Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_17909

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, 687

Length: 1146
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.22


Found at i:401 original size:228 final size:228

Alignment explanation


    Indices: 1--1109  Score: 1389
    Period size: 228  Copynumber: 4.9  Consensus size: 228

                          *        *  *              **    *  *     *  *  *  
          1 ATGCAAATTTTCGTCAAGACCCTCACCGGAAAGACCATCACATTGGAGGTGGAGAGTTCTGATAC
          1 ATGCAAATTTTCGTGAAGACCCTGACTGGAAAGACCATCACCCTGGAAGTTGAGAGCTCAGACAC

            *     *     *                 *        *  *              *   *   
         66 TATTGACAATGTAAAGGCCAAGATTCAGGACAAGGAAGGCATCCCCCCAGACCAGCAAAGGTTGA
         66 GATTGATAATGTTAAGGCCAAGATTCAGGATAAGGAAGGAATTCCCCCAGACCAGCAGAGGCTGA

             *  *     *                 ** *   *     *                       
        131 TCTTCGCTGGTAAGCAACTTGAGGATGGCCGCA-CGTTGGCTGATTACAACATCCAGAAGGAGTC
        131 TTTTTGCTGGGAAGCAACTTGAGGATGGGAGGACCCTT-GCAGATTACAACATCCAGAAGGAGTC

               *        *     *  *        *  *
        195 CACACTCCACTTAGTGCTTCGCCTCCGTGGAGGA
        195 CACCCTCCACTTGGTGCTCCGTCTCCGTGGCGGG

                       *  *     **       *        *  **    *  *     *     *  
        229 ATGCAAATTTTTGTTAAGACTTTGACTGGGAAGACCATTACATTGGAGGTAGAGAGTTCAGATAC
          1 ATGCAAATTTTCGTGAAGACCCTGACTGGAAAGACCATCACCCTGGAAGTTGAGAGCTCAGACAC

            *                 *  *        *     *                 *          
        294 CATTGATAATGTTAAGGCAAAAATTCAGGACAAGGAGGGAATTCCCCCAGACCAACAGAGGCTGA
         66 GATTGATAATGTTAAGGCCAAGATTCAGGATAAGGAAGGAATTCCCCCAGACCAGCAGAGGCTGA

                      *        *        ** *     *  *  *  *                  
        359 TTTTTGCTGGTAAGCAACTGGAGGATGGCCGTACCCTGGCTGACTATAACATCCAGAAGGAGTCC
        131 TTTTTGCTGGGAAGCAACTTGAGGATGGGAGGACCCTTGCAGATTACAACATCCAGAAGGAGTCC

                                   *     *  *
        424 ACCCTCCACTTGGTGCTCCGTCTTCGTGGTGGT
        196 ACCCTCCACTTGGTGCTCCGTCTCCGTGGCGGG

                 *     *        *  *     *                             *     
        457 ATGCAGATTTTTGTGAAGACACTTACTGGGAAGACCATCACCCTGGAAGTTGAGAGCTCTGACAC
          1 ATGCAAATTTTCGTGAAGACCCTGACTGGAAAGACCATCACCCTGGAAGTTGAGAGCTCAGACAC

            *  *                        *           *                        
        522 AATCGATAATGTTAAGGCCAA-AGTTCAAGATAAGGAAGGTA-TCCCTCCAGACCAGCAGAGGCT
         66 GATTGATAATGTTAAGGCCAAGA-TTCAGGATAAGGAAGGAATTCCC-CCAGACCAGCAGAGGCT

               *        *     *  *                                           
        585 GATATTTGCTGGAAAGCAGCTAGAGGATGGGAGGACCCTTGCAGATTACAACATCCAGAAGGAGT
        129 GATTTTTGCTGGGAAGCAACTTGAGGATGGGAGGACCCTTGCAGATTACAACATCCAGAAGGAGT

                            *                  
        650 CCACCCTCCACTTGGTTCTCCGTCTCCGTGGCGGG
        194 CCACCCTCCACTTGGTGCTCCGTCTCCGTGGCGGG

                                                                             
        685 ATGCAAATTTTCGTGAAGACCCTGACTGGAAAGACCATCACCCTGGAAGTTGAGAGCTCAGACAC
          1 ATGCAAATTTTCGTGAAGACCCTGACTGGAAAGACCATCACCCTGGAAGTTGAGAGCTCAGACAC

                                    *                    *                   
        750 GATTGATAATGTTAAGGCCAAGATCCAGGATAAGGAAGGAATTCCTCCAGACCAGCAGAGGCTGA
         66 GATTGATAATGTTAAGGCCAAGATTCAGGATAAGGAAGGAATTCCCCCAGACCAGCAGAGGCTGA

                                  *                                          
        815 TTTTTGCTGGGAAGCAACTTGAAGATGGGAGGACCCTTGCAGATTACAACATCCAGAAGGAGTCC
        131 TTTTTGCTGGGAAGCAACTTGAGGATGGGAGGACCCTTGCAGATTACAACATCCAGAAGGAGTCC

                          *  *               
        880 ACCCTCCACTTGGTTCTTCGTCTCCGTGGCGGG
        196 ACCCTCCACTTGGTGCTCCGTCTCCGTGGCGGG

                                                                             
        913 ATGCAAATTTTCGTGAAGACCCTGACTGGAAAGACCATCACCCTGGAAGTTGAGAGCTCAGACAC
          1 ATGCAAATTTTCGTGAAGACCCTGACTGGAAAGACCATCACCCTGGAAGTTGAGAGCTCAGACAC

                                    *                                        
        978 GATTGATAATGTTAAGGCCAAGATCCAGGATAAGGAAGGAA-TCCCACCAGACCAGCAGAGGCTG
         66 GATTGATAATGTTAAGGCCAAGATTCAGGATAAGGAAGGAATTCCC-CCAGACCAGCAGAGGCTG

                                   *                                      *  
       1042 ATTTTTGCTGGGAAGCAACTTGAAGATGGGAGGACCCTTGCAGATTACAACATCCAGAAGGAATC
        130 ATTTTTGCTGGGAAGCAACTTGAGGATGGGAGGACCCTTGCAGATTACAACATCCAGAAGGAGTC

               
       1107 CAC
        195 CAC

       1110 TTTGCACCTG


Statistics
Matches: 783,  Mismatches: 92, Indels: 12
        0.88            0.10        0.01

Matches are distributed among these distances:
 227    8  0.01
 228  769  0.98
 229    6  0.01

ACGTcount: A:0.29, C:0.23, G:0.26, T:0.22


Consensus pattern (228 bp):   
ATGCAAATTTTCGTGAAGACCCTGACTGGAAAGACCATCACCCTGGAAGTTGAGAGCTCAGACAC
GATTGATAATGTTAAGGCCAAGATTCAGGATAAGGAAGGAATTCCCCCAGACCAGCAGAGGCTGA
TTTTTGCTGGGAAGCAACTTGAGGATGGGAGGACCCTTGCAGATTACAACATCCAGAAGGAGTCC
ACCCTCCACTTGGTGCTCCGTCTCCGTGGCGGG

Done.