Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold3049

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, 483

Length: 805
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25


Found at i:136 original size:44 final size:44

Alignment explanation


    Indices: 1--138  Score: 124
    Period size: 44  Copynumber: 3.1  Consensus size: 44

                                                     *  
          1 TTGCCTCTCTCGGTTGTGATAGAGCTGGTTGAAGACAAAAGTTC
          1 TTGCCTCTCTCGGTTGTGATAGAGCTGGTTGAAGACAAAAGATC

                          *    ** * *                 *    * 
         45 TTGCCT-TC-CTGCATTGACAACAAAGCAT--TTCGAAGACACAA-ACC
          1 TTGCCTCTCTC-G-GTTG-TGATAGAGC-TGGTT-GAAGACAAAAGATC

                                                        
         89 TTGCCTCTCTCGGTTGTGATAGAGCTGGTTGAAGACAAAAGATC
          1 TTGCCTCTCTCGGTTGTGATAGAGCTGGTTGAAGACAAAAGATC

                  
        133 TTGCCT
          1 TTGCCT

        139 TCCTGCATTG


Statistics
Matches: 69,  Mismatches: 15, Indels: 20
        0.66            0.14        0.19

Matches are distributed among these distances:
  42    2  0.03
  43   17  0.25
  44   31  0.45
  45   17  0.25
  46    2  0.03

ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29


Consensus pattern (44 bp):   
TTGCCTCTCTCGGTTGTGATAGAGCTGGTTGAAGACAAAAGATC

Found at i:150 original size:88 final size:88

Alignment explanation


    Indices: 1--805  Score: 1081
    Period size: 88  Copynumber: 9.1  Consensus size: 88

                   *            *                    *                     * 
          1 TTGCCTCTCTCGGTTGTGATAGAGCTGGTTGAAGACAAAAGTTCTTGCCTTCCTGCATTGACAAC
          1 TTGCCTCCCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGC

            *     **               
         66 AAAGCATTTCGAAGACACAAACC
         66 GAAGCAGATCGAAGACACAAACC

                   *            *                                            
         89 TTGCCTCTCTCGGTTGTGATAGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGC
          1 TTGCCTCCCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGC

               *                   
        154 GAATCAGATCGAAGACACAAACC
         66 GAAGCAGATCGAAGACACAAACC

             *             *           *   *      *                          
        177 TAGCCTCCCTCGGTTCTGATGGAGCTGATTGTAGACAACAGATCTTGCCTTCCTGCATTGACAGC
          1 TTGCCTCCCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGC

                   * **            
        242 GAAGCAGGTTAAAGACACAAACC
         66 GAAGCAGATCGAAGACACAAACC

                                       *                                     
        265 TTGCCTCCCTCGGTTGTGATGGAGCTGATTGAAGACAAAAGATCTTGCCTTCCTGCATTGACA-C
          1 TTGCCTCCCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGC

                ** *                
        329 GGAATTAAATCGAAGACACAAACC
         66 -GAAGCAGATCGAAGACACAAACC

                       *                          *            *    *        
        353 TTGCCTCCCTCAGTTGTGATGGAGCTGGTTGAAGACAACAGATCTTGCCTTTCTGCTTTGACAGC
          1 TTGCCTCCCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGC

                   *  *            
        418 GAAGCAGGTCAAAGACACAAACC
         66 GAAGCAGATCGAAGACACAAACC

            *                      *                   *          *          
        441 CTGCCTCCCTCGGTTGTGATGGAACTGGTTGAAGACAAAAGATATTGCCTTCCTTCATTGACAGC
          1 TTGCCTCCCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGC

               *                   
        506 GAATCAGATCGAAGACACAAACC
         66 GAAGCAGATCGAAGACACAAACC

                       *   *                      *    *        *           *
        529 TTGCCTCCCTCAGTTCTGATGGAGCTGGTTGAAGACAACAGATATTGCCTTCTTGCATTGACAGG
          1 TTGCCTCCCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGC

                   *  *            
        594 GAAGCAGGTCAAAGACACAAACC
         66 GAAGCAGATCGAAGACACAAACC

                                       **      *                            *
        617 TTGCCTCCCTCGGTTGTGATGGAGCTGACTGAAGATAAAAGATCTTGCCTTCCTGCATTGACAGG
          1 TTGCCTCCCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGC

               ** *                
        682 GAATTAAATCGAAGACACAAACC
         66 GAAGCAGATCGAAGACACAAACC

                       *                          *    *               *     
        705 TTGCCTCCCTCAGTTGTGATGGAGCTGGTTGAAGACAACAGATGTTGCCTTCCTGCATTCACAGC
          1 TTGCCTCCCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGC

                   *  *           *
        770 GAAGCAGGTCAAAGACACAAACA
         66 GAAGCAGATCGAAGACACAAACC

              *    *     
        793 TTTCCTCTCTCGG
          1 TTGCCTCCCTCGG


Statistics
Matches: 626,  Mismatches: 89, Indels: 4
        0.87            0.12        0.01

Matches are distributed among these distances:
  87    1  0.00
  88  624  1.00
  89    1  0.00

ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25


Consensus pattern (88 bp):   
TTGCCTCCCTCGGTTGTGATGGAGCTGGTTGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGC
GAAGCAGATCGAAGACACAAACC

Found at i:303 original size:176 final size:176

Alignment explanation


    Indices: 1--805  Score: 1216
    Period size: 176  Copynumber: 4.6  Consensus size: 176

                   *   *        *                 *  *                     * 
          1 TTGCCTCTCTCGGTTGTGATAGAGCTGGTTGAAGACAAAAGTTCTTGCCTTCCTGCATTGACAAC
          1 TTGCCTCCCTCAGTTGTGATGGAGCTGGTTGAAGACAACAGATCTTGCCTTCCTGCATTGACAGC

            *     **  *                   *            *      *              
         66 AAAGCATTTCGAAGACACAAACCTTGCCTCTCTCGGTTGTGATAGAGCTGGTTGAAGACAAAAGA
         66 GAAGCAGGTCAAAGACACAAACCTTGCCTCCCTCGGTTGTGATGGAGCTGATTGAAGACAAAAGA

                                         *                
        131 TCTTGCCTTCCTGCATTGACAGCGAATCAGATCGAAGACACAAACC
        131 TCTTGCCTTCCTGCATTGACAGCGAATCAAATCGAAGACACAAACC

             *         *   *           *   *                                 
        177 TAGCCTCCCTCGGTTCTGATGGAGCTGATTGTAGACAACAGATCTTGCCTTCCTGCATTGACAGC
          1 TTGCCTCCCTCAGTTGTGATGGAGCTGGTTGAAGACAACAGATCTTGCCTTCCTGCATTGACAGC

                     *                                                       
        242 GAAGCAGGTTAAAGACACAAACCTTGCCTCCCTCGGTTGTGATGGAGCTGATTGAAGACAAAAGA
         66 GAAGCAGGTCAAAGACACAAACCTTGCCTCCCTCGGTTGTGATGGAGCTGATTGAAGACAAAAGA

                                        *                  
        307 TCTTGCCTTCCTGCATTGACA-CGGAATTAAATCGAAGACACAAACC
        131 TCTTGCCTTCCTGCATTGACAGC-GAATCAAATCGAAGACACAAACC

                                                               *    *        
        353 TTGCCTCCCTCAGTTGTGATGGAGCTGGTTGAAGACAACAGATCTTGCCTTTCTGCTTTGACAGC
          1 TTGCCTCCCTCAGTTGTGATGGAGCTGGTTGAAGACAACAGATCTTGCCTTCCTGCATTGACAGC

                                   *                      *   *              
        418 GAAGCAGGTCAAAGACACAAACCCTGCCTCCCTCGGTTGTGATGGAACTGGTTGAAGACAAAAGA
         66 GAAGCAGGTCAAAGACACAAACCTTGCCTCCCTCGGTTGTGATGGAGCTGATTGAAGACAAAAGA

             *          *                *                
        483 TATTGCCTTCCTTCATTGACAGCGAATCAGATCGAAGACACAAACC
        131 TCTTGCCTTCCTGCATTGACAGCGAATCAAATCGAAGACACAAACC

                           *                           *        *           *
        529 TTGCCTCCCTCAGTTCTGATGGAGCTGGTTGAAGACAACAGATATTGCCTTCTTGCATTGACAGG
          1 TTGCCTCCCTCAGTTGTGATGGAGCTGGTTGAAGACAACAGATCTTGCCTTCCTGCATTGACAGC

                                                               *      *      
        594 GAAGCAGGTCAAAGACACAAACCTTGCCTCCCTCGGTTGTGATGGAGCTGACTGAAGATAAAAGA
         66 GAAGCAGGTCAAAGACACAAACCTTGCCTCCCTCGGTTGTGATGGAGCTGATTGAAGACAAAAGA

                                  *    *                  
        659 TCTTGCCTTCCTGCATTGACAGGGAATTAAATCGAAGACACAAACC
        131 TCTTGCCTTCCTGCATTGACAGCGAATCAAATCGAAGACACAAACC

                                                       *               *     
        705 TTGCCTCCCTCAGTTGTGATGGAGCTGGTTGAAGACAACAGATGTTGCCTTCCTGCATTCACAGC
          1 TTGCCTCCCTCAGTTGTGATGGAGCTGGTTGAAGACAACAGATCTTGCCTTCCTGCATTGACAGC

                                  *  *    *     
        770 GAAGCAGGTCAAAGACACAAACATTTCCTCTCTCGG
         66 GAAGCAGGTCAAAGACACAAACCTTGCCTCCCTCGG


Statistics
Matches: 569,  Mismatches: 58, Indels: 4
        0.90            0.09        0.01

Matches are distributed among these distances:
 175    1  0.00
 176  567  1.00
 177    1  0.00

ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25


Consensus pattern (176 bp):   
TTGCCTCCCTCAGTTGTGATGGAGCTGGTTGAAGACAACAGATCTTGCCTTCCTGCATTGACAGC
GAAGCAGGTCAAAGACACAAACCTTGCCTCCCTCGGTTGTGATGGAGCTGATTGAAGACAAAAGA
TCTTGCCTTCCTGCATTGACAGCGAATCAAATCGAAGACACAAACC

Done.