Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_15065

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: 4824
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28


Found at i:878 original size:84 final size:84

Alignment explanation


    Indices: 675--1035  Score: 433
    Period size: 84  Copynumber: 4.3  Consensus size: 84

        665 AAGAAACAAG

                  *               **                         *               
        675 GAAGGCGGTTGAAGAAAGAAAATGTGCTGATTTGGAGATGGCTAAAGCAAAGGAGCAGAGGAAGA
          1 GAAGGCTGTTGAAGAAAGAAAACATGCTGATTTGGAGATGGCTAAAGCACAGGAGC--A-GAAGA

               *           *      
        740 AGACTGCAGAAGAATTGAAGAA
         63 AGATTGCAGAAGAATCGAAGAA

                                          *                         *   *    
        762 GAAGGCT-TCTGAAGAAAGAAAACATGCTGCTTTGGAGATGGCTAAAGCACAGGAGGAGAGGAAG
          1 GAAGGCTGT-TGAAGAAAGAAAACATGCTGATTTGGAGATGGCTAAAGCACAGGAGCAGAAGAAG

                       *        
        826 ATTGCAGAAGAGTCGAAGAA
         65 ATTGCAGAAGAATCGAAGAA

                                          *                                  
        846 GAAGGCTGTTGAAGAAAGAAAACATG-TGGCTTTGGAGATGGCTAAAGCACAGGAGCAGAAGAAG
          1 GAAGGCTGTTGAAGAAAGAAAACATGCT-GATTTGGAGATGGCTAAAGCACAGGAGCAGAAGAAG

                           *     
        910 ATTGCAGAAGAGAT-TAAGAA
         65 ATTGCAGAAGA-ATCGAAGAA

                  *         *                **        *     *   *           
        930 GAAGGCAGTTGAAGAACGAAAACATGCTGATTTACAGATGGCTGAAGCAGAGGCGCA-AAGAAAG
          1 GAAGGCTGTTGAAGAAAGAAAACATGCTGATTTGGAGATGGCTAAAGCACAGGAGCAGAAG-AAG

                        * *     
        994 ATTGCAGAAGAAACCAAGAA
         65 ATTGCAGAAGAATCGAAGAA

                          *       
       1014 GAAGGCTGTTGAAGCAAGAAAA
          1 GAAGGCTGTTGAAGAAAGAAAA

       1036 TGGGCCGATT


Statistics
Matches: 240,  Mismatches: 27, Indels: 17
        0.85            0.10        0.06

Matches are distributed among these distances:
  83    5  0.02
  84  182  0.76
  85    4  0.02
  86    1  0.00
  87   48  0.20

ACGTcount: A:0.42, C:0.11, G:0.32, T:0.15


Consensus pattern (84 bp):   
GAAGGCTGTTGAAGAAAGAAAACATGCTGATTTGGAGATGGCTAAAGCACAGGAGCAGAAGAAGA
TTGCAGAAGAATCGAAGAA

Done.