Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_D_gene_10034122

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, 649

Length: 1083
ACGTcount: A:0.39, C:0.21, G:0.22, T:0.18


Found at i:593 original size:168 final size:168

Alignment explanation


    Indices: 310--820  Score: 846
    Period size: 168  Copynumber: 3.0  Consensus size: 168

        300 CCCTGCAAGC

                *              *    * *                       * *            
        310 AACAGGAAGAGTACCACGAGTCACACAAATCGAAGGAGCACGAAGAGTACCAAAAAGAAAAACCC
          1 AACATGAAGAGTACCACGAATCACGCGAATCGAAGGAGCACGAAGAGTACGAGAAAGAAAAACCC

                       *                                                     
        375 GAGTTCCCCAAGTTGGAAAAGCCTAAAGAGCACGAGAAACACGAAGTCGAATATCCGAAAATACC
         66 GAGTTCCCCAAATTGGAAAAGCCTAAAGAGCACGAGAAACACGAAGTCGAATATCCGAAAATACC

                                                  
        440 CGAGTACAAGGAAAAGCAAGATGAGGGTAAGGAACATA
        131 CGAGTACAAGGAAAAGCAAGATGAGGGTAAGGAACATA

                                                     *                       
        478 AACATGAAGAGTACCACGAATCACGCGAATCGAAGGAGCACAAAGAGTACGAGAAAGAAAAACCC
          1 AACATGAAGAGTACCACGAATCACGCGAATCGAAGGAGCACGAAGAGTACGAGAAAGAAAAACCC

                          *                                                  
        543 G-GATTCCCCAAATGGGAAAAGCCTAAAGAGCACGAGAAACACGAAGTCGAATATCCGAAAATAC
         66 GAG-TTCCCCAAATTGGAAAAGCCTAAAGAGCACGAGAAACACGAAGTCGAATATCCGAAAATAC

                                         *          
        607 CCGAGTACAAGGTAAAA-CAAGATGAGGGCAAGGAACATA
        130 CCGAGTACAAGG-AAAAGCAAGATGAGGGTAAGGAACATA

                                                                             
        646 AACATGAAGAGTACCACGAATCACGCGAATCGAAGGAGCACGAAGAGTACGAGAAAGAAAAACCC
          1 AACATGAAGAGTACCACGAATCACGCGAATCGAAGGAGCACGAAGAGTACGAGAAAGAAAAACCC

                    *     *                  *                       *       
        711 GAGTTCCCTAAATTAGAAAAGCCTAAAGAGCACCAGAAACACGAAGTCGAATATCCGGAAATACC
         66 GAGTTCCCCAAATTGGAAAAGCCTAAAGAGCACGAGAAACACGAAGTCGAATATCCGAAAATACC

               *      *                           
        776 CGAATACAAGAAAAAGCAAGATGAGGGTAAGGAACATA
        131 CGAGTACAAGGAAAAGCAAGATGAGGGTAAGGAACATA

                   
        814 AACATGA
          1 AACATGA

        821 GTTCCCAAAG


Statistics
Matches: 320,  Mismatches: 19, Indels: 8
        0.92            0.05        0.02

Matches are distributed among these distances:
 167    5  0.02
 168  310  0.97
 169    5  0.02

ACGTcount: A:0.46, C:0.20, G:0.23, T:0.11


Consensus pattern (168 bp):   
AACATGAAGAGTACCACGAATCACGCGAATCGAAGGAGCACGAAGAGTACGAGAAAGAAAAACCC
GAGTTCCCCAAATTGGAAAAGCCTAAAGAGCACGAGAAACACGAAGTCGAATATCCGAAAATACC
CGAGTACAAGGAAAAGCAAGATGAGGGTAAGGAACATA

Found at i:664 original size:87 final size:87

Alignment explanation


    Indices: 405--664  Score: 197
    Period size: 87  Copynumber: 3.1  Consensus size: 87

        395 GCCTAAAGAG

                                                              *           *  
        405 CACGAGAAACACGAAGTCGAATATCCGAAAATACCCGAGTACAAGGAAAAGCAAGATGAGGGTAA
          1 CACGAGAAACACGAAGTCGAATATCCGAAAATACCCGAGTACAAGGAAAACCAAGATGAGGGCAA

                                  
        470 GGAACATAAACATGAAGAGTAC
         66 GGAACATAAACATGAAGAGTAC

                    *  *           * *                        *      **    **
        492 CACGA-ATCACGCGAA-TCGAAGGAGCAC-AAAGAGTA--CGAG-A-AAGAAAAACCCGGAT-TC
          1 CACGAGA-AACACGAAGTCGAA-TATC-CGAAA-A-TACCCGAGTACAAGGAAAACCAAGATGAG

            **       *      * *         *
        549 CCCAAATGGGA-A-AAGCCT-AA-AG-AG
         61 GGC-AA-GGAACATAAACATGAAGAGTAC

                                                                             
        573 CACGAGAAACACGAAGTCGAATATCCGAAAATACCCGAGTACAAGGTAAAA-CAAGATGAGGGCA
          1 CACGAGAAACACGAAGTCGAATATCCGAAAATACCCGAGTACAAGG-AAAACCAAGATGAGGGCA

                                   
        637 AGGAACATAAACATGAAGAGTAC
         65 AGGAACATAAACATGAAGAGTAC

                 
        660 CACGA
          1 CACGA

        665 ATCACGCGAA


Statistics
Matches: 120,  Mismatches: 32, Indels: 42
        0.62            0.16        0.22

Matches are distributed among these distances:
  79    2  0.02
  80    2  0.02
  81   21  0.17
  82   12  0.10
  83   12  0.10
  84   13  0.11
  85   16  0.13
  86   12  0.10
  87   26  0.22
  88    2  0.02
  89    2  0.02

ACGTcount: A:0.46, C:0.20, G:0.24, T:0.10


Consensus pattern (87 bp):   
CACGAGAAACACGAAGTCGAATATCCGAAAATACCCGAGTACAAGGAAAACCAAGATGAGGGCAA
GGAACATAAACATGAAGAGTAC
Done.