Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_12089

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, 414

Length: 690
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22


Found at i:404 original size:228 final size:227

Alignment explanation


    Indices: 1--662  Score: 774
    Period size: 228  Copynumber: 2.9  Consensus size: 227

                          *                       *  *                       
          1 ATGCAGATCTTTGTGAAAACCCTTACCGGCAAGACCATAACACTCGAGGTCGAAAGCTCCGACAC
          1 ATGCAGATCTTTGTCAAAA-CCTTACCGGCAAGACCATCACCCTCGAGGTCGAAAGCTCCGACAC

                        *           *              *        *                
         66 CATCGACAACGTCAAGGCCAAGATCCAAGACAAGGAAGGGATCCCACCCGACCAGCAGCGTCTCA
         65 CATCGACAACGTTAAGGCCAAGATTCAAGACAAGGAAGGAATCCCACCTGACCAGCAGCGTCTCA

             *              ** *     *  **                                   
        131 TTTTCGCTGGCAAACAGCTCGAAGACGGTCGGACCCTT-GCTGATTATAACATCCAGAAAGAATC
        130 TCTTCGCTGGCAAACAATTGGAAGATGGGAGGA-CCTTGGCTGATTATAACATCCAGAAAGAATC

                  *                            
        195 CACCCTCCACCTCGTCTT-ACGCCTTCGTGG-GGG
        194 CACCCTTCACCTCGTCTTGA-GCCTTCGTGGAGGG

                  *                                         *     *  *       
        228 CATGCAAATCTTTGTCAAAACCTTAACCGGCAAGACCATCACCCTCGAAGTCGAGAGTTCCGACA
          1 -ATGCAGATCTTTGTCAAAACCTT-ACCGGCAAGACCATCACCCTCGAGGTCGAAAGCTCCGACA

                                                                   *      * *
        293 CCATCGACAACGTTAAGGCCAAGATTCAAGACAAGGAAGGAATCCCACCTGACCAACAGCGTTTG
         64 CCATCGACAACGTTAAGGCCAAGATTCAAGACAAGGAAGGAATCCCACCTGACCAGCAGCGTCTC

                                                              *              
        358 ATCTTCGCTGGCAAACAATTGGAAGATGGGAGGACCTTGGCTGATTATAATATCCA-AAAGGAAT
        129 ATCTTCGCTGGCAAACAATTGGAAGATGGGAGGACCTTGGCTGATTATAACATCCAGAAA-GAAT

                         *  *     *            
        422 CCACCCTTCACCTTGTTTTGAGGCTTCGTGGAGGG
        193 CCACCCTTCACCTCGTCTTGAGCCTTCGTGGAGGG

                    *        *  *     *     *  *      * *     *           *  
        457 ATGCAGATTTTTGTCAAGACTTTGACAGGCAAAACAATCACCTTGGAGGTTGAAAGCTCCGATAC
          1 ATGCAGATCTTTGTCAAAACCTT-ACCGGCAAGACCATCACCCTCGAGGTCGAAAGCTCCGACAC

               *     *        *        *  *                    *     ** *    
        522 CATTGACAATGTTAAGGCAAAGATTCAGGATAAGGAAGGAATCCCACCTGATCAGCAAAGGCTCA
         65 CATCGACAACGTTAAGGCCAAGATTCAAGACAAGGAAGGAATCCCACCTGACCAGCAGCGTCTCA

                *  *                          *                 *        *  *
        587 TCTTTGCCGGCAAACAATTGGAAGATGGGAGGACTTTGGCTGATTATAACATTCAGAAAGAGTCT
        130 TCTTCGCTGGCAAACAATTGGAAGATGGGAGGACCTTGGCTGATTATAACATCCAGAAAGAATCC

                       
        652 ACCCTTCACCT
        195 ACCCTTCACCT

        663 TGTTCTTCGT


Statistics
Matches: 368,  Mismatches: 60, Indels: 12
        0.84            0.14        0.03

Matches are distributed among these distances:
 227   11  0.03
 228  350  0.95
 229    7  0.02

ACGTcount: A:0.31, C:0.26, G:0.22, T:0.21


Consensus pattern (227 bp):   
ATGCAGATCTTTGTCAAAACCTTACCGGCAAGACCATCACCCTCGAGGTCGAAAGCTCCGACACC
ATCGACAACGTTAAGGCCAAGATTCAAGACAAGGAAGGAATCCCACCTGACCAGCAGCGTCTCAT
CTTCGCTGGCAAACAATTGGAAGATGGGAGGACCTTGGCTGATTATAACATCCAGAAAGAATCCA
CCCTTCACCTCGTCTTGAGCCTTCGTGGAGGG

Done.