Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Ga01g01234.F19

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: 3475
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25


Found at i:310 original size:42 final size:42

Alignment explanation


    Indices: 260--349  Score: 126
    Period size: 42  Copynumber: 2.1  Consensus size: 42

        250 ATAGCAAACG

                            *                  *  *   
        260 GGAAGAGCCGTCTCAATCCCAACTGAAAATGGCTAGCAGAAA
          1 GGAAGAGCCGTCTCAAGCCCAACTGAAAATGGCTAACAAAAA

                          *  **                       
        302 GGAAGAGCCGTCTCCAGGGCAACTGAAAATGGCTAACAAAAA
          1 GGAAGAGCCGTCTCAAGCCCAACTGAAAATGGCTAACAAAAA

                  
        344 GGAAGA
          1 GGAAGA

        350 CCCTTCTGTA


Statistics
Matches: 42,  Mismatches: 6, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  42   42  1.00

ACGTcount: A:0.40, C:0.21, G:0.27, T:0.12


Consensus pattern (42 bp):   
GGAAGAGCCGTCTCAAGCCCAACTGAAAATGGCTAACAAAAA

Found at i:1776 original size:3 final size:3

Alignment explanation


    Indices: 1768--1821  Score: 63
    Period size: 3  Copynumber: 18.0  Consensus size: 3

       1758 GATGTATCCA

                             *       *      *    *                         
       1768 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

            *      
       1816 GTG ATG
          1 ATG ATG

       1822 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.