Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga01g01943.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: 1742
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Found at i:1038 original size:86 final size:86
Alignment explanation
Indices: 848--1255 Score: 475
Period size: 86 Copynumber: 4.7 Consensus size: 86
838 AAATTTAGCT
* * * * * * *
848 TGTTACCCTACTACTT-AGAGGGTTAAAGCCCATCATCTTCGATCTGTTTCCCTATTGCTTAGGG
1 TGTTACCCTACTGCTTAAG-GGGTTAAGGCTCTTCGTCTTCGATCTGCTTCCCTACTGCTTAGGG
* * *
912 -GTTAAGATCTGTAAATT-AGCC
65 AGATAAGATCTG-CAATTCAACC
* *
933 TGTTACCCTACTGCTTAAGGGGTTAAGGCCCTTTGTCTTCGATCTGCTTCCCTACTGCTTAGGGA
1 TGTTACCCTACTGCTTAAGGGGTTAAGGCTCTTCGTCTTCGATCTGCTTCCCTACTGCTTAGGGA
*
998 GATAAGATCTGTAATTCAACC
66 GATAAGATCTGCAATTCAACC
** * *
1019 TGTTACCCTACTGCTTAAGGATTTAAGGTTCTTCGTCTTCGATATGC-TCCACTACTGCTTAGGG
1 TGTTACCCTACTGCTTAAGGGGTTAAGGCTCTTCGTCTTCGATCTGCTTCC-CTACTGCTTAGGG
*
1083 AGATAAGATCTGCAATTCAACT
65 AGATAAGATCTGCAATTCAACC
* * * *
1105 TGTTACCCTACTGCTT-AGGGAGTTTAAGGTTCTTCGTTTTTGATCTGCTTCACTACTGCTTAGG
1 TGTTACCCTACTGCTTAAGGG-G-TTAAGGCTCTTCGTCTTCGATCTGCTTCCCTACTGCTTAGG
*
1169 GAGATAAGATCTGCAATTCAACT
64 GAGATAAGATCTGCAATTCAACC
* * * * * *
1192 TGTTACCCTACTGCTTAGGGGGTTAAGGCTCGTCATCTTCGATCTGTTTTCCTACTACTTAGGG
1 TGTTACCCTACTGCTTAAGGGGTTAAGGCTCTTCGTCTTCGATCTGCTTCCCTACTGCTTAGGG
1256 GGGGTTAGGA
Statistics
Matches: 281, Mismatches: 34, Indels: 15
0.85 0.10 0.05
Matches are distributed among these distances:
85 64 0.23
86 138 0.49
87 74 0.26
88 5 0.02
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (86 bp):
TGTTACCCTACTGCTTAAGGGGTTAAGGCTCTTCGTCTTCGATCTGCTTCCCTACTGCTTAGGGA
GATAAGATCTGCAATTCAACC
Found at i:1233 original size:173 final size:171
Alignment explanation
Indices: 846--1347 Score: 503
Period size: 173 Copynumber: 2.9 Consensus size: 171
836 GTAAATTTAG
* * * * * * *
846 CTTGTTACCCTACTACTTAGAGGGTTAAAGCCCATCATCTTCGATCTGTTTCCCTATTGCTTAGG
1 CTTGTTACCCTACTGCTTAGGGGGTTAAGGCTCATCATCTTCGATATGTCTCCCTACTGCTTAGG
* * *
911 GGTTAAGATCTGTAAATTAGCCTGTTACCCTACTGCTTAAGGGGTTAAGGCCCTTTGTCTTCGAT
66 GGATAAGATCTGTAAATTAACCTGTTACCCTACTGCTTAAGGGGTTAAGGCCCTTCGTCTTCGAT
* *
976 CTGCTTCCCTACTGCTTAGGGAGATAAGATCTGTAATTCAA
131 CTGCTTCACTACTGCTTAGGGAGATAAGATCTGCAATTCAA
* * ** * * *
1017 CCTGTTACCCTACTGCTTAAGGATTTAAGGTTCTTCGTCTTCGATATG-CTCCACTACTGCTTAG
1 CTTGTTACCCTACTGCTTAGGGGGTTAAGGCTCATCATCTTCGATATGTCTCC-CTACTGCTTAG
* * ** *
1081 GGAGATAAGATCTG-CAATTCAACTTGTTACCCTACTGCTT-AGGGAGTTTAAGGTTCTTCGTTT
65 GG-GATAAGATCTGTAAATT-AACCTGTTACCCTACTGCTTAAGGG-G-TTAAGGCCCTTCGTCT
*
1144 TTGATCTGCTTCACTACTGCTTAGGGAGATAAGATCTGCAATTCAA
126 TCGATCTGCTTCACTACTGCTTAGGGAGATAAGATCTGCAATTCAA
* * * * *
1190 CTTGTTACCCTACTGCTTAGGGGGTTAAGGCTCGTCATCTTCGATCTGTTTTCCTACTACTTAGG
1 CTTGTTACCCTACTGCTTAGGGGGTTAAGGCTCATCATCTTCGATATGTCTCCCTACTGCTTA--
* * * * * *
1255 GGGGGTTAGGATCTATAAA-T-ACGGCTTGTTACCCTACTGCTT-AGAGGGTTAAAGCCCGTCAT
64 -GGGGATAAGATCTGTAAATTAAC--C-TGTTACCCTACTGCTTAAG-GGGTTAAGGCCCTTCGT
* * *
1317 CTTTGATTTGCTCCACTACTGCTTAGGGAGA
124 CTTCGATCTGCTTCACTACTGCTTAGGGAGA
1348 CAAAATCACT
Statistics
Matches: 268, Mismatches: 49, Indels: 24
0.79 0.14 0.07
Matches are distributed among these distances:
170 3 0.01
171 56 0.21
172 29 0.11
173 106 0.40
174 2 0.01
175 46 0.17
176 24 0.09
177 2 0.01
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.35
Consensus pattern (171 bp):
CTTGTTACCCTACTGCTTAGGGGGTTAAGGCTCATCATCTTCGATATGTCTCCCTACTGCTTAGG
GGATAAGATCTGTAAATTAACCTGTTACCCTACTGCTTAAGGGGTTAAGGCCCTTCGTCTTCGAT
CTGCTTCACTACTGCTTAGGGAGATAAGATCTGCAATTCAA
Done.