Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_22275

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: 2991
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.30


Found at i:2890 original size:162 final size:164

Alignment explanation


    Indices: 2630--2936  Score: 356
    Period size: 162  Copynumber: 1.9  Consensus size: 164

       2620 GAGAGATGCA

                                                         *                   
       2630 ATAATTTGAAATATATCTTCCCAATGTCAGTTGATAATAGCCTTATGCAATTACATACTTTGAAG
          1 ATAATTTGAAATATATCTTCCCAATGTCAGTTGATAATAGCCTTAGGCAATTACATACTTTGAAG

                          *  *       *          *  *                         
       2695 ATAAAGAGTTGCAGGAGCTTAGAAGGCATAATCCAATACTCACAAGTCCCATACATAAG-C-CTC
         66 ATAAAGAGTTGCAGCAGATTAGAAGACATAATCCAAGACCCACAAGTCCCATACATAAGTCACTC

                  *                           
       2758 CAAAGTTTAAGGGAAATAGAAGTTGAAAATTGCG
        131 CAAAGTCTAAGGGAAATAGAAGTTGAAAATTGCG

                           *    *   *    *                         *    *    
       2792 ATAATTT-AAAGTATCTCTTTCCATTGTCGGTTGCA-AATAGCCTT-GGCCAATTGCATATTTTG
          1 ATAATTTGAAA-TATATCTTCCCAATGTCAGTTG-ATAATAGCCTTAGG-CAATTACATACTTTG

                            *       *     *                    **        *   
       2854 AAGATAAAGAGTTGCTCGCA-ATTGGAAGATATAATCCAAGACCCACAAGTGGCATACATATGTC
         63 AAGATAAAGAGTTGC-AGCAGATTAGAAGACATAATCCAAGACCCACAAGTCCCATACATAAGTC

                               
       2918 TACTCCAAAGTCTAAGGGA
        127 -ACTCCAAAGTCTAAGGGA

       2937 GGTATGTGTA


Statistics
Matches: 119,  Mismatches: 19, Indels: 11
        0.80            0.13        0.07

Matches are distributed among these distances:
 161    4  0.03
 162   95  0.80
 163    4  0.03
 165   16  0.13

ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29


Consensus pattern (164 bp):   
ATAATTTGAAATATATCTTCCCAATGTCAGTTGATAATAGCCTTAGGCAATTACATACTTTGAAG
ATAAAGAGTTGCAGCAGATTAGAAGACATAATCCAAGACCCACAAGTCCCATACATAAGTCACTC
CAAAGTCTAAGGGAAATAGAAGTTGAAAATTGCG
Done.