Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_23255

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: 3052
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.24


Found at i:107 original size:15 final size:15

Alignment explanation


    Indices: 87--120  Score: 50
    Period size: 15  Copynumber: 2.3  Consensus size: 15

         77 CCTCCAAACG

                  *        
         87 CCACAAGCATCGCCA
          1 CCACAAACATCGCCA

                        *  
        102 CCACAAACATCGTCA
          1 CCACAAACATCGCCA

                
        117 CCAC
          1 CCAC

        121 CGCCACCGCA


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  15   17  1.00

ACGTcount: A:0.35, C:0.47, G:0.09, T:0.09


Consensus pattern (15 bp):   
CCACAAACATCGCCA

Found at i:1020 original size:54 final size:55

Alignment explanation


    Indices: 962--1098  Score: 190
    Period size: 54  Copynumber: 2.5  Consensus size: 55

        952 GGGAGATTTA

                  *             *                      *     *      
        962 TGGTGAGAGGAGAAGGGAGAGGGAGCGAGCA-AGGAGTAGAGATAGAGACAT-GAG
          1 TGGTGAAAGGAGAAGGGAGAAGGAGCGAG-AGAGGAGTAGAGAGAGAGAAATGGAG

                                                   *               
       1016 TGGTGAAAGGAGAAGGGAGAAGGAGCGAGAGAGGAGTAGGGAGAGAGAAATGGAG
          1 TGGTGAAAGGAGAAGGGAGAAGGAGCGAGAGAGGAGTAGAGAGAGAGAAATGGAG

            *                            
       1071 AGG-GAAAGGAGAAGGGAGAAGGAGCGAG
          1 TGGTGAAAGGAGAAGGGAGAAGGAGCGAG

       1099 GGAAGAGCCG


Statistics
Matches: 75,  Mismatches: 6, Indels: 4
        0.88            0.07        0.05

Matches are distributed among these distances:
  53    1  0.01
  54   69  0.92
  55    5  0.07

ACGTcount: A:0.39, C:0.04, G:0.50, T:0.07


Consensus pattern (55 bp):   
TGGTGAAAGGAGAAGGGAGAAGGAGCGAGAGAGGAGTAGAGAGAGAGAAATGGAG

Found at i:1132 original size:54 final size:56

Alignment explanation


    Indices: 961--1146  Score: 179
    Period size: 54  Copynumber: 3.4  Consensus size: 56

        951 AGGGAGATTT

                   *             *            *   *  *  *     *      
        961 ATGGTGAGAGGAGAAGGGAGAGGGAGCGAGCA-AGGAGTAGAGATAGAGACAT-GAG
          1 ATGGTGAAAGGAGAAGGGAGAAGGAGCGAG-AGAAGAGCAGGGACAGAGAAATCGAG

                                             *   *     *        *   
       1016 -TGGTGAAAGGAGAAGGGAGAAGGAGCGAGAGAGGAGTAGGGAGAGAGAAATGGAG
          1 ATGGTGAAAGGAGAAGGGAGAAGGAGCGAGAGAAGAGCAGGGACAGAGAAATCGAG

                                          *       *          *   *  
       1071 A-GG-GAAAGGAGAAGGGAGAAGGAGCGAGGGAAGAGCCGGGACAG-G-GATCTAG
          1 ATGGTGAAAGGAGAAGGGAGAAGGAGCGAGAGAAGAGCAGGGACAGAGAAATCGAG

                                    
       1123 ATGGTGAAAGGAGAAGGGAGAAGG
          1 ATGGTGAAAGGAGAAGGGAGAAGG

       1147 TGCATGATAG


Statistics
Matches: 113,  Mismatches: 13, Indels: 11
        0.82            0.09        0.08

Matches are distributed among these distances:
  52    5  0.04
  53    4  0.04
  54   99  0.88
  55    5  0.04

ACGTcount: A:0.39, C:0.05, G:0.49, T:0.07


Consensus pattern (56 bp):   
ATGGTGAAAGGAGAAGGGAGAAGGAGCGAGAGAAGAGCAGGGACAGAGAAATCGAG
Done.