Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_4285

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: 15279
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.29


Found at i:7229 original size:47 final size:46

Alignment explanation


    Indices: 7070--7382  Score: 167
    Period size: 47  Copynumber: 6.7  Consensus size: 46

       7060 TGGATATTCG

                *        *   *          *  *    * *       
       7070 GCCAATGTAAGACGTGTTTGGGACATGCTTCGGCCACATTATGAGA
          1 GCCAGTGTAAGACATGTCTGGGACATGCATCAGCCATACTATGAGA

              *                    **                  * *  
       7116 GCTAGTGTAAGACCATGTCTGGGGTATGGCATCAG-CAT-CTAGGCGA
          1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCCATACTATGAGA

                *          *                              * 
       7162 GGACTAGTGTAAGACTTGTCTGGGACATGCATCAGCCATACTATGATA
          1 -G-CCAGTGTAAGACATGTCTGGGACATGCATCAGCCATACTATGAGA

                                            *                  
       7210 GCCAGTGTAAGACCATGTCTGGGACATGCATCGGCC-TCGAC-A-GAGATA
          1 GCCAGTGTAAGA-CATGTCTGGGACATGCATCAGCCAT--ACTATGAG--A

                         *   *             * *    **    * *
       7258 GCCAGTGTAAGACGTGTTTGGGACATGCAT-TGGC-TAAGA-GTTGT
          1 GCCAGTGTAAGACATGTCTGGGACATGCATCAGCCATACTATG-AGA

              * *   *                             *          
       7302 GCTACTGTGAGACATGTCTGGGACATGCATCAGCACGCGTA-TATGAGA
          1 GCCAGTGTAAGACATGTCTGGGACATGCATCAG--C-CATACTATGAGA

            *                                
       7350 CCCAGTGTAAGACCATGTCTGGGACATGGCATC
          1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATC

       7383 GACAATATAT


Statistics
Matches: 203,  Mismatches: 43, Indels: 38
        0.71            0.15        0.13

Matches are distributed among these distances:
  44   26  0.13
  45    3  0.01
  46   39  0.19
  47   66  0.33
  48   47  0.23
  49   17  0.08
  50    5  0.02

ACGTcount: A:0.26, C:0.20, G:0.29, T:0.24


Consensus pattern (46 bp):   
GCCAGTGTAAGACATGTCTGGGACATGCATCAGCCATACTATGAGA

Found at i:7265 original size:94 final size:94

Alignment explanation


    Indices: 7070--7287  Score: 244
    Period size: 94  Copynumber: 2.3  Consensus size: 94

       7060 TGGATATTCG

                *                       *  *      *         *                
       7070 GCCAATGTAAGACGTGTTTGGGACATGCTTCGGCCACATTATGAGAGCTAGTGTAAGACCATGTC
          1 GCCAGTGTAAGACGTGTTTGGGACATGCATCAGCCACACTATGAGAGCCAGTGTAAGACCATGTC

                **                 *      
       7135 TGGGGTATGGCATCAGCATCTAGGCGAGGA
         66 TGGGACATGGCATCAGCA-CTAGACGAGGA

              *          *   *                  *       *                    
       7165 -CTAGTGTAAGACTTGTCTGGGACATGCATCAGCCATACTATGATAGCCAGTGTAAGACCATGTC
          1 GCCAGTGTAAGACGTGTTTGGGACATGCATCAGCCACACTATGAGAGCCAGTGTAAGACCATGTC

                          *     *        * 
       7229 TGGGACAT-GCATCGGC-CTCGACAGAGATA
         66 TGGGACATGGCATCAGCACTAGAC-GAG-GA

                                          
       7258 GCCAGTGTAAGACGTGTTTGGGACATGCAT
          1 GCCAGTGTAAGACGTGTTTGGGACATGCAT

       7288 TGGCTAAGAG


Statistics
Matches: 101,  Mismatches: 19, Indels: 7
        0.80            0.15        0.06

Matches are distributed among these distances:
  91    4  0.04
  92    3  0.03
  93    8  0.08
  94   86  0.85

ACGTcount: A:0.26, C:0.20, G:0.29, T:0.24


Consensus pattern (94 bp):   
GCCAGTGTAAGACGTGTTTGGGACATGCATCAGCCACACTATGAGAGCCAGTGTAAGACCATGTC
TGGGACATGGCATCAGCACTAGACGAGGA
Done.