Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold1899

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, 730

Length: 1217
ACGTcount: A:0.18, C:0.19, G:0.11, T:0.17

Warning! 427 characters in sequence are not A, C, G, or T


Found at i:68 original size:46 final size:46

Alignment explanation


    Indices: 1--322  Score: 414
    Period size: 46  Copynumber: 7.0  Consensus size: 46

                                  *          *       *    
          1 GCCAAATACAGGAAGACAAGATTTGCTATCTTCTATCCCCTTCGCT
          1 GCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCT

                     * *             *   *  *         *   
         47 GCCAAATACCGAAAGACAAGATCTGATATTTTTGATCCCCTCTGCT
          1 GCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCT

                            *                    * *      
         93 GCCAAATACAGGAAGATAAGATCTGCTATCTTCGATCGCGTCCGCT
          1 GCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCT

                          *                               
        139 -CCAAATACAGGAACACAAGATCTGCTATCTTCGAT-CCCTCCGCT
          1 GCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCT

                    *       * *      *                    
        183 GCCAAATATAGGAAGAGAGGATCTGATATCTTCGATCCCCTCCGCT
          1 GCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCT

                                   *        **     * *  * 
        229 GCCAAATACAGGAAGACAAGATCAGCTATCTTTTATCCCTTTCGTT
          1 GCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCT

                   *                                      
        275 GCCAAATTCAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCT
          1 GCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCT

              
        321 GC
          1 GC

        323 NNNNNNNNNN


Statistics
Matches: 230,  Mismatches: 44, Indels: 4
        0.83            0.16        0.01

Matches are distributed among these distances:
  44    7  0.03
  45   63  0.27
  46  160  0.70

ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26


Consensus pattern (46 bp):   
GCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCCTCCGCT

Found at i:877 original size:46 final size:46

Alignment explanation


    Indices: 750--1217  Score: 618
    Period size: 46  Copynumber: 10.2  Consensus size: 46

        740 NNNNNNNNNN

                                                           
        750 TCCGCTGCCAAATACAGGAAGACAAGATCTGCTATC-TCTGATCCCC
          1 TCCGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTC-GATCCCC

             *      *           *   *   *              *  
        796 TTCGCTG-TAAATACAGGAAAACATGATATGCTATCTTCGATCTCC
          1 TCCGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCC

             *    *            *           *              
        841 TTCGCTACCAAATACAGGATGACAAGATCTGATATCTTCGATCCCC
          1 TCCGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCC

                                     *       *          * *
        887 TCCGCTGCCAAATACAGGAAGACAATATCTGCTGTCTGT-GATCTCT
          1 TCCGCTGCCAAATACAGGAAGACAAGATCTGCTATCT-TCGATCCCC

                                                   *      
        933 TCCGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCAATCCCC
          1 TCCGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCC

                  *      *         **                     
        979 TCCGCTCCCAAATTCAGGAAGACCTGATCTGCTATCTTCGATCCCC
          1 TCCGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCC

                 *             *           *             *
       1025 TCCGCGGCCAAATACAGGATGACAAGATCTGATATCTTCGATCCCT
          1 TCCGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCC

             *           *                         *      
       1071 TTCGCTGCCAAATTCAGGAAGACAAGATCTGCTATCTTCTATCCCC
          1 TCCGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCC

                            *                      *      
       1117 TCCGCTGCCAAATACAAGAAGACAAGATCTGCTATCTTCAATCCCC
          1 TCCGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCC

                  *      *          *                     
       1163 TCCGCTCCCAAATTCAGGAAGACATGATCTGCTATCTTCGATCCCC
          1 TCCGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCC

                     
       1209 TCCGCTGCC
          1 TCCGCTGCC


Statistics
Matches: 361,  Mismatches: 57, Indels: 8
        0.85            0.13        0.02

Matches are distributed among these distances:
  45   37  0.10
  46  323  0.89
  47    1  0.00

ACGTcount: A:0.27, C:0.31, G:0.16, T:0.25


Consensus pattern (46 bp):   
TCCGCTGCCAAATACAGGAAGACAAGATCTGCTATCTTCGATCCCC

Done.