Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_38139

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: 1809
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25


Found at i:1687 original size:24 final size:25

Alignment explanation


    Indices: 1660--1717  Score: 77
    Period size: 24  Copynumber: 2.4  Consensus size: 25

       1650 GTCTTCGCAG

                           *  *      
       1660 CAGCCA-CAGCCACAGTCTCAGCCT
          1 CAGCCAGCAGCCACAATCCCAGCCT

                                     
       1684 CAG-CAGCAGCCACAATCCCAGCCT
          1 CAGCCAGCAGCCACAATCCCAGCCT

                       
       1708 CAG-CAGCAGC
          1 CAGCCAGCAGC

       1718 AGCAGCCAGC


Statistics
Matches: 31,  Mismatches: 2, Indels: 2
        0.89            0.06        0.06

Matches are distributed among these distances:
  23    2  0.06
  24   29  0.94

ACGTcount: A:0.28, C:0.45, G:0.19, T:0.09


Consensus pattern (25 bp):   
CAGCCAGCAGCCACAATCCCAGCCT

Found at i:1710 original size:30 final size:30

Alignment explanation


    Indices: 1656--1725  Score: 88
    Period size: 30  Copynumber: 2.3  Consensus size: 30

       1646 CTCAGTCTTC

                               *      **  
       1656 GCAGCAGCCACAGCCACAGTCTCAGCCTCA
          1 GCAGCAGCCACAGCCACAGCCTCAGCAGCA

                         *                 
       1686 GCAGCAGCCACAATCC-CAGCCTCAGCAGCA
          1 GCAGCAGCCAC-AGCCACAGCCTCAGCAGCA

                      
       1716 GCAGCAGCCA
          1 GCAGCAGCCA

       1726 GCCACTGGAG


Statistics
Matches: 35,  Mismatches: 4, Indels: 2
        0.85            0.10        0.05

Matches are distributed among these distances:
  30   32  0.91
  31    3  0.09

ACGTcount: A:0.29, C:0.43, G:0.21, T:0.07


Consensus pattern (30 bp):   
GCAGCAGCCACAGCCACAGCCTCAGCAGCA
Done.