Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga14g01387.P3
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: 8778
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Found at i:3950 original size:26 final size:24
Alignment explanation
Indices: 3864--3995 Score: 210
Period size: 25 Copynumber: 5.2 Consensus size: 24
3854 TGATACAAAT
3864 TGATAATAGGTTAGGTAAATGTTCA
1 TGATAAT-GGTTAGGTAAATGTTCA
3889 TGATAATGGTTAGGTAAATGTTCA
1 TGATAATGGTTAGGTAAATGTTCA
3913 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAAT-GGTTAGGTAAATGTT-CA
3939 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAAT-GGTTAGGTAAATG-TTCA
3965 TGATAATGGTTAGGTAAATGTTTCA
1 TGATAATGGTTAGGTAAATG-TTCA
3990 TGATAA
1 TGATAA
3996 GAATATCATG
Statistics
Matches: 103, Mismatches: 1, Indels: 6
0.94 0.01 0.05
Matches are distributed among these distances:
24 24 0.23
25 46 0.45
26 31 0.30
27 2 0.02
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.37
Consensus pattern (24 bp):
TGATAATGGTTAGGTAAATGTTCA
Found at i:3976 original size:51 final size:49
Alignment explanation
Indices: 3864--3995 Score: 221
Period size: 51 Copynumber: 2.6 Consensus size: 49
3854 TGATACAAAT
3864 TGATAATAGGTTAGGTAAATGTTCATGATAATGGTTAGGTAAATGTTCA
1 TGATAATAGGTTAGGTAAATGTTCATGATAATGGTTAGGTAAATGTTCA
3913 TGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTT-CATGATAAT-GGTTAGGTAAATG-TTCA
3965 TGATAAT-GGTTAGGTAAATGTTTCATGATAA
1 TGATAATAGGTTAGGTAAATG-TTCATGATAA
3996 GAATATCATG
Statistics
Matches: 79, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
49 23 0.29
50 9 0.11
51 34 0.43
52 13 0.16
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.37
Consensus pattern (49 bp):
TGATAATAGGTTAGGTAAATGTTCATGATAATGGTTAGGTAAATGTTCA
Found at i:6017 original size:137 final size:137
Alignment explanation
Indices: 5771--6045 Score: 514
Period size: 137 Copynumber: 2.0 Consensus size: 137
5761 GAGTAGTCTC
5771 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
5836 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTATAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTATAATCTGAAAAGGGCTCTGGCCCAGTACC
5901 ACTGTTA
131 ACTGTTA
*
5908 CCCAAATGGGCTTGCATATGTTTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
* * *
5973 TGTTATCTGAATAAGGGGTTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTATC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTATAATCTGAAAAGGGCTCTGGCCCAGTACC
6038 ACTGTTA
131 ACTGTTA
6045 C
1 C
6046 TGAATGGGCT
Statistics
Matches: 134, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
137 134 1.00
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.32
Consensus pattern (137 bp):
CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTATAATCTGAAAAGGGCTCTGGCCCAGTACC
ACTGTTA
Done.