Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_12437

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, 723

Length: 1206
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31


Found at i:376 original size:117 final size:117

Alignment explanation


    Indices: 162--1107  Score: 1285
    Period size: 117  Copynumber: 8.1  Consensus size: 117

        152 CACTAATGAC

                 *        *     **                 *                         
        162 ATCGATATCTTCATTACTTTCAAAGAGTTCAAA-TTCTAGGATTCTACCTACAGGTGTGCCTATT
          1 ATCGACATCTTCATCACTTTTGAAGAGTTCAAATTTC-AAGATTCTACCTACAGGTGTGCCTATT

                                        *                *       
        226 CCTCCGTCAGGACCTAGTGGAAGTACATTAGATCCACCTCCTCCATCGTCAAT
         65 CCTCCGTCAGGACCTAGTGGAAGTACATCAGATCCACCTCCTCCACCGTCAAT

              *                     *                         *      *       
        279 ATTGACATCTTCATCACTTTTGAAAAGTTCAAATTTCAAGATTCTACCTATAGGTGTTCCTATTC
          1 ATCGACATCTTCATCACTTTTGAAGAGTTCAAATTTCAAGATTCTACCTACAGGTGTGCCTATTC

                   *                          *  *      *       
        344 CTCCGTCGGGACCTAGTGGAAGTACATCAGATCCGCCACCTCCATCGTCAAT
         66 CTCCGTCAGGACCTAGTGGAAGTACATCAGATCCACCTCCTCCACCGTCAAT

                 *  *                                                  *     
        396 ATCGAAATTTTCATCACTTTTGAAGAGTTCAAATTTCAAGATTCTACCTACAGGTGTGCATATTC
          1 ATCGACATCTTCATCACTTTTGAAGAGTTCAAATTTCAAGATTCTACCTACAGGTGTGCCTATTC

                           *  *              **  *      *       
        461 CTCCGTCAGGACCTAATGAAAGTACATCAGATCTGCCACCTCCATCGTCAAT
         66 CTCCGTCAGGACCTAGTGGAAGTACATCAGATCCACCTCCTCCACCGTCAAT

             *                 *         *                            *      
        513 AACGACATCTTCATCACTTGTGAAGAGTTTAAATTTCAAGATTCTACCTACAGGTGTGGCTATTC
          1 ATCGACATCTTCATCACTTTTGAAGAGTTCAAATTTCAAGATTCTACCTACAGGTGTGCCTATTC

               *   *                          *  *              
        578 CTCTGTCGGGACCTAGTGGAAGTACATCAGATCCGCCACCTCCACCGTCAAT
         66 CTCCGTCAGGACCTAGTGGAAGTACATCAGATCCACCTCCTCCACCGTCAAT

                                                * *    *              **     
        630 ATCGACATCTTCATCACTTTTGAAGAGTTCAAATTTTAGGATTATACCTACAGGTGTGGTTATTC
          1 ATCGACATCTTCATCACTTTTGAAGAGTTCAAATTTCAAGATTCTACCTACAGGTGTGCCTATTC

                   *                                          * 
        695 CTCCGTCGGGACCTAGTGGAAGTACATCAGATCCACCTCCTCCACCGTCAGT
         66 CTCCGTCAGGACCTAGTGGAAGTACATCAGATCCACCTCCTCCACCGTCAAT

                                                  *                          
        747 ATCGACATCTTCATCACTTTTGAAGAGTTCAAATTTCAGGATTCTACCTACAGGTGTGCCTATTC
          1 ATCGACATCTTCATCACTTTTGAAGAGTTCAAATTTCAAGATTCTACCTACAGGTGTGCCTATTC

                 * *                               *          * 
        812 CTCCGCCGGGACCTAGTGGAAGTACATCAGATCCACCTCATCCACCGTCAGT
         66 CTCCGTCAGGACCTAGTGGAAGTACATCAGATCCACCTCCTCCACCGTCAAT

                                                * *       *                  
        864 ATCGACATCTTCATCACTTTTGAAGAGTTCAAATTTTAGGATTCTATCTACAGGTGTGCCTATTC
          1 ATCGACATCTTCATCACTTTTGAAGAGTTCAAATTTCAAGATTCTACCTACAGGTGTGCCTATTC

                *                                           *   
        929 CTCCATCAGGACCTAGTGGAAGTACATCAGATCCACCTCCTCCACCGTTAAT
         66 CTCCGTCAGGACCTAGTGGAAGTACATCAGATCCACCTCCTCCACCGTCAAT

              *                  *                        *    *             
        981 ATTG--A----CATCACTTTTAAAGAGTTCAAATTTCAAGATTCTATCTACTGGTGTGCCTATTC
          1 ATCGACATCTTCATCACTTTTGAAGAGTTCAAATTTCAAGATTCTACCTACAGGTGTGCCTATTC

                    *         *          *              **  *   
       1040 CTCCGTCAAGACCTAGTGAAAGTACATCATATCCACCTCCTCCATTGTTAAT
         66 CTCCGTCAGGACCTAGTGGAAGTACATCAGATCCACCTCCTCCACCGTCAAT

               *       *    
       1092 ATCAACATCTTTATCA
          1 ATCGACATCTTCATCA

       1108 ATTTCAAAAA


Statistics
Matches: 746,  Mismatches: 76, Indels: 14
        0.89            0.09        0.02

Matches are distributed among these distances:
 111   98  0.13
 113    1  0.00
 115    1  0.00
 117  643  0.86
 118    3  0.00

ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31


Consensus pattern (117 bp):   
ATCGACATCTTCATCACTTTTGAAGAGTTCAAATTTCAAGATTCTACCTACAGGTGTGCCTATTC
CTCCGTCAGGACCTAGTGGAAGTACATCAGATCCACCTCCTCCACCGTCAAT

Done.