Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga01g01234.F15

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: 3448
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25


Found at i:314 original size:42 final size:42

Alignment explanation


    Indices: 260--391  Score: 194
    Period size: 42  Copynumber: 3.1  Consensus size: 42

        250 ATAGCAAACG

                          * * *                       
        260 GGAAGAGCCGTCTCAATCCCAACTGAAAATGGCTAGCAGAAA
          1 GGAAGAGCCGTCTCCAGCGCAACTGAAAATGGCTAGCAGAAA

                                                       
        302 GGAAGA-CTCGTCTCCAGCGCAACTGAAAATGGCTAGCAGAAA
          1 GGAAGAGC-CGTCTCCAGCGCAACTGAAAATGGCTAGCAGAAA

                             *                 *  *   
        344 GGAAGAGCCGTCTCCAGGGCAACTGAAAATGGCTAACAAAAA
          1 GGAAGAGCCGTCTCCAGCGCAACTGAAAATGGCTAGCAGAAA

                  
        386 GGAAGA
          1 GGAAGA

        392 CCCTTCTGTA


Statistics
Matches: 82,  Mismatches: 6, Indels: 4
        0.89            0.07        0.04

Matches are distributed among these distances:
  41    1  0.01
  42   80  0.98
  43    1  0.01

ACGTcount: A:0.39, C:0.22, G:0.27, T:0.13


Consensus pattern (42 bp):   
GGAAGAGCCGTCTCCAGCGCAACTGAAAATGGCTAGCAGAAA

Found at i:1749 original size:3 final size:3

Alignment explanation


    Indices: 1741--1794  Score: 63
    Period size: 3  Copynumber: 18.0  Consensus size: 3

       1731 GATGTATCCA

                             *       *      *    *                         
       1741 ATG ATG ATG ATG AGG ATG AGG ATG GTG ACG ATG ATG ATG ATG ATG ATG
          1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG

            *      
       1789 GTG ATG
          1 ATG ATG

       1795 CAGCAAGTGA


Statistics
Matches: 41,  Mismatches: 10, Indels: 0
        0.80            0.20        0.00

Matches are distributed among these distances:
   3   41  1.00

ACGTcount: A:0.30, C:0.02, G:0.41, T:0.28


Consensus pattern (3 bp):   
ATG

Done.