Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_17541

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: 3678
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.28


Found at i:1434 original size:210 final size:210

Alignment explanation


    Indices: 1070--1909  Score: 1240
    Period size: 210  Copynumber: 4.0  Consensus size: 210

       1060 CAATCTATAA

                                                            *                
       1070 TTGAATCCTCTGCCTCATCCAATATCATTTCAAGCAATGAGATCTCCATGAGTTTACCTGATCCA
          1 TTGAATCCTCTGCCTCATCCAATATCATTTCAAGCAATGAGATCTCCACGAGTTTACCTGATCCA

               *                       *                *                    
       1135 GTTCCCTCAGC-GAATTTTGCCAGTGAGCAGATGTTGCAAATCTTAGGGAAATCTTCTGATCCTG
         66 GTTTCCTCA-CAGAATTTTGCCAGTGAACAGATGTTGCAAATCTCAGGGAAATCTTCTGATCCTG

                                *                                         *  
       1199 ACAATTTATCCCAT-T-CTGGTTTATACATGAGTGATGAAATTCATAAAAATTCACAAGTGGTAT
        130 ACAATTTA-CCC-TGTACTGATTTATACATGAGTGATGAAATTCATAAAAATTCACAAGTGGAAT

                       *      
       1262 CTGTCATCAGTAATCCAT
        193 CTGTCATCAGTGATCCAT

                                *         *    *                             
       1280 TTGAATCCTCTGCCTCATCCGATATCATTTTAAGTGAA-GAGATCTCCACGAGTTTACCTGATCC
          1 TTGAATCCTCTGCCTCATCCAATATCATTTCAAG-CAATGAGATCTCCACGAGTTTACCTGATCC

                     *                    *                              *   
       1344 AGTTTCCTCGCAGAATTTTGCCAGTGAACATATGTTGCAAATCTCAGGGAAATCTTCTGATACTG
         65 AGTTTCCTCACAGAATTTTGCCAGTGAACAGATGTTGCAAATCTCAGGGAAATCTTCTGATCCTG

                                                       *        *            
       1409 ACAATTTACCCTGTACTGATTTATACATGAGTGATGAAATTCAAAAAAATTCTCAAGTGGAATCT
        130 ACAATTTACCCTGTACTGATTTATACATGAGTGATGAAATTCATAAAAATTCACAAGTGGAATCT

                   *        
       1474 GTCATCAATGATCCAT
        195 GTCATCAGTGATCCAT

                                         *         *         *               
       1490 TTGAATCCTCTGCCTCATCCAATATCATTGCAAGCAATGGGATCTCCACAAGTTTACCTGATCCA
          1 TTGAATCCTCTGCCTCATCCAATATCATTTCAAGCAATGAGATCTCCACGAGTTTACCTGATCCA

            *                         *                 *                   *
       1555 ATTTCCTCACAGAATTTTGCCAGTGAGCAGATGTTGCAAATCTCTGGGAAATCTTCTGATCCTGT
         66 GTTTCCTCACAGAATTTTGCCAGTGAACAGATGTTGCAAATCTCAGGGAAATCTTCTGATCCTGA

                                            *                                
       1620 CAATTTACCCTGTACTGATTTATACATGAGTGGTGAAATTCATAAAAATTCACAAGTGGAATCTG
        131 CAATTTACCCTGTACTGATTTATACATGAGTGATGAAATTCATAAAAATTCACAAGTGGAATCTG

                *          
       1685 TCATTAGTGATCCAT
        196 TCATCAGTGATCCAT

               *                        *           *        *               
       1700 TTGTATCCTCTGCCTCATCCAATATCATCTCTAA-CAATGGGATCTCCATGAGTTTACCTGATCC
          1 TTGAATCCTCTGCCTCATCCAATATCATTTC-AAGCAATGAGATCTCCACGAGTTTACCTGATCC

                                  *       *          *   *   *               
       1764 AGTTTCCTCACAGAATTTTGCCGGTGAACATATGTTGCAAAACTCGGGGGAATCTTCTGATCCTG
         65 AGTTTCCTCACAGAATTTTGCCAGTGAACAGATGTTGCAAATCTCAGGGAAATCTTCTGATCCTG

                      *             *  **                   *                
       1829 ACAATTTACCATGTACTGATTTATGCACAAGTGATGAAATTCATAAAATTTCACAAGTGGAATCT
        130 ACAATTTACCCTGTACTGATTTATACATGAGTGATGAAATTCATAAAAATTCACAAGTGGAATCT

                     *      
       1894 GTCATCAGTCATCCAT
        195 GTCATCAGTGATCCAT

       1910 CATCATCCTC


Statistics
Matches: 569,  Mismatches: 55, Indels: 12
        0.89            0.09        0.02

Matches are distributed among these distances:
 208    1  0.00
 209    7  0.01
 210  557  0.98
 211    4  0.01

ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33


Consensus pattern (210 bp):   
TTGAATCCTCTGCCTCATCCAATATCATTTCAAGCAATGAGATCTCCACGAGTTTACCTGATCCA
GTTTCCTCACAGAATTTTGCCAGTGAACAGATGTTGCAAATCTCAGGGAAATCTTCTGATCCTGA
CAATTTACCCTGTACTGATTTATACATGAGTGATGAAATTCATAAAAATTCACAAGTGGAATCTG
TCATCAGTGATCCAT

Done.