Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_04977

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: 2760
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.28


Found at i:2015 original size:54 final size:55

Alignment explanation


    Indices: 1856--2027  Score: 174
    Period size: 54  Copynumber: 3.2  Consensus size: 55

       1846 ACTTCCGTTG

                       *  *                                 * * *  
       1856 GGATCATTACTGGAGATCA-AATTTCTAGAAGGGAATCAACCTTCACTCCCGGTA
          1 GGATCATTACTCGAAATCAGAATTTCTAGAAGGGAATCAACCTTCACTTCTGATA

                *   *                      *             * *       
       1910 GGATGATTGCTCGAAATCAGAA-TTCTAGAAAGGAATCAACCTTCGCCTCTGATA
          1 GGATCATTACTCGAAATCAGAATTTCTAGAAGGGAATCAACCTTCACTTCTGATA

                         *                                          *
       1964 GGATCATTAC-CATAAATC-GAATTTCTAGAAGGGAATCAACC-TCTACTTCTGATG
          1 GGATCATTACTC-GAAATCAGAATTTCTAGAAGGGAATCAACCTTC-ACTTCTGATA

              *       
       2018 GGGTCATTAC
          1 GGATCATTAC

       2028 GAAAAACCAA


Statistics
Matches: 96,  Mismatches: 18, Indels: 8
        0.79            0.15        0.07

Matches are distributed among these distances:
  53    6  0.06
  54   88  0.92
  55    2  0.02

ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27


Consensus pattern (55 bp):   
GGATCATTACTCGAAATCAGAATTTCTAGAAGGGAATCAACCTTCACTTCTGATA
Done.