Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_D_gene_10040043

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, 536

Length: 894
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29


Found at i:379 original size:60 final size:60

Alignment explanation


    Indices: 311--429  Score: 175
    Period size: 60  Copynumber: 2.0  Consensus size: 60

        301 GAACAAGGAA

                                **   * *              *         *       
        311 TGCCAAGGCCTCCATTTGGTGTGGGTAGCTCCTCAAATGTTGTTGCTAATGGCTTGGGGT
          1 TGCCAAGGCCTCCATTTGGTAAGGGCAACTCCTCAAATGTTGCTGCTAATGGATTGGGGT

                                                           *           
        371 TGCCAAGGCCTCCATTTGGTAAGGGCAACTCCTCAAATGTTGCTGCTTATGGATTGGGG
          1 TGCCAAGGCCTCCATTTGGTAAGGGCAACTCCTCAAATGTTGCTGCTAATGGATTGGGG

        430 CTACCAAGCC


Statistics
Matches: 52,  Mismatches: 7, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  60   52  1.00

ACGTcount: A:0.18, C:0.21, G:0.30, T:0.31


Consensus pattern (60 bp):   
TGCCAAGGCCTCCATTTGGTAAGGGCAACTCCTCAAATGTTGCTGCTAATGGATTGGGGT

Found at i:674 original size:120 final size:120

Alignment explanation


    Indices: 460--677  Score: 276
    Period size: 120  Copynumber: 1.8  Consensus size: 120

        450 TGAGGGTAGC

                                     *    *       *             *            
        460 GTTGTTGATCACTTAGGGCTACCAATGCCTTCATTTGGTGAGGGTAGCTCCTTAAATGTTGCTTC
          1 GTTGTTGATCACTTAGGGCTACCAAGGCCTCCATTTGGGGAGGGTAGCTCCTCAAATGTTGCTTC

                         *   *   * **                              
        525 TGATCACTTAGGATTACCAAGGCTTCCATTTGGTGAAGGTCGCTCCTCAAATATT
         66 TGATCACTTAGGACTACAAAGACCACCATTTGGTGAAGGTCGCTCCTCAAATATT

                       *  *         *       *                                
        580 GTTGTTGATCATTTGGGGCTACCAGGGCCTCCGTTTGGGGAGGGTAGCTCCTCAAATGTTG-TTG
          1 GTTGTTGATCACTTAGGGCTACCAAGGCCTCCATTTGGGGAGGGTAGCTCCTCAAATGTTGCTT-

            *         *  *                    
        644 TTGATCACTTGGGGCTACAAAGACCACCATTTGG
         65 CTGATCACTTAGGACTACAAAGACCACCATTTGG

        678 CGGTAGTTCA


Statistics
Matches: 81,  Mismatches: 16, Indels: 2
        0.82            0.16        0.02

Matches are distributed among these distances:
 119    2  0.02
 120   79  0.98

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


Consensus pattern (120 bp):   
GTTGTTGATCACTTAGGGCTACCAAGGCCTCCATTTGGGGAGGGTAGCTCCTCAAATGTTGCTTC
TGATCACTTAGGACTACAAAGACCACCATTTGGTGAAGGTCGCTCCTCAAATATT

Found at i:677 original size:60 final size:60

Alignment explanation


    Indices: 460--677  Score: 231
    Period size: 60  Copynumber: 3.6  Consensus size: 60

        450 TGAGGGTAGC

                                  *  *    *                     *       
        460 GTTGTTGATCACTTAGGGCTACCAATGCCTTCATTTGGTGAGGGTAGCTCCTTAAATGTT
          1 GTTGTTGATCACTTAGGGCTACAAAGGCCTCCATTTGGTGAGGGTAGCTCCTCAAATGTT

                 *            **   *     *            *   *           *  
        520 GCTT-CTGATCACTTAGGATTACCAAGGCTTCCATTTGGTGAAGGTCGCTCCTCAAATATT
          1 G-TTGTTGATCACTTAGGGCTACAAAGGCCTCCATTTGGTGAGGGTAGCTCCTCAAATGTT

                       *  *       * *       *     *                     
        580 GTTGTTGATCATTTGGGGCTACCAGGGCCTCCGTTTGGGGAGGGTAGCTCCTCAAATGTT
          1 GTTGTTGATCACTTAGGGCTACAAAGGCCTCCATTTGGTGAGGGTAGCTCCTCAAATGTT

                          *           *  *        
        640 GTTGTTGATCACTTGGGGCTACAAAGACCACCATTTGG
          1 GTTGTTGATCACTTAGGGCTACAAAGGCCTCCATTTGG

        678 CGGTAGTTCA


Statistics
Matches: 128,  Mismatches: 28, Indels: 4
        0.80            0.17        0.03

Matches are distributed among these distances:
  59    2  0.02
  60  124  0.97
  61    2  0.02

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


Consensus pattern (60 bp):   
GTTGTTGATCACTTAGGGCTACAAAGGCCTCCATTTGGTGAGGGTAGCTCCTCAAATGTT
Done.