Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_A_19736

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: 3093
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28


Found at i:735 original size:54 final size:51

Alignment explanation


    Indices: 537--847  Score: 331
    Period size: 51  Copynumber: 6.0  Consensus size: 51

        527 ATCTTTTTCA

                 *     *   *  *      *    *      *            *
        537 GGAAATTGTATTGAGCAAACCATCTAAGAAGTTACTCTCCAAGGAGAAAAC
          1 GGAAACTGTATCGAGGAAGCCATCTGAGAAATTACTCCCCAAGGAGAAAAT

                 *                      **       *             
        588 GGAAATTGTATC---GAAGCCATCTGAGGGATTACTCTCCAAGGAGAAAAT
          1 GGAAACTGTATCGAGGAAGCCATCTGAGAAATTACTCCCCAAGGAGAAAAT

                 *  *  *       *                  *            
        636 GGAAATTGAATGGAGGAAGTCATCTGAGAAATTACTCCACAAGGAGAAAAT
          1 GGAAACTGTATCGAGGAAGCCATCTGAGAAATTACTCCCCAAGGAGAAAAT

                  *                      *                        
        687 GGAAACCGTATCGAGGAAGAAACCATCTGGGAAATTACTCCCCAAGGAGAAAAT
          1 GGAAACTGTATCGAGGAAG---CCATCTGAGAAATTACTCCCCAAGGAGAAAAT

                                     *           *                
        741 GGAAACTGTATCGAGGAAGAAGCCAACTGAGAAATTAATCCCCAAGGAGAAAAT
          1 GGAAACTGTATCGA-G--GAAGCCATCTGAGAAATTACTCCCCAAGGAGAAAAT

                   *    *                                *     
        795 GGAAACTATATCAAGGAAGCCATCTGAGAAATTACTCCCCAAGGAAAAAAT
          1 GGAAACTGTATCGAGGAAGCCATCTGAGAAATTACTCCCCAAGGAGAAAAT

              
        846 GG
          1 GG

        848 TTGGGGAGTC


Statistics
Matches: 220,  Mismatches: 31, Indels: 18
        0.82            0.12        0.07

Matches are distributed among these distances:
  48   39  0.18
  51   92  0.42
  53    1  0.00
  54   83  0.38
  55    1  0.00
  57    4  0.02

ACGTcount: A:0.41, C:0.17, G:0.23, T:0.18


Consensus pattern (51 bp):   
GGAAACTGTATCGAGGAAGCCATCTGAGAAATTACTCCCCAAGGAGAAAAT

Found at i:757 original size:105 final size:104

Alignment explanation


    Indices: 600--847  Score: 311
    Period size: 105  Copynumber: 2.4  Consensus size: 104

        590 AAATTGTATC

                         **       *                  *     *         *  *    
        600 GAAGCCATCTGAGGGATTACTCTCCAAGGAGAAAATGGAAATTGAATGGA-G-GAAGTCATCTGA
          1 GAAGCCATCTGAGAAATTACTCCCCAAGGAGAAAATGGAAACTGAATCGAGGAGAAGCCAACTGA

                   *                       *    *  
        663 GAAATTACTCCACAAGGAGAAAATGGAAACCGTATCGAG
         66 GAAATTAATCCACAAGGAGAAAATGGAAACCATATCAAG

                          *                                *                 
        702 GAAGAAACCATCTGGGAAATTACTCCCCAAGGAGAAAATGGAAACTGTATCGAGGAAGAAGCCAA
          1 GAAG---CCATCTGAGAAATTACTCCCCAAGGAGAAAATGGAAACTGAATCGAGG-AGAAGCCAA

                           *                  *        
        767 CTGAGAAATTAATCCCCAAGGAGAAAATGGAAACTATATCAAG
         62 CTGAGAAATTAATCCACAAGGAGAAAATGGAAACCATATCAAG

                                          *       
        810 GAAGCCATCTGAGAAATTACTCCCCAAGGAAAAAATGG
          1 GAAGCCATCTGAGAAATTACTCCCCAAGGAGAAAATGG

        848 TTGGGGAGTC


Statistics
Matches: 124,  Mismatches: 16, Indels: 9
        0.83            0.11        0.06

Matches are distributed among these distances:
 102    4  0.03
 105   71  0.57
 106    1  0.01
 108   48  0.39

ACGTcount: A:0.42, C:0.17, G:0.24, T:0.17


Consensus pattern (104 bp):   
GAAGCCATCTGAGAAATTACTCCCCAAGGAGAAAATGGAAACTGAATCGAGGAGAAGCCAACTGA
GAAATTAATCCACAAGGAGAAAATGGAAACCATATCAAG
Done.