Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold3755

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, 400

Length: 668
ACGTcount: A:0.20, C:0.24, G:0.16, T:0.39


Found at i:182 original size:9 final size:9

Alignment explanation


    Indices: 168--236  Score: 68
    Period size: 9  Copynumber: 7.7  Consensus size: 9

        158 TCATCTTGAT

                    *
        168 TTTTTTCTC
          1 TTTTTTCTG

                  *  
        177 TTTTTTTTG
          1 TTTTTTCTG

                     
        186 TTTTTT-TG
          1 TTTTTTCTG

                *    
        194 TTTTGTCTG
          1 TTTTTTCTG

                      
        203 TTTTTTTCTG
          1 -TTTTTTCTG

                  * *
        213 TTTTTTGTT
          1 TTTTTTCTG

                    *
        222 TTTTTTCTA
          1 TTTTTTCTG

                  
        231 TTTTTT
          1 TTTTTT

        237 TTGCTTGTTT


Statistics
Matches: 50,  Mismatches: 8, Indels: 4
        0.81            0.13        0.06

Matches are distributed among these distances:
   8    7  0.14
   9   35  0.70
  10    8  0.16

ACGTcount: A:0.01, C:0.07, G:0.09, T:0.83


Consensus pattern (9 bp):   
TTTTTTCTG

Found at i:182 original size:10 final size:9

Alignment explanation


    Indices: 167--237  Score: 56
    Period size: 10  Copynumber: 7.8  Consensus size: 9

        157 TTCATCTTGA

                     
        167 TTTTTTTCT
          1 TTTTTTTCT

                      
        176 CTTTTTTT-T
          1 -TTTTTTTCT

            *        
        185 GTTTTTT-T
          1 TTTTTTTCT

            *    *   
        193 GTTTTGTCT
          1 TTTTTTTCT

                      
        202 GTTTTTTTCT
          1 -TTTTTTTCT

            *      * 
        212 GTTTTTTGT
          1 TTTTTTTCT

                     
        221 TTTTTTTCT
          1 TTTTTTTCT

                    
        230 ATTTTTTT
          1 -TTTTTTT

        238 TGCTTGTTTT


Statistics
Matches: 50,  Mismatches: 8, Indels: 6
        0.78            0.12        0.09

Matches are distributed among these distances:
   8   13  0.26
   9   16  0.32
  10   21  0.42

ACGTcount: A:0.01, C:0.07, G:0.08, T:0.83


Consensus pattern (9 bp):   
TTTTTTTCT

Found at i:197 original size:17 final size:17

Alignment explanation


    Indices: 168--237  Score: 77
    Period size: 17  Copynumber: 3.9  Consensus size: 17

        158 TCATCTTGAT

                              
        168 TTTTTTCTCTTTTTTTTG
          1 TTTTTT-TCTTTTTTTTG

                   *    * *  
        186 TTTTTTTGTTTTGTCTG
          1 TTTTTTTCTTTTTTTTG

                     *       
        203 TTTTTTTCTGTTTTTTG
          1 TTTTTTTCTTTTTTTTG

                              
        220 TTTTTTTTCTATTTTTTT
          1 -TTTTTTTCT-TTTTTTT

        238 TGCTTGTTTT


Statistics
Matches: 42,  Mismatches: 8, Indels: 3
        0.79            0.15        0.06

Matches are distributed among these distances:
  17   21  0.50
  18   15  0.36
  19    6  0.14

ACGTcount: A:0.01, C:0.07, G:0.09, T:0.83


Consensus pattern (17 bp):   
TTTTTTTCTTTTTTTTG
Done.