Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_04385

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: 2424
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.27


Found at i:974 original size:510 final size:512

Alignment explanation


    Indices: 15--1060  Score: 1898
    Period size: 510  Copynumber: 2.0  Consensus size: 512

          5 CAATTGCATG

                                                                             
         15 GCCAAGGTTTATGGTGCTCAAATGTGAGGCGAGGAACAAATATTTGAGCTATATGCATGAGAGTT
          1 GCCAAGGTTTATGGTGCTCAAATGTGAGGCGAGGAACAAATATTTGAGCTATATGCATGAGAGTT

                    *            *                                           
         80 ACGATTGTCATGGGTATCTCAGATTTTCGGAAACTTTGGCTTGCAGTCCATACACAAAATTTGAG
         66 ACGATTGTAATGGGTATCTCAAATTTTCGGAAACTTTGGCTTGCAGTCCATACACAAAATTTGAG

                 *                                                  *     *  
        145 GTGGAGAGGGCCAAATGCAGTGGGGAAGATGGGTTGGTGCACATAAAGAGCTGCCAGAACAACAA
        131 GTGGAAAGGGCCAAATGCAGTGGGGAAGATGGGTTGGTGCACATAAAGAGCTGCCACAACAAAAA

                                                                             
        210 ATACTGCAAACGAGTCAAAAATGTTTCCATCACTGGAAACTCAAAAGAGCAGTATTGGATTTCTG
        196 ATACTGCAAACGAGTCAAAAATGTTTCCATCACTGGAAACTCAAAAGAGCAGTATTGGATTTCTG

                                                                   *         
        275 CAGCAGCAGACAAACCGGAGGAAGGCCGATCCGAGGAGTCGTGCACGTTGTTCAAGCTTATCCCA
        261 CAGCAGCAGACAAACCGGAGGAAGGCCGATCCGAGGAGTCGTGCACGTTGTTCAAACTTATCCCA

                                                                             
        340 GTGGACACTGCAACAAATAAGATCCGAATTATGCATGTGCAATCAGGTTGCTATTTATGCTTATG
        326 GTGGACACTGCAACAAATAAGATCCGAATTATGCATGTGCAATCAGGTTGCTATTTATGCTTATG

                                                                             
        405 GTGGGTAGATTCTCCAACGTTTAATAACTGTGTGTTGGCAAACTACAAAGTTTTCGATGGTAATT
        391 GTGGGTAGATTCTCCAACGTTTAATAACTGTGTGTTGGCAAACTACAAAGTTTTCGATGGTAATT

                                                                     
        470 CCTGTGATCTCTTCACAGTCATCGACT-G-GTCGCTTGCGAATAAGCCATTTGCGTC
        456 CCTGTGATCTCTTCACAGTCATCGACTGGAGTCGCTTGCGAATAAGCCATTTGCGTC

                                                                             
        525 GCCAAGGTTTATGGTGCTCAAATGTGAGGCGAGGAACAAATATTTGAGCTATATGCATGAGAGTT
          1 GCCAAGGTTTATGGTGCTCAAATGTGAGGCGAGGAACAAATATTTGAGCTATATGCATGAGAGTT

                                                      *                      
        590 ACGATTGTAATGGGTATCTCAAATTTTCGGAAACTTTGGCTTTCAGTCCATACACAAAATTTGAG
         66 ACGATTGTAATGGGTATCTCAAATTTTCGGAAACTTTGGCTTGCAGTCCATACACAAAATTTGAG

                              *                                              
        655 GTGGAAAGGGCCAAATGCGGTGGGGAAGATGGGTTGGTGCACATAAAGAGCTGCCACAACAAAAA
        131 GTGGAAAGGGCCAAATGCAGTGGGGAAGATGGGTTGGTGCACATAAAGAGCTGCCACAACAAAAA

                                                        *                    
        720 ATACTGCAAACGAGTCAAAAATGTTTCCATCACTGGAAACTCAACAGAGCAGTATTGGATTTCTG
        196 ATACTGCAAACGAGTCAAAAATGTTTCCATCACTGGAAACTCAAAAGAGCAGTATTGGATTTCTG

                   *     *    *                                             *
        785 CAGCAGCCGACAAGCCGGTGGAAGGCCGATCCGAGGAGTCGTGCACGTTGTTCAAACTTATCCCG
        261 CAGCAGCAGACAAACCGGAGGAAGGCCGATCCGAGGAGTCGTGCACGTTGTTCAAACTTATCCCA

                                                     *                       
        850 GTGGACACTGCAACAAATAAGATCCGAATTATGCATGTGCAGTCAGGTTGCTATTTATGCTTATG
        326 GTGGACACTGCAACAAATAAGATCCGAATTATGCATGTGCAATCAGGTTGCTATTTATGCTTATG

                                                                             
        915 GTGGGTAGATTCTCCAACGTTTAATAACTGTGTGTTGGCAAACTACAAAGTTTTCGATGGTAATT
        391 GTGGGTAGATTCTCCAACGTTTAATAACTGTGTGTTGGCAAACTACAAAGTTTTCGATGGTAATT

                            *     *          *                        
        980 CCTGTGATCTCTTCACTGTCATTGACTGGGAGTTGCTTGCGAATAAGCCATTTGCGTC
        456 CCTGTGATCTCTTCACAGTCATCGACT-GGAGTCGCTTGCGAATAAGCCATTTGCGTC

                        *   *      
       1038 GCCAAGGTTTATCGTGATCAAAT
          1 GCCAAGGTTTATGGTGCTCAAAT

       1061 CCCATCAGAA


Statistics
Matches: 514,  Mismatches: 19, Indels: 3
        0.96            0.04        0.01

Matches are distributed among these distances:
 510  466  0.91
 512    1  0.00
 513   47  0.09

ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27


Consensus pattern (512 bp):   
GCCAAGGTTTATGGTGCTCAAATGTGAGGCGAGGAACAAATATTTGAGCTATATGCATGAGAGTT
ACGATTGTAATGGGTATCTCAAATTTTCGGAAACTTTGGCTTGCAGTCCATACACAAAATTTGAG
GTGGAAAGGGCCAAATGCAGTGGGGAAGATGGGTTGGTGCACATAAAGAGCTGCCACAACAAAAA
ATACTGCAAACGAGTCAAAAATGTTTCCATCACTGGAAACTCAAAAGAGCAGTATTGGATTTCTG
CAGCAGCAGACAAACCGGAGGAAGGCCGATCCGAGGAGTCGTGCACGTTGTTCAAACTTATCCCA
GTGGACACTGCAACAAATAAGATCCGAATTATGCATGTGCAATCAGGTTGCTATTTATGCTTATG
GTGGGTAGATTCTCCAACGTTTAATAACTGTGTGTTGGCAAACTACAAAGTTTTCGATGGTAATT
CCTGTGATCTCTTCACAGTCATCGACTGGAGTCGCTTGCGAATAAGCCATTTGCGTC
Done.