Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_D_gene_10038870

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, 228

Length: 381
ACGTcount: A:0.24, C:0.27, G:0.25, T:0.24


Found at i:254 original size:45 final size:45

Alignment explanation


    Indices: 190--321  Score: 169
    Period size: 45  Copynumber: 3.0  Consensus size: 45

        180 AAGGCTGGAG

                                                         
        190 TTTTTGATCTGCTTCGCTGCCGGTACAGGAAGGCAAGATCTGCTA
          1 TTTTTGATCTGCTTCGCTGCCGGTACAGGAAGGCAAGATCTGCTA

                   *     *      * *      *        *   * *
        235 TTTTTGACCTGCTCCGCTGCAGCT-CAGGGAGGCAAG-GCTGGTG
          1 TTTTTGATCTGCTTCGCTGCCGGTACAGGAAGGCAAGATCTGCTA

             *                                          
        278 TCTTTGATCTGCTTCGCTGCCGGTACAGGAAGGCAAGATCTGCT
          1 TTTTTGATCTGCTTCGCTGCCGGTACAGGAAGGCAAGATCTGCT

        322 GTCTTCATTG


Statistics
Matches: 69,  Mismatches: 16, Indels: 4
        0.78            0.18        0.04

Matches are distributed among these distances:
  43   23  0.33
  44   22  0.32
  45   24  0.35

ACGTcount: A:0.17, C:0.24, G:0.30, T:0.29


Consensus pattern (45 bp):   
TTTTTGATCTGCTTCGCTGCCGGTACAGGAAGGCAAGATCTGCTA

Found at i:312 original size:44 final size:44

Alignment explanation


    Indices: 179--314  Score: 166
    Period size: 44  Copynumber: 3.1  Consensus size: 44

        169 CTCAGGGAGA

                     *                                  
        179 CAAGGCTGGAGTTTTTGATCTGCTTCGCTGCCGGTACAGGAAGG
          1 CAAGGCTGGTGTTTTTGATCTGCTTCGCTGCCGGTACAGGAAGG

                 *   * *       *     *      * *      *   
        223 CAAGATCTGCTATTTTTGACCTGCTCCGCTGCAGCT-CAGGGAGG
          1 CAAG-GCTGGTGTTTTTGATCTGCTTCGCTGCCGGTACAGGAAGG

                        *                               
        267 CAAGGCTGGTGTCTTTGATCTGCTTCGCTGCCGGTACAGGAAGG
          1 CAAGGCTGGTGTTTTTGATCTGCTTCGCTGCCGGTACAGGAAGG

                
        311 CAAG
          1 CAAG

        315 ATCTGCTGTC


Statistics
Matches: 72,  Mismatches: 18, Indels: 4
        0.77            0.19        0.04

Matches are distributed among these distances:
  43   23  0.32
  44   26  0.36
  45   23  0.32

ACGTcount: A:0.18, C:0.24, G:0.32, T:0.26


Consensus pattern (44 bp):   
CAAGGCTGGTGTTTTTGATCTGCTTCGCTGCCGGTACAGGAAGG
Done.