Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_09689

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, 563

Length: 939
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.23


Found at i:764 original size:375 final size:375

Alignment explanation


    Indices: 74--824  Score: 1322
    Period size: 375  Copynumber: 2.0  Consensus size: 375

         64 CCTACTAAAT

                                  *  *                                       
         74 CTTGCAAAGCTAGGGGTTCTGATCTTCGTGTTCATTTTAAGAATACACGAGAAACTGCATTCGCA
          1 CTTGCAAAGCTAGGGGTTCTGACCTACGTGTTCATTTTAAGAATACACGAGAAACTGCATTCGCA

                                            *                       *        
        139 ATCCGAAAGCTACCTTTGACAAAGGCAAAAAGGTACTTGGAGGATGTTATTGCCCATAAGCAAGC
         66 ATCCGAAAGCTACCTTTGACAAAGGCAAAAAGATACTTGGAGGATGTTATTGCCCACAAGCAAGC

                                                                             
        204 AATTCCATTCCGCCGCTTCTGTGGAGGAGTTGGGCGAACCGCACAGGCTAAGAATCGACATTCTA
        131 AATTCCATTCCGCCGCTTCTGTGGAGGAGTTGGGCGAACCGCACAGGCTAAGAATCGACATTCTA

                                                                      *      
        269 ATGGACAAGGCCGCTGGCCCGTGAAATCTGCAAAATTCATTCTCGATTTGCTCAAGAATGCCGAG
        196 ATGGACAAGGCCGCTGGCCCGTGAAATCTGCAAAATTCATTCTCGATTTGCTCAAGAACGCCGAG

                    *                                                        
        334 AGCAATGCTGAGGTAAAAGGTTTGGATGTAGACTCACTTATCATATCTCACATCCAAGTGAACCA
        261 AGCAATGCCGAGGTAAAAGGTTTGGATGTAGACTCACTTATCATATCTCACATCCAAGTGAACCA

                                                              
        399 AGCACAGAAGCAAAGGCGCCGAACATATCGTGCACACGGAAGGATTAACC
        326 AGCACAGAAGCAAAGGCGCCGAACATATCGTGCACACGGAAGGATTAACC

                                                                      *  *  *
        449 CTTGCAAAGCTAGGGGTTCTGACCTACGTGTTCATTTTAAGAATACACGAGAAACTGCCTTTGCC
          1 CTTGCAAAGCTAGGGGTTCTGACCTACGTGTTCATTTTAAGAATACACGAGAAACTGCATTCGCA

                                         *                                   
        514 ATCCGAAAGCTACCTTTGACAAAGGCAAAGAGATACTTGGAGGATGTTATTGCCCACAAGCAAGC
         66 ATCCGAAAGCTACCTTTGACAAAGGCAAAAAGATACTTGGAGGATGTTATTGCCCACAAGCAAGC

                  *     *           *              *                 *       
        579 AATTCCGTTCCGGCGCTTCTGTGGTGGAGTTGGGCGAACTGCACAGGCTAAGAATCGCCATTCTA
        131 AATTCCATTCCGCCGCTTCTGTGGAGGAGTTGGGCGAACCGCACAGGCTAAGAATCGACATTCTA

                      *        *                                         *   
        644 ATGGACAAGGTCGCTGGCCTGTGAAATCTGCAAAATTCATTCTCGATTTGCTCAAGAACGCTGAG
        196 ATGGACAAGGCCGCTGGCCCGTGAAATCTGCAAAATTCATTCTCGATTTGCTCAAGAACGCCGAG

                          *                                                  
        709 AGCAATGCCGAGGTGAAAGGTTTGGATGTAGACTCACTTATCATATCTCACATCCAAGTGAACCA
        261 AGCAATGCCGAGGTAAAAGGTTTGGATGTAGACTCACTTATCATATCTCACATCCAAGTGAACCA

                                                *             
        774 AGCACAGAAGCAAAGGCGCCGAACATATCGTGCACATGGAAGGATTAACC
        326 AGCACAGAAGCAAAGGCGCCGAACATATCGTGCACACGGAAGGATTAACC

             
        824 C
          1 C

        825 CTACATGTCT


Statistics
Matches: 356,  Mismatches: 20, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
 375  356  1.00

ACGTcount: A:0.30, C:0.23, G:0.24, T:0.23


Consensus pattern (375 bp):   
CTTGCAAAGCTAGGGGTTCTGACCTACGTGTTCATTTTAAGAATACACGAGAAACTGCATTCGCA
ATCCGAAAGCTACCTTTGACAAAGGCAAAAAGATACTTGGAGGATGTTATTGCCCACAAGCAAGC
AATTCCATTCCGCCGCTTCTGTGGAGGAGTTGGGCGAACCGCACAGGCTAAGAATCGACATTCTA
ATGGACAAGGCCGCTGGCCCGTGAAATCTGCAAAATTCATTCTCGATTTGCTCAAGAACGCCGAG
AGCAATGCCGAGGTAAAAGGTTTGGATGTAGACTCACTTATCATATCTCACATCCAAGTGAACCA
AGCACAGAAGCAAAGGCGCCGAACATATCGTGCACACGGAAGGATTAACC
Done.