Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_30266

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: 3209
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26


Found at i:2246 original size:33 final size:32

Alignment explanation


    Indices: 2142--2262  Score: 111
    Period size: 33  Copynumber: 3.7  Consensus size: 32

       2132 TAAGTAGAAC

                     *        *  *         * 
       2142 GGATGATGCTCCTATAAGTAGTCCTAGTAGTAG
          1 GGATGATGCCCCTATAAGCAGGCCTAGTAG-CG

                         * *               *   
       2175 GGATGATGCCCCTGTGAGCA--CCTCAAGTACCTG
          1 GGATGATGCCCCTATAAGCAGGCCT--AGTAGC-G

                     *                      
       2208 GGATGATGCTCCTATAAGCAGGCCTAGTAGCG
          1 GGATGATGCCCCTATAAGCAGGCCTAGTAGCG

                                   
       2240 GTGATGATGCCCCTATAAGCAGG
          1 G-GATGATGCCCCTATAAGCAGG

       2263 TTAAGTATGG


Statistics
Matches: 71,  Mismatches: 11, Indels: 12
        0.76            0.12        0.13

Matches are distributed among these distances:
  31    3  0.04
  32    2  0.03
  33   63  0.89
  35    3  0.04

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


Consensus pattern (32 bp):   
GGATGATGCCCCTATAAGCAGGCCTAGTAGCG

Found at i:2348 original size:98 final size:100

Alignment explanation


    Indices: 2224--2449  Score: 343
    Period size: 98  Copynumber: 2.3  Consensus size: 100

       2214 TGCTCCTATA

                    *     **                                           *     
       2224 AGCAGGCCTAGTAGCGGTGATGATGCCCCTATAAGCAGGTTAAGTATGGGGGAAAATGCTCCTGT
          1 AGCAGGCCAAGTAGAAGTGATGATGCCCCTATAAGCAGGTTAAGTATGGGGGAAAATGCCCCTGT

                                               
       2289 AAGTGGACCAACTGCTGGTGAAGATT-ACCC-TTT
         66 AAGTGGACCAACTGCTGGTGAAGATTGACCCGTTT

                               *                           *                 
       2322 AGCAGGCCAAGTAGAAGTGTTGATGCCCCTATAAGCAGGTTAAGTATTGGGGAAAATGCCCCTGT
          1 AGCAGGCCAAGTAGAAGTGATGATGCCCCTATAAGCAGGTTAAGTATGGGGGAAAATGCCCCTGT

                                       *       
       2387 AAGTGGACCAACTGCTGGTGAAGATTGTCCCGTTT
         66 AAGTGGACCAACTGCTGGTGAAGATTGACCCGTTT

                               *          
       2422 -GCAGGCCAAGTAGCAA-TAATGATGCCCC
          1 AGCAGGCCAAGTAG-AAGTGATGATGCCCC

       2450 CATGAGCTGT


Statistics
Matches: 116,  Mismatches: 9, Indels: 5
        0.89            0.07        0.04

Matches are distributed among these distances:
  98   85  0.73
  99   26  0.22
 100    5  0.04

ACGTcount: A:0.27, C:0.20, G:0.29, T:0.23


Consensus pattern (100 bp):   
AGCAGGCCAAGTAGAAGTGATGATGCCCCTATAAGCAGGTTAAGTATGGGGGAAAATGCCCCTGT
AAGTGGACCAACTGCTGGTGAAGATTGACCCGTTT
Done.