Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: CotAD_47067

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, 289

Length: 483
ACGTcount: A:0.28, C:0.29, G:0.25, T:0.18


Found at i:137 original size:39 final size:39

Alignment explanation


    Indices: 80--365  Score: 308
    Period size: 39  Copynumber: 7.3  Consensus size: 39

         70 AACCACGATA

                         *     *      *     *    * 
         80 ATGAGCCACCACAACACCCTGGACCTAGTGGTTGGGGGG
          1 ATGAGCCACCACACCACCCCGGACCTGGTGGTAGGGGAG

                               * *    *             
        119 ATGAGCCACCACACCACCCTGAACCTAGTGGTATGGGGA-
          1 ATGAGCCACCACACCACCCCGGACCTGGTGGTA-GGGGAG

                *        *                *    *   
        158 ATGAACCACCACATCACCCCGGACCTGGTGATAGGAGAG
          1 ATGAGCCACCACACCACCCCGGACCTGGTGGTAGGGGAG

                                       *             
        197 A-GAAGCCACCACACCACCCCGGACCTAGTGGTATGGGG-G
          1 ATG-AGCCACCACACCACCCCGGACCTGGTGGTA-GGGGAG

                         *                    *    
        236 ATGAGCCACCACATCACCCCGGACCTGGTGGTAGAGGAG
          1 ATGAGCCACCACACCACCCCGGACCTGGTGGTAGGGGAG

             *                 *              *    
        275 AGGAGCCACCACACCACCCAGGACCTGGTGGTAGTGGAG
          1 ATGAGCCACCACACCACCCCGGACCTGGTGGTAGGGGAG

             *                 *           *    *  
        314 AGGAGCCACCACACCACCCTGGACCTGGTGGCAGGGAAG
          1 ATGAGCCACCACACCACCCCGGACCTGGTGGTAGGGGAG

             *  *        
        353 AGGAACCACCACA
          1 ATGAGCCACCACA

        366 TGGGAAAAAA


Statistics
Matches: 213,  Mismatches: 28, Indels: 12
        0.84            0.11        0.05

Matches are distributed among these distances:
  38    8  0.04
  39  197  0.92
  40    8  0.04

ACGTcount: A:0.27, C:0.31, G:0.30, T:0.12


Consensus pattern (39 bp):   
ATGAGCCACCACACCACCCCGGACCTGGTGGTAGGGGAG

Found at i:293 original size:117 final size:117

Alignment explanation


    Indices: 83--344  Score: 350
    Period size: 117  Copynumber: 2.2  Consensus size: 117

         73 CACGATAATG

                      *                                            *         
         83 AGCCACCACAACACCCTGGACCTAGTGGTTGGGGGGATGAGCCACCACACCACCCTGAACCTAGT
          1 AGCCACCACACCACCCTGGACCTAGTGGTTGGGGGGATGAGCCACCACACCACCCCGAACCTAGT

                  *    *           *     *                       
        148 GGTATGGGGAATGAACCACCACATCACCCCGGACCTGGTGATAG-GAGAGAGA
         66 GGTATGAGGAAGGAACCACCACACCACCCAGGACCTGGTGATAGTG-GAGAGA

                            *                                 *       *    * 
        200 AGCCACCACACCACCCCGGACCTAGTGGTAT-GGGGGATGAGCCACCACATCACCCCGGACCTGG
          1 AGCCACCACACCACCCTGGACCTAGTGGT-TGGGGGGATGAGCCACCACACCACCCCGAACCTAG

                            *                         *          *
        264 TGGTA-GAGGAGAGGAGCCACCACACCACCCAGGACCTGGTGGTAGTGGAGAGG
         65 TGGTATGAGGA-AGGAACCACCACACCACCCAGGACCTGGTGATAGTGGAGAGA

                                   *    
        317 AGCCACCACACCACCCTGGACCTGGTGG
          1 AGCCACCACACCACCCTGGACCTAGTGG

        345 CAGGGAAGAG


Statistics
Matches: 127,  Mismatches: 15, Indels: 6
        0.86            0.10        0.04

Matches are distributed among these distances:
 116    4  0.03
 117  121  0.95
 118    2  0.02

ACGTcount: A:0.26, C:0.32, G:0.30, T:0.12


Consensus pattern (117 bp):   
AGCCACCACACCACCCTGGACCTAGTGGTTGGGGGGATGAGCCACCACACCACCCCGAACCTAGT
GGTATGAGGAAGGAACCACCACACCACCCAGGACCTGGTGATAGTGGAGAGA

Done.