Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_36851

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, 997

Length: 1662
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23


Found at i:52 original size:18 final size:18

Alignment explanation


    Indices: 31--108  Score: 66
    Period size: 18  Copynumber: 4.3  Consensus size: 18

         21 TACGGGTCCT

                   *       *  
         31 CCTGCAAGTACAGATGCA
          1 CCTGCAACTACAGATCCA

                       *      
         49 CCTGCAACTACGGATCCA
          1 CCTGCAACTACAGATCCA

               *    *  *     *
         67 CCTACAACAACTGATCCG
          1 CCTGCAACTACAGATCCA

               *   *      *   
         85 CCTACAAGTACAGAGCCA
          1 CCTGCAACTACAGATCCA

                  
        103 CCTGCA
          1 CCTGCA

        109 GGTGATGTAG


Statistics
Matches: 47,  Mismatches: 13, Indels: 0
        0.78            0.22        0.00

Matches are distributed among these distances:
  18   47  1.00

ACGTcount: A:0.32, C:0.36, G:0.17, T:0.15


Consensus pattern (18 bp):   
CCTGCAACTACAGATCCA

Found at i:1473 original size:81 final size:81

Alignment explanation


    Indices: 1343--1537  Score: 223
    Period size: 81  Copynumber: 2.4  Consensus size: 81

       1333 TCCCCACCTT

                      *             *     *    *  *   *         *      * *   
       1343 TAAAGAAAGAGAGTGAAGAAGCTTCCAAAAATGAAGTCGAAGCTCCTGAAGCCAACCCAGCTTCA
          1 TAAAGAAAGATAGTGAAGAAGCTTGCAAAACTGAAATCAAAGATCCTGAAGCAAACCCACCATCA

                      *     
       1408 CAAGAAGTTCCACCA-
         66 CAAGAAGTTCAACCAG

              *                                          *          *        
       1423 TCGAAGAAAGATAGTGAAGAAGCTTGCAAAACTGAAATCAAAGATTCTGAAGCAAAGCCACCATC
          1 T-AAAGAAAGATAGTGAAGAAGCTTGCAAAACTGAAATCAAAGATCCTGAAGCAAACCCACCATC

                      *      
       1488 ACAAGAAGTTGAACCAG
         65 ACAAGAAGTTCAACCAG

                             *                
       1505 TAAAGAAAGATAGTGAACAAGCTTTG-AAAACTG
          1 TAAAGAAAGATAGTGAAGAAGC-TTGCAAAACTG

       1538 TTGTCAAGGA


Statistics
Matches: 96,  Mismatches: 16, Indels: 5
        0.82            0.14        0.04

Matches are distributed among these distances:
  80    1  0.01
  81   91  0.95
  82    4  0.04

ACGTcount: A:0.44, C:0.19, G:0.21, T:0.16


Consensus pattern (81 bp):   
TAAAGAAAGATAGTGAAGAAGCTTGCAAAACTGAAATCAAAGATCCTGAAGCAAACCCACCATCA
CAAGAAGTTCAACCAG
Done.