Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_12207

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, 288

Length: 480
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33


Found at i:206 original size:15 final size:15

Alignment explanation


    Indices: 184--374  Score: 184
    Period size: 15  Copynumber: 12.7  Consensus size: 15

        174 CTCTACCATT

                      *    
        184 GTACCAAATGTTGCG
          1 GTACCAAATGCTGCG

             *            *
        199 GCACCAAATGCTGCA
          1 GTACCAAATGCTGCG

                       *  *
        214 GTACCAAATGCAGCT
          1 GTACCAAATGCTGCG

                        *  
        229 GTACCAAATGCTACG
          1 GTACCAAATGCTGCG

            *        *    *
        244 ATACCAAATACTGCT
          1 GTACCAAATGCTGCG

              *       *  **
        259 GTTCCAAATGTTGTT
          1 GTACCAAATGCTGCG

                    * *    
        274 GTACCAAACGTTGCG
          1 GTACCAAATGCTGCG

                          *
        289 GTACCAAATGCTGCT
          1 GTACCAAATGCTGCG

                  *   *    
        304 GTACCAGATGTTGCG
          1 GTACCAAATGCTGCG

                      *   *
        319 GTACCAAATGTTGCT
          1 GTACCAAATGCTGCG

                      *    
        334 GTACCAAATGTTGCG
          1 GTACCAAATGCTGCG

            *              
        349 ATACCAAATGCTGCG
          1 GTACCAAATGCTGCG

                       
        364 GTACCAAATGC
          1 GTACCAAATGC

        375 GAACGAGAAA


Statistics
Matches: 142,  Mismatches: 34, Indels: 0
        0.81            0.19        0.00

Matches are distributed among these distances:
  15  142  1.00

ACGTcount: A:0.29, C:0.24, G:0.21, T:0.25


Consensus pattern (15 bp):   
GTACCAAATGCTGCG

Found at i:220 original size:30 final size:30

Alignment explanation


    Indices: 183--373  Score: 213
    Period size: 30  Copynumber: 6.4  Consensus size: 30

        173 CCTCTACCAT

                             *            
        183 TGTACCAAATGTTGCGGCACCAAATGCTGC
          1 TGTACCAAATGTTGCGGTACCAAATGCTGC

            *          **  *            * 
        213 AGTACCAAATGCAGCTGTACCAAATGCTAC
          1 TGTACCAAATGTTGCGGTACCAAATGCTGC

                       **   *  *       *  *
        243 -GATACCAAATACTGCTGTTCCAAATGTTGT
          1 TG-TACCAAATGTTGCGGTACCAAATGCTGC

                     *                    
        273 TGTACCAAACGTTGCGGTACCAAATGCTGC
          1 TGTACCAAATGTTGCGGTACCAAATGCTGC

                   *                  *   
        303 TGTACCAGATGTTGCGGTACCAAATGTTGC
          1 TGTACCAAATGTTGCGGTACCAAATGCTGC

                            *             
        333 TGTACCAAATGTTGCGATACCAAATGCTGC
          1 TGTACCAAATGTTGCGGTACCAAATGCTGC

            *          
        363 GGTACCAAATG
          1 TGTACCAAATG

        374 CGAACGAGAA


Statistics
Matches: 133,  Mismatches: 26, Indels: 4
        0.82            0.16        0.02

Matches are distributed among these distances:
  29    1  0.01
  30  131  0.98
  31    1  0.01

ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26


Consensus pattern (30 bp):   
TGTACCAAATGTTGCGGTACCAAATGCTGC

Found at i:250 original size:45 final size:45

Alignment explanation


    Indices: 183--373  Score: 213
    Period size: 45  Copynumber: 4.2  Consensus size: 45

        173 CCTCTACCAT

                             *            *           *  
        183 TGTACCAAATGTTGCGGCACCAAATGCTGCAGTACCAAATGCAGC
          1 TGTACCAAATGTTGCGGTACCAAATGCTGCTGTACCAAATGCTGC

                       * *  *        *       *       *  *
        228 TGTACCAAATGCTACGATACCAAATACTGCTGTTCCAAATGTTGT
          1 TGTACCAAATGTTGCGGTACCAAATGCTGCTGTACCAAATGCTGC

                     *                           *   *   
        273 TGTACCAAACGTTGCGGTACCAAATGCTGCTGTACCAGATGTTGC
          1 TGTACCAAATGTTGCGGTACCAAATGCTGCTGTACCAAATGCTGC

            *              *          *                   
        318 GGTACCAAATGTTGCTGTACCAAATGTTGC-GATACCAAATGCTGC
          1 TGTACCAAATGTTGCGGTACCAAATGCTGCTG-TACCAAATGCTGC

            *          
        363 GGTACCAAATG
          1 TGTACCAAATG

        374 CGAACGAGAA


Statistics
Matches: 121,  Mismatches: 24, Indels: 2
        0.82            0.16        0.01

Matches are distributed among these distances:
  44    1  0.01
  45  120  0.99

ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26


Consensus pattern (45 bp):   
TGTACCAAATGTTGCGGTACCAAATGCTGCTGTACCAAATGCTGC
Done.