Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga14g01387.P1
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: 9803
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Found at i:1123 original size:137 final size:137
Alignment explanation
Indices: 837--1111 Score: 487
Period size: 137 Copynumber: 2.0 Consensus size: 137
827 GAGTAGTCTC
*
837 CCCAAATGGGCTTGCATATGTTTACTGATGTTACATGTATTTTGAAATGGGCCTATGGGTCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTACATGTATTTTGAAATGGGCCTATGGGCCATAC
902 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTATAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTATAATCTGAAAAGGGCTCTGGCCCAGTACC
967 ACTGTTA
131 ACTGTTA
* * *
974 CCCAAATGGGCTTGCATATGTTTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAT
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTACATGTATTTTGAAATGGGCCTATGGGCCATAC
* * *
1039 TGTTATCTGAATAAGGGGTTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTATC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTATAATCTGAAAAGGGCTCTGGCCCAGTACC
1104 ACTGTTA
131 ACTGTTA
1111 C
1 C
1112 TTGAATGGGC
Statistics
Matches: 131, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
137 131 1.00
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.33
Consensus pattern (137 bp):
CCCAAATGGGCTTGCATATGTTTACTGATGTTACATGTATTTTGAAATGGGCCTATGGGCCATAC
TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTATAATCTGAAAAGGGCTCTGGCCCAGTACC
ACTGTTA
Found at i:4975 original size:26 final size:24
Alignment explanation
Indices: 4889--5020 Score: 210
Period size: 25 Copynumber: 5.2 Consensus size: 24
4879 TGATACAAAT
4889 TGATAATAGGTTAGGTAAATGTTCA
1 TGATAAT-GGTTAGGTAAATGTTCA
4914 TGATAATGGTTAGGTAAATGTTCA
1 TGATAATGGTTAGGTAAATGTTCA
4938 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAAT-GGTTAGGTAAATGTT-CA
4964 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAAT-GGTTAGGTAAATG-TTCA
4990 TGATAATGGTTAGGTAAATGTTTCA
1 TGATAATGGTTAGGTAAATG-TTCA
5015 TGATAA
1 TGATAA
5021 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:5001 original size:51 final size:49
Alignment explanation
Indices: 4889--5020 Score: 221
Period size: 51 Copynumber: 2.6 Consensus size: 49
4879 TGATACAAAT
4889 TGATAATAGGTTAGGTAAATGTTCATGATAATGGTTAGGTAAATGTTCA
1 TGATAATAGGTTAGGTAAATGTTCATGATAATGGTTAGGTAAATGTTCA
4938 TGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTT-CATGATAAT-GGTTAGGTAAATG-TTCA
4990 TGATAAT-GGTTAGGTAAATGTTTCATGATAA
1 TGATAATAGGTTAGGTAAATG-TTCATGATAA
5021 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:7042 original size:137 final size:137
Alignment explanation
Indices: 6796--7070 Score: 514
Period size: 137 Copynumber: 2.0 Consensus size: 137
6786 GAGTAGTCTC
6796 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
6861 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTATAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTATAATCTGAAAAGGGCTCTGGCCCAGTACC
6926 ACTGTTA
131 ACTGTTA
*
6933 CCCAAATGGGCTTGCATATGTTTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
* * *
6998 TGTTATCTGAATAAGGGGTTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTATC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTATAATCTGAAAAGGGCTCTGGCCCAGTACC
7063 ACTGTTA
131 ACTGTTA
7070 C
1 C
7071 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.