Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_35833

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, 1000

Length: 2748
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.32


Found at i:1702 original size:213 final size:213

Alignment explanation


    Indices: 686--1700  Score: 1442
    Period size: 213  Copynumber: 4.8  Consensus size: 213

        676 TTTCCAATAA

                                       *     **                              
        686 TCATGGACACCATGGAGA-GTTTGAGGCATCTTTCTTTAAGCGGAACGGCTTTGAAGGAATTACC
          1 TCATGGACACCATGGAGATG-TTGAGGGATCTTGATTTAAGCGGAACGGCTTTGAAGGAATTACC

                   *   **  *            *                                    
        750 ATCCTCAATTGAAAACCTTATTGGTCTTAAGCAATTGAGATTGAAAAACTGTGAAAACCTTGTTT
         65 ATCCTCATTTGGCAATCTTATTGGTCTTGAGCAATTGAGATTGAAAAACTGTGAAAACCTTGTTT

                                               *           *                 
        815 GCCTTCCTGACAGCTTTTATAAATTGAAATCTCTCGAGAGATTCGA-TCTTAAAGGTTGCTCAAG
        130 GCCTTCCTGACAGCTTTTATAAATTGAAATCTCTCAAGAGATTC-ACACTTAAAGGTTGCTCAAG

                               *
        879 ATTGGAGATTTTCCCAGAAA
        194 ATTGGAGATTTTCCCAGAAG

                     *              **  *         * *       *      *         
        899 TCATGGACATCATGGAGATGTTGATAGAACTTGATTTAGGTGGAACGGGTTTGAAAGAATTACCA
          1 TCATGGACACCATGGAGATGTTGAGGGATCTTGATTTAAGCGGAACGGCTTTGAAGGAATTACCA

                  *   **          *    * *                           *       
        964 TCCTCAATTGATAATCTTATTGATCTTAATCAATTGAGATTGAAAAACTGTGAAAACTTTGTTTG
         66 TCCTCATTTGGCAATCTTATTGGTCTTGAGCAATTGAGATTGAAAAACTGTGAAAACCTTGTTTG

                        *                                                  * 
       1029 CCTTCCTGACAGTTTTTATAAATTGAAATCTCTCAAGAGATTCA-ATCTTAAAGGTTGCTCAATA
        131 CCTTCCTGACAGCTTTTATAAATTGAAATCTCTCAAGAGATTCACA-CTTAAAGGTTGCTCAAGA

                               
       1093 TTGGAGATTTTCCCAGAAG
        195 TTGGAGATTTTCCCAGAAG

                                      *                                      
       1112 TCATGGACACCATGGAGATGTTGAGGTATCTTGATTTAAGCGGAACGGCTTTGAAGGAATTACCA
          1 TCATGGACACCATGGAGATGTTGAGGGATCTTGATTTAAGCGGAACGGCTTTGAAGGAATTACCA

                                                               *    *        
       1177 TCCTCATTTGGCAATCTTATTGGTCTTGAGCAATTGAGATTGAAAAACTGTAAAAAGCTTGTTTG
         66 TCCTCATTTGGCAATCTTATTGGTCTTGAGCAATTGAGATTGAAAAACTGTGAAAACCTTGTTTG

                                        *     *   *     **              *    
       1242 CCTTCCTGACAGCTTTTATAAATTGAAACCTCTCGAGATATTCAGTCTTAAAGGTTGCTCGAGAT
        131 CCTTCCTGACAGCTTTTATAAATTGAAATCTCTCAAGAGATTCACACTTAAAGGTTGCTCAAGAT

             *                
       1307 TAGAGATTTTCCCAGAAG
        196 TGGAGATTTTCCCAGAAG

                   *               *                                         
       1325 TCATGGATACCATGGAGATGTTGTGGGATCTTGATTTAAGCGGAACGGCTTTGAAGGAATTACCA
          1 TCATGGACACCATGGAGATGTTGAGGGATCTTGATTTAAGCGGAACGGCTTTGAAGGAATTACCA

                                        *                      *    *        
       1390 TCCTCATTTGGCAATCTTATTGGTCTTGGGCAATTGAGATTGAAAAACTGTAAAAAGCTTGTTTG
         66 TCCTCATTTGGCAATCTTATTGGTCTTGAGCAATTGAGATTGAAAAACTGTGAAAACCTTGTTTG

                                  *          *    *       *  *          *    
       1455 CCTTCCTGACAGCTTTTATAAACTGAAATCTCTTAAGACATTCACAGTTCAAGGTTGCTCGAGAT
        131 CCTTCCTGACAGCTTTTATAAATTGAAATCTCTCAAGAGATTCACACTTAAAGGTTGCTCAAGAT

                              
       1520 TGGAGATTTTCCCAGAAG
        196 TGGAGATTTTCCCAGAAG

              *                                           *               *  
       1538 TCTTGGACACCATGGAGATGTTGAGGGATCTTGATTTAAGCGGAACAGCTTTGAAGGAATTATCA
          1 TCATGGACACCATGGAGATGTTGAGGGATCTTGATTTAAGCGGAACGGCTTTGAAGGAATTACCA

                                          *      *    * **                   
       1603 TCCTCATTTGGCAATCTTATTGGTCTTGAGAAATTGATATTGGACCACTGTGAAAACCTTGTTTG
         66 TCCTCATTTGGCAATCTTATTGGTCTTGAGCAATTGAGATTGAAAAACTGTGAAAACCTTGTTTG

                   *              *  *       
       1668 CCTTCCTTACAGCTTTTATAAACTGGAATCTCT
        131 CCTTCCTGACAGCTTTTATAAATTGAAATCTCT

       1701 TAGGAGACTT


Statistics
Matches: 723,  Mismatches: 76, Indels: 6
        0.90            0.09        0.01

Matches are distributed among these distances:
 212    1  0.00
 213  721  1.00
 214    1  0.00

ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33


Consensus pattern (213 bp):   
TCATGGACACCATGGAGATGTTGAGGGATCTTGATTTAAGCGGAACGGCTTTGAAGGAATTACCA
TCCTCATTTGGCAATCTTATTGGTCTTGAGCAATTGAGATTGAAAAACTGTGAAAACCTTGTTTG
CCTTCCTGACAGCTTTTATAAATTGAAATCTCTCAAGAGATTCACACTTAAAGGTTGCTCAAGAT
TGGAGATTTTCCCAGAAG
Done.