Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga11g01239.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: 5142
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Found at i:4065 original size:271 final size:271
Alignment explanation
Indices: 3517--4020 Score: 834
Period size: 271 Copynumber: 1.9 Consensus size: 271
3507 TGAGATTGAA
* * *
3517 AAAATATGGCATGATGATCAACTTCTTACTGTGTCTTGTGGTGTTCAAAATTTAACACATTTGCT
1 AAAAGATGGCATGATGATCAACTTCTTACAGTGTCTTGTGGTGTTCAAAATTTAACACATTTGCA
*** * *
3582 AGTGTGGGGATGCCGTAAGTTGAAGTGTGTATTTACTTCCTCTATGGTTAAAAGCTTTGTGAACC
66 AGTGTGCCAATGCCATAAGCTGAAGTGTGTATTTACTTCCTCTATGGTTAAAAGCTTTGTGAACC
* *
3647 TGAAAACACTTAGAGGTCAGAAATTGTTATGGAAAGGAAGACATAATAGAAGGAATACTAGGTGG
131 TGAAAACACTTAAAGGTCAGAAATTGTAATGGAAAGGAAGACATAATAGAAGGAATACTAGGTGG
3712 GGAAGAAAGGATTAACAACAGCTTAAGCGTGTTCCCTAAGCTTGACTCGGTGGCACTCTACAATC
196 GGAAGAAAGGATTAACAACAGCTTAAGCGTGTTCCCTAAGCTTGACTCGGTGGCACTCTACAATC
3777 TTCTAAATCTC
261 TTCTAAATCTC
*
3788 AAAAGATGGCATGATGATCAACTTCTTACAGTGTCTTGTGGTGTTCAAAATTTAACACATTTGGA
1 AAAAGATGGCATGATGATCAACTTCTTACAGTGTCTTGTGGTGTTCAAAATTTAACACATTTGCA
*
3853 AGTGT-CCAATTGTCATAAGCTGAAGTGTGTATTTACTTCCTCTATGGTTAAAAGCTTTGTGAAC
66 AGTGTGCCAA-TGCCATAAGCTGAAGTGTGTATTTACTTCCTCTATGGTTAAAAGCTTTGTGAAC
* *
3917 CTGAAAACACTTAAAGGTTAGACATTGTAAT-GAAATGGAAGACATAATAGAAGGAATACTAGGT
130 CTGAAAACACTTAAAGGTCAGAAATTGTAATGGAAA-GGAAGACATAATAGAAGGAATACTAGGT
3981 GGGGAAGAAAGGATTAACAACAGCATTAAG-GTGTTCCCTA
194 GGGGAAGAAAGGATTAACAACAGC-TTAAGCGTGTTCCCTA
4021 CTCTTACCGT
Statistics
Matches: 216, Mismatches: 14, Indels: 6
0.92 0.06 0.03
Matches are distributed among these distances:
270 5 0.02
271 206 0.95
272 5 0.02
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.30
Consensus pattern (271 bp):
AAAAGATGGCATGATGATCAACTTCTTACAGTGTCTTGTGGTGTTCAAAATTTAACACATTTGCA
AGTGTGCCAATGCCATAAGCTGAAGTGTGTATTTACTTCCTCTATGGTTAAAAGCTTTGTGAACC
TGAAAACACTTAAAGGTCAGAAATTGTAATGGAAAGGAAGACATAATAGAAGGAATACTAGGTGG
GGAAGAAAGGATTAACAACAGCTTAAGCGTGTTCCCTAAGCTTGACTCGGTGGCACTCTACAATC
TTCTAAATCTC
Found at i:4760 original size:21 final size:21
Alignment explanation
Indices: 4736--4782 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 21
4726 TAGTATGGTA
4736 GAAGAATCTGAAAATTCTTG-G
1 GAAGAATCTGAAAATTC-TGAG
4757 GAAGAATCTGAAAATTCTGAG
1 GAAGAATCTGAAAATTCTGAG
4778 GAAGA
1 GAAGA
4783 TCTAAGCGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.43, C:0.09, G:0.26, T:0.23
Consensus pattern (21 bp):
GAAGAATCTGAAAATTCTGAG
Done.