Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_16407

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: 2751
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.24


Found at i:1279 original size:126 final size:127

Alignment explanation


    Indices: 1083--1425  Score: 499
    Period size: 126  Copynumber: 2.7  Consensus size: 127

       1073 CAGCCAACTC

                               *              *                              
       1083 TAAGTTCGAGGCATGCCAGACAACTTCCTCTACAGTAATGGATGATTTGGAGCAACCTCAGATTG
          1 TAAGTTCGAGGCATGCCAGCCAACTTCCTCT--ATTAATGGATGATTTGGAGCAACCTCAGATTG

                                                   *     *       *    *     
       1148 ACAACAGTACATCTGACATAAAAGAGGGTGAAGAGAATCTGATTATCTACAACGCAACTGACTT
         64 ACAACAGTACATCTGACATAAAAGAGGGTGAAGAGAATCGGATTACCTACAACACAACCGACTT

                        *           *                         *              
       1212 TAAGTTCGAGGCTTGCCAGCCAACATCCTCT-TTAATGGATGATTTGGAGAAACCTCAGATTGAC
          1 TAAGTTCGAGGCATGCCAGCCAACTTCCTCTATTAATGGATGATTTGGAGCAACCTCAGATTGAC

                                                            * *   *       
       1276 AACAGTACATCTGACATAAAAGAGGGTGAAGAGAATCGGATTACCTACGATACAGCCGACTT
         66 AACAGTACATCTGACATAAAAGAGGGTGAAGAGAATCGGATTACCTACAACACAACCGACTT

                  *                                                          
       1338 TAAGTTTGAGGCATGCCAGCCAACTTCCTCTTCATTAATGGATGATTTGGAGCAACCTCAGATTG
          1 TAAGTTCGAGGCATGCCAGCCAACTTCCTC-T-ATTAATGGATGATTTGGAGCAACCTCAGATTG

                    * *      *     
       1403 ACAACAGTGCGTCTGACCTAAAA
         64 ACAACAGTACATCTGACATAAAA

       1426 CAGACCTCTC


Statistics
Matches: 192,  Mismatches: 19, Indels: 6
        0.88            0.09        0.03

Matches are distributed among these distances:
 126  113  0.59
 127    1  0.01
 129   78  0.41

ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25


Consensus pattern (127 bp):   
TAAGTTCGAGGCATGCCAGCCAACTTCCTCTATTAATGGATGATTTGGAGCAACCTCAGATTGAC
AACAGTACATCTGACATAAAAGAGGGTGAAGAGAATCGGATTACCTACAACACAACCGACTT
Done.