Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold982

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: 3629
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.31


Found at i:556 original size:44 final size:43

Alignment explanation


    Indices: 503--1136  Score: 240
    Period size: 44  Copynumber: 14.7  Consensus size: 43

        493 CTTAGTTTAT

                      *            *                      
        503 TCCATTGCAATTTCAGGGAGATAGGATTAT-CAGCT-TTAATCTGC
          1 TCCATTGCAACTTCAGGGAGATAAGATT-TGC--CTATTAATCTGC

              *            * *                    *     
        547 TCTATTGCAACTTCAAGAAGATAAGATTTGCCTACTTAGTCTGC
          1 TCCATTGCAACTTCAGGGAGATAAGATTTGCCTA-TTAATCTGC

                                      * *       *     * 
        591 TCCATTGCAACTTCAGGGAGATAAGACTAG---ATGCAATCTAC
          1 TCCATTGCAACTTCAGGGAGATAAGATTTGCCTAT-TAATCTGC

                             *                * *      *  
        632 T-C-TCTGCAACTTCAGAGAGATAAGATCTGTG-ATTTTAATCCGC
          1 TCCAT-TGCAACTTCAGGGAGATAAGAT-T-TGCCTATTAATCTGC

               **                   *        *          * 
        675 TCCCCTGCAACTTCAAGGG-GATAGGATTATCGGCT-TTAATCTAC
          1 TCCATTGCAACTTC-AGGGAGATAAGATT-T-GCCTATTAATCTGC

                *               *             *    *     
        719 TCCACTGCAACTTCAGGGAGGTAAGATTTGCCATCTTCAGTCTGC
          1 TCCATTGCAACTTCAGGGAGATAAGATTTGCC-TATT-AATCTGC

                 *  *     *             *    *      *     
        764 -CTCACTGGAACTTTA-GGAGGATAAGACTTGCTTACTTAGTCTGC
          1 TC-CATTGCAACTTCAGGGA-GATAAGATTTGCCTA-TTAATCTGC

                                      * *       ** *    
        808 TCCATTGCAACTTCAGGGAGATAAGACTAG---ATGCGACCTGC
          1 TCCATTGCAACTTCAGGGAGATAAGATTTGCCTAT-TAATCTGC

                             *                * *      *  
        849 T-C-TCTGCAACTTCAGAGAGATAAGATCTGTG-ATTTTAATCCGC
          1 TCCAT-TGCAACTTCAGGGAGATAAGAT-T-TGCCTATTAATCTGC

                *                  *        *            
        892 TCCACTGCAACTTCAGGGAGATAGGATTATTGGCT-TTAATCTGC
          1 TCCATTGCAACTTCAGGGAGATAAGA-T-TTGCCTATTAATCTGC

                *                           * *    *     
        936 TCCACTGCAACTTCAGGGAGATAAGATTTGTCATCTTCAGTCTGC
          1 TCCATTGCAACTTCAGGGAGATAAGATTTG-CCTATT-AATCTGC

                 *                      *  * *      **    
        981 -CTCACTGCAACTTCA-GGAGGATAAGACTTACTTACTTAGCCTGC
          1 TC-CATTGCAACTTCAGGGA-GATAAGATTTGCCTA-TTAATCTGC

                *                     * *  *  ***      
       1025 TCCACTGCAACTTCAGGGAGATAAGACTAG-GT-GCGATCTGC
          1 TCCATTGCAACTTCAGGGAGATAAGATTTGCCTATTAATCTGC

                             *                * *   * *   
       1066 T-C-TCTGCAACTTCAGAGAGATAAGATCTGTG-ATTTTAGTTTGC
          1 TCCAT-TGCAACTTCAGGGAGATAAGAT-T-TGCCTATTAATCTGC

                *                       
       1109 TCCACTGCAACTTCAGGGAGATAAGATT
          1 TCCATTGCAACTTCAGGGAGATAAGATT

       1137 ATCGACTACG


Statistics
Matches: 452,  Mismatches: 91, Indels: 95
        0.71            0.14        0.15

Matches are distributed among these distances:
  39    2  0.00
  40   65  0.14
  41   21  0.05
  42   11  0.02
  43   29  0.06
  44  251  0.56
  45   73  0.16

ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30


Consensus pattern (43 bp):   
TCCATTGCAACTTCAGGGAGATAAGATTTGCCTATTAATCTGC

Found at i:941 original size:217 final size:217

Alignment explanation


    Indices: 552--1140  Score: 964
    Period size: 217  Copynumber: 2.7  Consensus size: 217

        542 TCTGCTCTAT

                      *  *       *    *                                      
        552 TGCAACTTCAAGAAGATAAGATTTGCCTACTTAGTCTGCTCCATTGCAACTTCAGGGAGATAAGA
          1 TGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCATTGCAACTTCAGGGAGATAAGA

                    *    *                                               *   
        617 CTAGATGCAATCTACTCTCTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCCGCTCCCCTG
         66 CTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCCGCTCCACTG

                                                                      *      
        682 CAACTTCAAGGG-GATAGGATTATCGGCTTTAATCTACTCCACTGCAACTTCAGGGAGGTAAGAT
        131 CAACTTC-AGGGAGATAGGATTATCGGCTTTAATCTACTCCACTGCAACTTCAGGGAGATAAGAT

                                   
        746 TTGCCATCTTCAGTCTGCCTCAC
        195 TTGCCATCTTCAGTCTGCCTCAC

              *     *                                                        
        769 TGGAACTTTAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCATTGCAACTTCAGGGAGATAAGA
          1 TGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCATTGCAACTTCAGGGAGATAAGA

                      *                                                      
        834 CTAGATGCGACCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCCGCTCCACTG
         66 CTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCCGCTCCACTG

                                   *           *                             
        899 CAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT
        131 CAACTTCAGGGAGATAGGATTATCGGCTTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATT

              *                   
        964 TGTCATCTTCAGTCTGCCTCAC
        196 TGCCATCTTCAGTCTGCCTCAC

                                    *         *        *                     
        986 TGCAACTTCAGGAGGATAAGACTTACTTACTTAGCCTGCTCCACTGCAACTTCAGGGAGATAAGA
          1 TGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCATTGCAACTTCAGGGAGATAAGA

                *                                               * **         
       1051 CTAGGTGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGTGATTTTAGTTTGCTCCACTG
         66 CTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCCGCTCCACTG

                            *        
       1116 CAACTTCAGGGAGATAAGATTATCG
        131 CAACTTCAGGGAGATAGGATTATCG

       1141 ACTACGGATT


Statistics
Matches: 345,  Mismatches: 26, Indels: 2
        0.92            0.07        0.01

Matches are distributed among these distances:
 216    4  0.01
 217  341  0.99

ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29


Consensus pattern (217 bp):   
TGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCATTGCAACTTCAGGGAGATAAGA
CTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCCGCTCCACTG
CAACTTCAGGGAGATAGGATTATCGGCTTTAATCTACTCCACTGCAACTTCAGGGAGATAAGATT
TGCCATCTTCAGTCTGCCTCAC
Done.