Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_3399

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: 18864
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31


Found at i:659 original size:40 final size:40

Alignment explanation


    Indices: 529--675  Score: 149
    Period size: 39  Copynumber: 3.8  Consensus size: 40

        519 ATGAAAACGC

                                *  ** *   *     *   
        529 GGCTAAGTCCCGAAGGC-ATCTGCACTAGTGACTAATCCG
          1 GGCTAAGTCCCGAAGGCAATTTGTGCGAGTTACTAAACCG

            *          *                         *  
        568 AGCTAAGTCCCAAAGGCAA-TTGTGCGAGTTACTAAATCG
          1 GGCTAAGTCCCGAAGGCAATTTGTGCGAGTTACTAAACCG

                                               *     
        607 GGCTAAGTCCCG-AGGCAATTTGTGCGAGTTACTCTAACCG
          1 GGCTAAGTCCCGAAGGCAATTTGTGCGAGTTACT-AAACCG

                 *                 *      
        647 GGCTATGTCCCGAAGGC-ATTTGAGCGAGT
          1 GGCTAAGTCCCGAAGGCAATTTGTGCGAGT

        676 AGTTATATCG


Statistics
Matches: 89,  Mismatches: 15, Indels: 7
        0.80            0.14        0.06

Matches are distributed among these distances:
  38    6  0.07
  39   52  0.58
  40   27  0.30
  41    4  0.04

ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23


Consensus pattern (40 bp):   
GGCTAAGTCCCGAAGGCAATTTGTGCGAGTTACTAAACCG

Found at i:9003 original size:13 final size:13

Alignment explanation


    Indices: 8985--9030  Score: 85
    Period size: 13  Copynumber: 3.6  Consensus size: 13

       8975 CTTAGCACAT

                         
       8985 GCCCGTGTCTATA
          1 GCCCGTGTCTATA

                         
       8998 GCCCGTGTCTATA
          1 GCCCGTGTCTATA

                         
       9011 GCCCGTGTCTAT-
          1 GCCCGTGTCTATA

                    
       9023 GCCCGTGT
          1 GCCCGTGT

       9031 ATAAAAACCT


Statistics
Matches: 33,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  12    8  0.24
  13   25  0.76

ACGTcount: A:0.11, C:0.33, G:0.26, T:0.30


Consensus pattern (13 bp):   
GCCCGTGTCTATA

Found at i:15745 original size:47 final size:48

Alignment explanation


    Indices: 15588--15858  Score: 305
    Period size: 48  Copynumber: 5.6  Consensus size: 48

      15578 AGGGTAAGAT

                   *        *        *      *             *  
      15588 GCCGATGTCATGCTCCAAG-CATGGCCTTACAGTAGCCCACATATCGAG
          1 GCCGATGCCATG-TCCCAGACATGGTCTTACACTAGCCCACATATCAAG

                    *                                       
      15636 GCCGATGCAATGTCCCAGACATGGTCTTACACTAGCCCACATATCAAG
          1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCCCACATATCAAG

               *                                            
      15684 GCCAATGCCATGTCCCAGACATGGTCTTACACTAGCCCA-ATATCAAG
          1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCCCACATATCAAG

                                             *  * *     *  *
      15731 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATAAAT
          1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCCCACATATCAAG

            *            *   *    *          *       *   * * *
      15779 ACCGATG-CATGTTCCAAACATAGTCTTACACTGGCTCTCATATACCGAT
          1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGC-C-CACATATCAAG

                                           
      15828 GCCGATGCCATGTCCCAGACATGGTCTTACA
          1 GCCGATGCCATGTCCCAGACATGGTCTTACA

      15859 ATGGCTCACA


Statistics
Matches: 190,  Mismatches: 28, Indels: 8
        0.84            0.12        0.04

Matches are distributed among these distances:
  47   73  0.38
  48   85  0.45
  49   12  0.06
  50   20  0.11

ACGTcount: A:0.27, C:0.31, G:0.19, T:0.24


Consensus pattern (48 bp):   
GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCCCACATATCAAG

Found at i:15774 original size:95 final size:95

Alignment explanation


    Indices: 15602--15870  Score: 324
    Period size: 95  Copynumber: 2.8  Consensus size: 95

      15592 ATGTCATGCT

                *     *      *                        *                      
      15602 CCAAGCATGGCCTTACAGTAGCCCACATATCGAGGCCGATGCAATGTCCCAGACATGGTCTTACA
          1 CCAAACATGGTCTTACACTAGCCCACATATCGAGGCCGATGCCATGTCCCAGACATGGTCTTACA

              *  *       *   *             
      15667 CTAGCCCACATATCAAGGCCAATGCCATGTC
         66 CTGGCTCACATATAAAGACCAATG-CATGTC

               *                           *                                 
      15698 CCAGACATGGTCTTACACTAGCCCA-ATATCAAGGCCGATGCCATGTCCCAGACATGGTCTTACA
          1 CCAAACATGGTCTTACACTAGCCCACATATCGAGGCCGATGCCATGTCCCAGACATGGTCTTACA

                   *        *   *        *
      15762 CTGGCTCTCATATAAATACCGATGCATGTT
         66 CTGGCTCACATATAAAGACCAATGCATGTC

                    *          *       *   *   *                             
      15792 CCAAACATAGTCTTACACTGGCTCTCATATACCGATGCCGATGCCATGTCCCAGACATGGTCTTA
          1 CCAAACATGGTCTTACACTAGC-C-CACATATCGAGGCCGATGCCATGTCCCAGACATGGTCTTA

              *           
      15857 CAATGGCTCACATA
         64 CACTGGCTCACATA

      15871 ACCCTAGTAT


Statistics
Matches: 148,  Mismatches: 22, Indels: 5
        0.85            0.13        0.03

Matches are distributed among these distances:
  94   24  0.16
  95   55  0.37
  96   23  0.16
  97   46  0.31

ACGTcount: A:0.28, C:0.30, G:0.18, T:0.23


Consensus pattern (95 bp):   
CCAAACATGGTCTTACACTAGCCCACATATCGAGGCCGATGCCATGTCCCAGACATGGTCTTACA
CTGGCTCACATATAAAGACCAATGCATGTC
Done.