Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_38575

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: 3612
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25


Found at i:1779 original size:6 final size:6

Alignment explanation


    Indices: 1760--1814  Score: 92
    Period size: 6  Copynumber: 9.2  Consensus size: 6

       1750 CAGCAGCAGC

                 *           *                                     
       1760 CTCAGC CTCAGT CTCTGT CTCAGT CTCAGT CTCAGT CTCAGT CTCAGT
          1 CTCAGT CTCAGT CTCAGT CTCAGT CTCAGT CTCAGT CTCAGT CTCAGT

                    
       1808 CTCAGT C
          1 CTCAGT C

       1815 ACATTCGCAG


Statistics
Matches: 46,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   6   46  1.00

ACGTcount: A:0.15, C:0.36, G:0.16, T:0.33


Consensus pattern (6 bp):   
CTCAGT

Found at i:1831 original size:6 final size:6

Alignment explanation


    Indices: 1822--1878  Score: 114
    Period size: 6  Copynumber: 9.5  Consensus size: 6

       1812 GTCACATTCG

                                                                   
       1822 CAGCCA CAGCCA CAGCCA CAGCCA CAGCCA CAGCCA CAGCCA CAGCCA
          1 CAGCCA CAGCCA CAGCCA CAGCCA CAGCCA CAGCCA CAGCCA CAGCCA

                      
       1870 CAGCCA CAG
          1 CAGCCA CAG

       1879 GCACCTCCAC


Statistics
Matches: 51,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   51  1.00

ACGTcount: A:0.33, C:0.49, G:0.18, T:0.00


Consensus pattern (6 bp):   
CAGCCA

Done.