Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1541

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: 10126
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29


Found at i:5043 original size:41 final size:40

Alignment explanation


    Indices: 4986--5075  Score: 144
    Period size: 41  Copynumber: 2.2  Consensus size: 40

       4976 CTAAATCCCA

                    *        *                       
       4986 AGGGTAACTATTCTAAATCTAGTTTGATAAAAGCAATGATG
          1 AGGGTAACCATTCTAAACCTAGTTTGAT-AAAGCAATGATG

                                                    
       5027 AGGGTAACCATTCTAAACCTAGTTTGATAAAGCAATGATG
          1 AGGGTAACCATTCTAAACCTAGTTTGATAAAGCAATGATG

               *     
       5067 AGGATAACC
          1 AGGGTAACC

       5076 CCACTTTACG


Statistics
Matches: 46,  Mismatches: 3, Indels: 1
        0.92            0.06        0.02

Matches are distributed among these distances:
  40   20  0.43
  41   26  0.57

ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28


Consensus pattern (40 bp):   
AGGGTAACCATTCTAAACCTAGTTTGATAAAGCAATGATG

Done.