Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Cotton_D_gene_10019269

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, 462

Length: 771
ACGTcount: A:0.28, C:0.15, G:0.34, T:0.23


Found at i:170 original size:42 final size:42

Alignment explanation


    Indices: 104--246  Score: 173
    Period size: 42  Copynumber: 3.4  Consensus size: 42

         94 GTATATGGCC

                           *   *                   *  
        104 TTGGATATGGCATTGAAGATGGGAACCAGTTAGGTACAGCCA
          1 TTGGATATGGCATTGGAGAAGGGAACCAGTTAGGTACAGGCA

                                         *            
        146 TTGGATATGGCATTGGAGAAGGGAACCAGGTAGGTACAGGCA
          1 TTGGATATGGCATTGGAGAAGGGAACCAGTTAGGTACAGGCA

                 *                              * **    
        188 TTGGAAATGGCA-TGG-GAAGTGGGAACCAGTTAGGAATGGGCA
          1 TTGGATATGGCATTGGAGAA--GGGAACCAGTTAGGTACAGGCA

                *            
        230 TTGGGTATGGCATTGGA
          1 TTGGATATGGCATTGGA

        247 AATGGGGGTC


Statistics
Matches: 86,  Mismatches: 11, Indels: 6
        0.83            0.11        0.06

Matches are distributed among these distances:
  40    3  0.03
  41    3  0.03
  42   77  0.90
  43    3  0.03

ACGTcount: A:0.29, C:0.11, G:0.37, T:0.22


Consensus pattern (42 bp):   
TTGGATATGGCATTGGAGAAGGGAACCAGTTAGGTACAGGCA

Found at i:265 original size:42 final size:42

Alignment explanation


    Indices: 218--342  Score: 103
    Period size: 42  Copynumber: 3.0  Consensus size: 42

        208 GGGAACCAGT

                                                      
        218 TAGGAATGGGCATTGGGTATGGCATTGGAAATGGGGGTCA-A
          1 TAGGAATGGGCATTGGGTATGGCATTGGAAATGGGGGTCAGA

                      *          *   *  *       * ***    
        259 TCAGGAAAT-AGCA-TGGGATTTGGTATCGGAAATGCGAACCAGA
          1 T-AGG-AATGGGCATTGGG-TATGGCATTGGAAATGGGGGTCAGA

             *        *  *                           
        302 TGGGAATGGGTATCGGGTATGGCATTGGAAATGGGGGTCAG
          1 TAGGAATGGGCATTGGGTATGGCATTGGAAATGGGGGTCAG

        343 GCCGGAAATA


Statistics
Matches: 59,  Mismatches: 19, Indels: 11
        0.66            0.21        0.12

Matches are distributed among these distances:
  41    8  0.14
  42   43  0.73
  43    8  0.14

ACGTcount: A:0.28, C:0.10, G:0.39, T:0.23


Consensus pattern (42 bp):   
TAGGAATGGGCATTGGGTATGGCATTGGAAATGGGGGTCAGA

Found at i:429 original size:42 final size:42

Alignment explanation


    Indices: 370--473  Score: 163
    Period size: 42  Copynumber: 2.5  Consensus size: 42

        360 ATATGGCATA

                    *                          *      
        370 GGATATGGCACTGGAAATGGGAACCAGTTAGGAACTGGTATT
          1 GGATATGGTACTGGAAATGGGAACCAGTTAGGAACCGGTATT

                      *                               
        412 GGATATGGTATTGGAAATGGGAACCAGTTAGGAACCGGTATT
          1 GGATATGGTACTGGAAATGGGAACCAGTTAGGAACCGGTATT

                *      *        
        454 GGATTTGGTACCGGAAATGG
          1 GGATATGGTACTGGAAATGG

        474 AGGTCAGTCA


Statistics
Matches: 56,  Mismatches: 6, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  42   56  1.00

ACGTcount: A:0.30, C:0.11, G:0.35, T:0.25


Consensus pattern (42 bp):   
GGATATGGTACTGGAAATGGGAACCAGTTAGGAACCGGTATT

Done.