Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Gorai.006G011500.1-JGI_221_v2.1

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: 3184
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27


Found at i:1655 original size:6 final size:6

Alignment explanation


    Indices: 1640--1696  Score: 53
    Period size: 6  Copynumber: 9.5  Consensus size: 6

       1630 TGGAGAATCC

                 *            *      *      *      *               
       1640 GAAGAG GAAGAA GAAGCA GAAGCA GAAGCA GAAGCA GAAGAA GAA-AA
          1 GAAGAA GAAGAA GAAGAA GAAGAA GAAGAA GAAGAA GAAGAA GAAGAA

                       
       1687 GGAAGAA GAA
          1 -GAAGAA GAA

       1697 AAACTTAAGC


Statistics
Matches: 46,  Mismatches: 3, Indels: 4
        0.87            0.06        0.08

Matches are distributed among these distances:
   5    2  0.04
   6   42  0.91
   7    2  0.04

ACGTcount: A:0.58, C:0.07, G:0.35, T:0.00


Consensus pattern (6 bp):   
GAAGAA

Found at i:1691 original size:18 final size:18

Alignment explanation


    Indices: 1640--1684  Score: 63
    Period size: 18  Copynumber: 2.5  Consensus size: 18

       1630 TGGAGAATCC

                 *            
       1640 GAAGAGGAAGAAGAAGCA
          1 GAAGAAGAAGAAGAAGCA

                *     *       
       1658 GAAGCAGAAGCAGAAGCA
          1 GAAGAAGAAGAAGAAGCA

                     
       1676 GAAGAAGAA
          1 GAAGAAGAA

       1685 AAGGAAGAAG


Statistics
Matches: 23,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  18   23  1.00

ACGTcount: A:0.56, C:0.09, G:0.36, T:0.00


Consensus pattern (18 bp):   
GAAGAAGAAGAAGAAGCA
Done.