAGGGTGTTTGACAAATATC-ATTCTTTGAAAATCTATTGCTTTGTGCCTTGTTCTTTTTAAT
1 GGAAGGGGGTTGGACAAATATCAATT-TTTGAAAATCTATTGCTTTGCGCCTTGTTCTTTTTAAT
* * *
2171 TCTCACTTTATTGTTCTTCCATTACAATATTTGAAGAGTTGTCTTTGTTTTAATGGTGAGGAAAT
65 TCTCACTTAAGTGTTCTTCCATTACAATATTTGAAGAGTTGTCTTTGTTTTAATGGTGAAGAAAT
2236 GATTCATTTTGCCAATTTAAGATTATTCATGACTTTGATTGTTTATTAAATTGCATAGGGAGACA
130 GATTCATTTTGCCAATTTAAGATTATTCATGACTTTGATTGTTTATTAAATTGCATAGGGAGACA
*
2301 ACGTTCCAGCACCATTCATAAG
195 ACATTCCAGCACCATTCATAAG
2323 ATTTGAAGAT
Statistics
Matches: 206, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
216 3 0.01
217 203 0.99
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (217 bp):
GGAAGGGGGTTGGACAAATATCAATTTTTGAAAATCTATTGCTTTGCGCCTTGTTCTTTTTAATT
CTCACTTAAGTGTTCTTCCATTACAATATTTGAAGAGTTGTCTTTGTTTTAATGGTGAAGAAATG
ATTCATTTTGCCAATTTAAGATTATTCATGACTTTGATTGTTTATTAAATTGCATAGGGAGACAA
CATTCCAGCACCATTCATAAGG
Found at i:3587 original size:33 final size:33
Alignment explanation
Indices: 3545--3633 Score: 142
Period size: 33 Copynumber: 2.7 Consensus size: 33
3535 GGATTCTGGA
3545 GGCCGTGGTGGAATGAGGGATGGAGGCTTTGGT
1 GGCCGTGGTGGAATGAGGGATGGAGGCTTTGGT
*
3578 GGCCGTGGTGGAATGAGGGATGGGGGCTTTGGT
1 GGCCGTGGTGGAATGAGGGATGGAGGCTTTGGT
* * *
3611 GGACGTGGTGGCATGAGAGATGG
1 GGCCGTGGTGGAATGAGGGATGG
3634 TTTTGGCGGT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.16, C:0.09, G:0.53, T:0.22
Consensus pattern (33 bp):
GGCCGTGGTGGAATGAGGGATGGAGGCTTTGGT
Found at i:3935 original size:6 final size:6
Alignment explanation
Indices: 3924--3951 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
3914 CGAACTTGGC
3924 GCCGTA GCCGTA GCCGTA GCCGTA GCCG
1 GCCGTA GCCGTA GCCGTA GCCGTA GCCG
3952 CAGTGGGAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.36, G:0.36, T:0.14
Consensus pattern (6 bp):
GCCGTA
Found at i:3966 original size:6 final size:6
Alignment explanation
Indices: 3957--4006 Score: 55
Period size: 6 Copynumber: 7.8 Consensus size: 6
3947 AGCCGCAGTG
* *
3957 GGAGTC GGAGTT GGAGTA GTAGGAGTA GGAGTA GGAGTA GGAGTA GGAGT
1 GGAGTA GGAGTA GGAGTA G--G-AGTA GGAGTA GGAGTA GGAGTA GGAGT
4007 CGAAGCAGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
6 32 0.82
7 1 0.03
8 1 0.03
9 5 0.13
ACGTcount: A:0.28, C:0.02, G:0.50, T:0.20
Consensus pattern (6 bp):
GGAGTA
Found at i:3987 original size:21 final size:21
Alignment explanation
Indices: 3957--3996 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3947 AGCCGCAGTG
* *
3957 GGAGTCGGAGTTGGAGTAGTA
1 GGAGTAGGAGTAGGAGTAGTA
3978 GGAGTAGGAGTAGGAGTAG
1 GGAGTAGGAGTAGGAGTAG
3997 GAGTAGGAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.03, G:0.50, T:0.20
Consensus pattern (21 bp):
GGAGTAGGAGTAGGAGTAGTA
Found at i:3989 original size:12 final size:12
Alignment explanation
Indices: 3974--4006 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
3964 GAGTTGGAGT
3974 AGTAGGAGTAGG
1 AGTAGGAGTAGG
3986 AGTAGGAGTAGG
1 AGTAGGAGTAGG
3998 AGTAGGAGT
1 AGTAGGAGT
4007 CGAAGCAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.48, T:0.18
Consensus pattern (12 bp):
AGTAGGAGTAGG
Found at i:4237 original size:63 final size:63
Alignment explanation
Indices: 4138--4293 Score: 226
Period size: 63 Copynumber: 2.5 Consensus size: 63
4128 GCTATGAGCG
* ** *
4138 GAAGGATGTTGCAAAGCGGGCATTTGATTCTCCTCCTGGTTCCAACGAACATAACTT-GCAACA
1 GAAGGATGTTGCAAAGCGAGCATTTGATTCTCCTCCTCCTTCCAACGAACAGAACTTCG-AACA
* *
4201 GAAGGATGTTGCGAAGCGAGCATTTGATTCTCCTCCTCCTTCCAACGAACAGAACTTCGAGCA
1 GAAGGATGTTGCAAAGCGAGCATTTGATTCTCCTCCTCCTTCCAACGAACAGAACTTCGAACA
4264 GAAGGATGTTGCAAAGC-AGGCATTTGATTC
1 GAAGGATGTTGCAAAGCGA-GCATTTGATTC
4294 ACCTGGTGCA
Statistics
Matches: 84, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
62 1 0.01
63 82 0.98
64 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (63 bp):
GAAGGATGTTGCAAAGCGAGCATTTGATTCTCCTCCTCCTTCCAACGAACAGAACTTCGAACA
Done.