Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_08496

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: 2385
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.25


Found at i:738 original size:69 final size:69

Alignment explanation


    Indices: 618--779  Score: 229
    Period size: 69  Copynumber: 2.3  Consensus size: 69

        608 CCTCTGCGAA

                      *                                                      
        618 TCCTCATCCTAGCACTGACGAAGGAAACATGGATAATGTTGTATCAGCTTCTGCTCAAGTCCCCT
          1 TCCTCATCCTTGCACTGACGAAGGAAACATGGATAATGTTGTATCAGCTTCTGCTCAAGTCCCCT

                
        683 CGAG
         66 CGAG

                          *                            *    *                
        687 TCCTCATCCTTGCATTGACGAAAGG-AACATGGATAATGTTGTCT-ATTCTTCTGCTCAAGTCCC
          1 TCCTCATCCTTGCACTGACG-AAGGAAACATGGATAATGTTGTATCA-GCTTCTGCTCAAGTCCC

            *     
        750 TTCGAG
         64 CTCGAG

                         *    *     
        756 TCCTCATCCTTGCTCTGATGAAGG
          1 TCCTCATCCTTGCACTGACGAAGG

        780 GAATAAGATT


Statistics
Matches: 83,  Mismatches: 8, Indels: 5
        0.86            0.08        0.05

Matches are distributed among these distances:
  68    5  0.06
  69   74  0.89
  70    4  0.05

ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30


Consensus pattern (69 bp):   
TCCTCATCCTTGCACTGACGAAGGAAACATGGATAATGTTGTATCAGCTTCTGCTCAAGTCCCCT
CGAG

Found at i:1727 original size:243 final size:243

Alignment explanation


    Indices: 1299--1785  Score: 884
    Period size: 243  Copynumber: 2.0  Consensus size: 243

       1289 CAAGTGTTGT

                         *                                                   
       1299 TGATTTGACAGCTTCTGTTACTGATCCCCTCCCTAAAGCCTTAGAAGTTGCTGAGAGATTAGTAT
          1 TGATTTGACAGCTACTGTTACTGATCCCCTCCCTAAAGCCTTAGAAGTTGCTGAGAGATTAGTAT

                                         *                                   
       1364 CTTTCATGGAAGCAGCTAAAAGTTTAAGTGCAGAAGGTGCTGAAGGGGATGTAAGGAAGGAAAAG
         66 CTTTCATGGAAGCAGCTAAAAGTTTAAGTACAGAAGGTGCTGAAGGGGATGTAAGGAAGGAAAAG

                                                 *                           
       1429 GGTGTTCCTGCAGCACCTATGAATTGTAATTTTGAACGGGCTCAAGCTGAGAGGAGGGAACCTGA
        131 GGTGTTCCTGCAGCACCTATGAATTGTAATTTTGAACAGGCTCAAGCTGAGAGGAGGGAACCTGA

                                                            
       1494 CAAGGCCATCAGAGAAGACCAGGACAAGATGAACAGGAGTGTTCCTGC
        196 CAAGGCCATCAGAGAAGACCAGGACAAGATGAACAGGAGTGTTCCTGC

                               *     *                                       
       1542 TGATTTGACAGCTACTGTTGCTGATTCCCTCCCTAAAGCCTTAGAAGTTGCTGAGAGATTAGTAT
          1 TGATTTGACAGCTACTGTTACTGATCCCCTCCCTAAAGCCTTAGAAGTTGCTGAGAGATTAGTAT

                     *                     *                                 
       1607 CTTTCATGGCAGCAGCTAAAAGTTTAAGTACTGAAGGTGCTGAAGGGGATGTAAGGAAGGAAAAG
         66 CTTTCATGGAAGCAGCTAAAAGTTTAAGTACAGAAGGTGCTGAAGGGGATGTAAGGAAGGAAAAG

                                                                      *      
       1672 GGTGTTCCTGCAGCACCTATGAATTGTAATTTTGAACAGGCTCAAGCTGAGAGGAGGGCACCTGA
        131 GGTGTTCCTGCAGCACCTATGAATTGTAATTTTGAACAGGCTCAAGCTGAGAGGAGGGAACCTGA

                                           **               
       1737 CAAGGCCATCAGAGAAGACCAGGACAAGATGGGCAGGAGTGTTCCTGC
        196 CAAGGCCATCAGAGAAGACCAGGACAAGATGAACAGGAGTGTTCCTGC

             
       1785 T
          1 T

       1786 TCGTCTGTTG


Statistics
Matches: 234,  Mismatches: 10, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
 243  234  1.00

ACGTcount: A:0.30, C:0.18, G:0.29, T:0.24


Consensus pattern (243 bp):   
TGATTTGACAGCTACTGTTACTGATCCCCTCCCTAAAGCCTTAGAAGTTGCTGAGAGATTAGTAT
CTTTCATGGAAGCAGCTAAAAGTTTAAGTACAGAAGGTGCTGAAGGGGATGTAAGGAAGGAAAAG
GGTGTTCCTGCAGCACCTATGAATTGTAATTTTGAACAGGCTCAAGCTGAGAGGAGGGAACCTGA
CAAGGCCATCAGAGAAGACCAGGACAAGATGAACAGGAGTGTTCCTGC
Done.