Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_35787

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, 414

Length: 690
ACGTcount: A:0.30, C:0.25, G:0.24, T:0.21


Found at i:679 original size:228 final size:227

Alignment explanation


    Indices: 1--683  Score: 722
    Period size: 228  Copynumber: 3.0  Consensus size: 227

                          *  *              *     *  ** *                    
          1 ATGCAGATCTTCGTTAAGACCCTGACCGGCAAGACCATCACCCTCGAAGTCGAGAGTTCCGACAC
          1 ATGCAGATCTTCGTCAAAACCCTGACCGGCAAAACCATAACTTTGGAAGTCGAGAGTTCCGACAC

                                 *                 *              *    *     
         66 GATCGACAACGTTAAGGCGAAAATCCAAGACAAGGAAGGGATCCCACCAGACCAAC-AACGTCTC
         66 GATCGACAACGTTAAGGCGAAGATCCAAGACAAGGAAGGAATCCCACCAGACCAGCAAAGGT-TC

              *        *     *           *                                   
        130 ATCTTCGCCGGAAAACAGCTCGAAGATGGCCGGACCTTGGCCGATTACAACATCCAGAAGGAGTC
        130 ATTTTCGCCGGGAAACAACTCGAAGATGGACGGACCTTGGCCGATTACAACATCCAGAAGGAGTC

                  *     *   * *     *         
        195 CACCCTACATCTCGTCCTCCGTCTACGTGGTGGC
        195 CACCCTCCA-CTTGTCTTGCGTCTTCGTGGTGGC

                                            *                    *  *  *     
        229 ATGCAGATCTTCGTCAAAACCCTGACCGGCAAGACCATAACTTTGGAAGTCGAAAGCTCTGACAC
          1 ATGCAGATCTTCGTCAAAACCCTGACCGGCAAAACCATAACTTTGGAAGTCGAGAGTTCCGACAC

            *  *        *     *                    *                     *   
        294 CATTGACAACGTCAAGGCAAAGATCCAAGACAAGGAAGGCATCCCACCAGACCAGCAAAGGCTCA
         66 GATCGACAACGTTAAGGCGAAGATCCAAGACAAGGAAGGAATCCCACCAGACCAGCAAAGGTTCA

                                   *  *  *  *                                
        359 TATTT-GCCGGGAAACAACTCGAGGACGGTCGCACCTTGGCCGATTACAACATCCAGAAGGAGTC
        131 T-TTTCGCCGGGAAACAACTCGAAGATGGACGGACCTTGGCCGATTACAACATCCAGAAGGAGTC

                     *     *   * *           *
        423 CACCCTCCATTTGGTATTGAGGCTTCGTGGTGGG
        195 CACCCTCCACTT-GTCTTGCGTCTTCGTGGTGGC

                    *        *  **    *  *                 *  *           *  
        457 ATGCAGATTTTCGTCAAGACGTTGACTGGGAAAACCATAACTTTGGAGGTGGAGAGTTCCGATAC
          1 ATGCAGATCTTCGTCAAAACCCTGACCGGCAAAACCATAACTTTGGAAGTCGAGAGTTCCGACAC

                     *              *  *     *        *        *           * 
        522 GATCGACAATGTTAAGGCGAAGATTCAGGACAAAGAAGGAATTCCACCAGATCAGCAAAGGTTGA
         66 GATCGACAACGTTAAGGCGAAGATCCAAGACAAGGAAGGAATCCCACCAGACCAGCAAAGGTTCA

                   *         * *         *    *     *        *  *        *   
        587 TTTTCGCTGGGAAACAATTGGAAGATGGAAGGACTTTGGCTGATTACAATATTCAGAAGGAATCC
        131 TTTTCGCCGGGAAACAACTCGAAGATGGACGGACCTTGGCCGATTACAACATCCAGAAGGAGTCC

              *                             
        652 ACTCTCCACCTTGTCTTGCGTCTTCGTGGTGG
        196 ACCCTCCA-CTTGTCTTGCGTCTTCGTGGTGG

        684 TTTCTAA


Statistics
Matches: 371,  Mismatches: 79, Indels: 10
        0.81            0.17        0.02

Matches are distributed among these distances:
 227    4  0.01
 228  360  0.97
 229    7  0.02

ACGTcount: A:0.30, C:0.25, G:0.24, T:0.20


Consensus pattern (227 bp):   
ATGCAGATCTTCGTCAAAACCCTGACCGGCAAAACCATAACTTTGGAAGTCGAGAGTTCCGACAC
GATCGACAACGTTAAGGCGAAGATCCAAGACAAGGAAGGAATCCCACCAGACCAGCAAAGGTTCA
TTTTCGCCGGGAAACAACTCGAAGATGGACGGACCTTGGCCGATTACAACATCCAGAAGGAGTCC
ACCCTCCACTTGTCTTGCGTCTTCGTGGTGGC
Done.