Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3294

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: 13048
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.31


Found at i:2752 original size:39 final size:40

Alignment explanation


    Indices: 2663--2872  Score: 269
    Period size: 37  Copynumber: 5.5  Consensus size: 40

       2653 TGGATGATAA

                                                    
       2663 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATTT
          1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATTT

            *                                       
       2703 TCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-TATTT
          1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATTT

                                             *      
       2742 CCGGGCTAAGTCCCGAAGGCA-TTGTGCGAGTTGCTATTT
          1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATTT

                                                  **
       2781 --GGGCTAAGTCCCGAAGGCA-TTGTGCGAGTTACTATAA
          1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATTT

                               *     *             * 
       2818 CCGGGCTAAGT-CCGAA-GAATTTGAGCGAG-TAGCTATAT
          1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATTT

                      *        
       2856 CC-GGCTAA-ACCCGAAGG
          1 CCGGGCTAAGTCCCGAAGG

       2873 TACTTGGTTG


Statistics
Matches: 153,  Mismatches: 10, Indels: 16
        0.85            0.06        0.09

Matches are distributed among these distances:
  37   49  0.32
  38   32  0.21
  39   39  0.25
  40   33  0.22

ACGTcount: A:0.23, C:0.21, G:0.29, T:0.26


Consensus pattern (40 bp):   
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATTT

Found at i:2822 original size:76 final size:79

Alignment explanation


    Indices: 2659--2847  Score: 282
    Period size: 76  Copynumber: 2.5  Consensus size: 79

       2649 TACTTGGATG

                                                                             
       2659 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATTTTCGGGCTAAGTCCCGAAGGCA
          1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATTTTCGGGCTAAGTCCCGAAGGCA

                          
       2724 TTTGTGCGAGTTAT
         66 TTTGTGCGAGTTAT

              **                                 *                           
       2738 ATTTCCGGGCTAAGTCCCGAAGGCA-TTGTGCGAGTTGCTA-TTT-GGGCTAAGTCCCGAAGGCA
          1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATTTTCGGGCTAAGTCCCGAAGGCA

                           
       2800 -TTGTGCGAGTTACT
         66 TTTGTGCGAGTTA-T

                                   *     *      
       2814 ATAACCGGGCTAAGT-CCGAA-GAATTTGAGCGAGT
          1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT

       2848 AGCTATATCC


Statistics
Matches: 101,  Mismatches: 7, Indels: 8
        0.87            0.06        0.07

Matches are distributed among these distances:
  74    2  0.02
  75   26  0.26
  76   33  0.33
  77    3  0.03
  78   14  0.14
  79   23  0.23

ACGTcount: A:0.23, C:0.20, G:0.29, T:0.28


Consensus pattern (79 bp):   
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATTTTCGGGCTAAGTCCCGAAGGCA
TTTGTGCGAGTTAT

Found at i:2862 original size:76 final size:77

Alignment explanation


    Indices: 2659--2872  Score: 269
    Period size: 76  Copynumber: 2.8  Consensus size: 77

       2649 TACTTGGATG

                                                                             
       2659 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATTTTCGGGCTAAGTCCCGAAGGC
          1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TAGCTA--TTCGGGCTAAGTCCCGAAGGC

                           
       2723 ATTTGTGCGAGTTAT
         63 ATTTGTGCGAGTTAT

              **                                *      *                     
       2738 ATTTCCGGGCTAAGTCCCGAAGGCA-TTGTGCGAGTTGCTATTTGGGCTAAGTCCCGAAGGCA-T
          1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGCTATTCGGGCTAAGTCCCGAAGGCATT

                         
       2801 TGTGCGAGTTACT
         66 TGTGCGAGTTA-T

                                   *     *               *       *        
       2814 ATAACCGGGCTAAGT-CCGAA-GAATTTGAGCGAGTAGCTATATCCGGCTAA-ACCCGAAGG
          1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGCTAT-TCGGGCTAAGTCCCGAAGG

       2873 TACTTGGTTG


Statistics
Matches: 119,  Mismatches: 12, Indels: 12
        0.83            0.08        0.08

Matches are distributed among these distances:
  74    2  0.02
  75   39  0.33
  76   42  0.35
  77    1  0.01
  78   12  0.10
  79   23  0.19

ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26


Consensus pattern (77 bp):   
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGCTATTCGGGCTAAGTCCCGAAGGCATT
TGTGCGAGTTAT

Found at i:10978 original size:39 final size:40

Alignment explanation


    Indices: 10841--10978  Score: 190
    Period size: 40  Copynumber: 3.5  Consensus size: 40

      10831 CGGATGATAA

                                                  * 
      10841 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATTT
          1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT

                        *        *                 *
      10881 CCGGGCTAAGTCTCGAAGGCAATTGTGCGAGTTACTATAA
          1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT

                                     *               
      10921 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
          1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT

                     **        
      10961 CC-GGCTAAACCCCGAAGG
          1 CCGGGCTAAGTCCCGAAGG

      10979 TACTTGGTTG


Statistics
Matches: 87,  Mismatches: 10, Indels: 3
        0.87            0.10        0.03

Matches are distributed among these distances:
  39   16  0.18
  40   71  0.82

ACGTcount: A:0.25, C:0.24, G:0.28, T:0.23


Consensus pattern (40 bp):   
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Done.