Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1798

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: 290850
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32


File 2 of 2

Found at i:275543 original size:77 final size:77

Alignment explanation


    Indices: 275370--275544  Score: 178
    Period size: 77  Copynumber: 2.3  Consensus size: 77

     275360 AGGTTCAGAA

                                   * **                                 *    
     275370 AAAAAAGAGTATAG-AAAAAAAATTGTTTCGTGAAATTCAAGTATTATATTGTATTCATCTTTTT
          1 AAAAAA-A-TATAGAAAAAAAAACTACTTCGTGAAATTCAAGTATTATATTGTATTCATCATTTT

             *            
     275434 AGTAGTTTATAAAC
         64 AATAGTTTATAAAC

                       * *                  *           * *                  
     275448 AAAAAAATATATACAAAAAAACTACTTCGTGAGATTCAAGTATTGTGTTGTAATT-ATCATTTTA
          1 AAAAAAATATAGAAAAAAAAACTACTTCGTGAAATTCAAGTATTATATTGT-ATTCATCATTTTA

                         
     275512 ATAG-TTATAAA-
         65 ATAGTTTATAAAC

                  *               
     275523 AAAAAGTATATAAGAAAAAAAA
          1 AAAAA-AATAT-AGAAAAAAAA

     275545 TCAAAACAAA


Statistics
Matches: 80,  Mismatches: 13, Indels: 9
        0.78            0.13        0.09

Matches are distributed among these distances:
  75    5  0.06
  76   15  0.19
  77   51  0.64
  78    9  0.11

ACGTcount: A:0.48, C:0.06, G:0.11, T:0.34


Consensus pattern (77 bp):   
AAAAAAATATAGAAAAAAAAACTACTTCGTGAAATTCAAGTATTATATTGTATTCATCATTTTAA
TAGTTTATAAAC

Done.