Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2146

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: 28236
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34


Found at i:6289 original size:17 final size:17

Alignment explanation


    Indices: 6246--6291  Score: 58
    Period size: 17  Copynumber: 2.6  Consensus size: 17

       6236 TAATGGAATT

                             
       6246 AAAAGTAGAAAAATGAA
          1 AAAAGTAGAAAAATGAA

               *              
       6263 AAAGGATAGAAAAAT-AA
          1 AAAAG-TAGAAAAATGAA

                        
       6280 ATAAAGTAGAAA
          1 A-AAAGTAGAAA

       6292 GAAGTTTGTG


Statistics
Matches: 25,  Mismatches: 2, Indels: 4
        0.81            0.06        0.13

Matches are distributed among these distances:
  17   13  0.52
  18   12  0.48

ACGTcount: A:0.70, C:0.00, G:0.17, T:0.13


Consensus pattern (17 bp):   
AAAAGTAGAAAAATGAA

Found at i:6854 original size:18 final size:19

Alignment explanation


    Indices: 6831--6866  Score: 56
    Period size: 18  Copynumber: 1.9  Consensus size: 19

       6821 TTAACTTTCG

                    *          
       6831 ATTTTTTATA-TTATTTTT
          1 ATTTTTTAGATTTATTTTT

                              
       6849 ATTTTTTAGATTTATTTT
          1 ATTTTTTAGATTTATTTT

       6867 AATAAAATAG


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    9  0.56
  19    7  0.44

ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75


Consensus pattern (19 bp):   
ATTTTTTAGATTTATTTTT

Found at i:7009 original size:27 final size:29

Alignment explanation


    Indices: 6965--7018  Score: 67
    Period size: 28  Copynumber: 1.9  Consensus size: 29

       6955 AAATTTTTAC

                         *    *          
       6965 TTATTTTACTATTTTAAATA-TAAAATAT
          1 TTATTTTACTATTGTAAAAATTAAAATAT

                    *                  
       6993 TTATTTT-GTATTGTAAAAATTAAAAT
          1 TTATTTTACTATTGTAAAAATTAAAAT

       7019 TAATTATATA


Statistics
Matches: 22,  Mismatches: 3, Indels: 2
        0.81            0.11        0.07

Matches are distributed among these distances:
  27    9  0.41
  28   13  0.59

ACGTcount: A:0.43, C:0.02, G:0.04, T:0.52


Consensus pattern (29 bp):   
TTATTTTACTATTGTAAAAATTAAAATAT

Found at i:21108 original size:31 final size:31

Alignment explanation


    Indices: 21048--21108  Score: 72
    Period size: 31  Copynumber: 2.0  Consensus size: 31

      21038 GGCTATATAA

                 *                  *      
      21048 AAAATTTTAATAAATAAAAAAATATTAAATT
          1 AAAATATTAATAAATAAAAAAATAATAAATT

                                            
      21079 AAAATATT-ATAAATAATTAAAAA-AATAAAT
          1 AAAATATTAATAAATAA--AAAAATAATAAAT

      21109 GGACTTGAAA


Statistics
Matches: 26,  Mismatches: 2, Indels: 4
        0.81            0.06        0.12

Matches are distributed among these distances:
  30    8  0.31
  31   13  0.50
  32    5  0.19

ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33


Consensus pattern (31 bp):   
AAAATATTAATAAATAAAAAAATAATAAATT
Done.