Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga11g00552.F2
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, 634
Length: 1057
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Found at i:469 original size:197 final size:198
Alignment explanation
Indices: 134--527 Score: 668
Period size: 197 Copynumber: 2.0 Consensus size: 198
124 TTCTTCTAGT
* * * *
134 TGATATCCAAACATTTTAACATTTAAAGATGCATATTGCAGGCGTAAAAAATGATTATTTGCAGG
1 TGATATCCAAACATTTTAACATTTAAACATGCATATCGCAGACGTAAAAAATGACTATTTGCAGG
* *
199 TATTTTATCAAGGTCGGATATCAAGTTATCGTTTTGTATTGGAGGTGAATTTTATTTTTGCTGAT
66 TAATTTATCAAGGTCGGATATCAAGTTATCGTTTTGTACTGGAGGTGAATTTTATTTTTGCTGAT
*
264 TGTTTATTTGTATGGTTGATT-TTTTTTGTTTGTGTTCAGTGGATATTTGCATTGATTCTGCAAC
131 TGTTTATTTGTATGGTTGATTATTTTTTGTTTGTGCTCAGTGGATATTTGCATTGATTCTGCAAC
328 TTG
196 TTG
331 TGATATCCAAACATTTTAACATTTAAACATGCATATCGCAGACGTAAAAAATGACTATTTGCAGG
1 TGATATCCAAACATTTTAACATTTAAACATGCATATCGCAGACGTAAAAAATGACTATTTGCAGG
* *
396 TAATTTATCAAGG-CTGGATAT-AAGGTTATTGTTTTGTACTGGAGGTGAATTTTATTTTTGTTG
66 TAATTTATCAAGGTC-GGATATCAA-GTTATCGTTTTGTACTGGAGGTGAATTTTATTTTTGCTG
459 ATTGTTTATTTGTATGGTTGATTATTTTTTGTTTGTGCTCAGTGGATATTTGCATTGATTCTGCA
129 ATTGTTTATTTGTATGGTTGATTATTTTTTGTTTGTGCTCAGTGGATATTTGCATTGATTCTGCA
524 ACTT
194 ACTT
528 ATGTGCGTGT
Statistics
Matches: 185, Mismatches: 9, Indels: 5
0.93 0.05 0.03
Matches are distributed among these distances:
196 3 0.02
197 138 0.75
198 44 0.24
ACGTcount: A:0.26, C:0.10, G:0.20, T:0.44
Consensus pattern (198 bp):
TGATATCCAAACATTTTAACATTTAAACATGCATATCGCAGACGTAAAAAATGACTATTTGCAGG
TAATTTATCAAGGTCGGATATCAAGTTATCGTTTTGTACTGGAGGTGAATTTTATTTTTGCTGAT
TGTTTATTTGTATGGTTGATTATTTTTTGTTTGTGCTCAGTGGATATTTGCATTGATTCTGCAAC
TTG
Found at i:981 original size:96 final size:96
Alignment explanation
Indices: 817--1008 Score: 375
Period size: 96 Copynumber: 2.0 Consensus size: 96
807 AACTTGCAAG
817 CATTTGCACTAGACATTCTGAAGAATGATATCAAATTTGATATATTTTCCATTACCAAGAAAATG
1 CATTTGCACTAGACATTCTGAAGAATGATATCAAATTTGATATATTTTCCATTACCAAGAAAATG
*
882 GAAAAACAAGTATTTGTATTGACACTGGTGT
66 GAAAAACAAGTATTTGTATTCACACTGGTGT
913 CATTTGCACTAGACATTCTGAAGAATGATATCAAATTTGATATATTTTCCATTACCAAGAAAATG
1 CATTTGCACTAGACATTCTGAAGAATGATATCAAATTTGATATATTTTCCATTACCAAGAAAATG
978 GAAAAACAAGTATTTGTATTCACACTGGTGT
66 GAAAAACAAGTATTTGTATTCACACTGGTGT
1009 TCCTTGCAAA
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 95 1.00
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (96 bp):
CATTTGCACTAGACATTCTGAAGAATGATATCAAATTTGATATATTTTCCATTACCAAGAAAATG
GAAAAACAAGTATTTGTATTCACACTGGTGT
Done.