Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold896

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: 24762
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36


Found at i:6867 original size:20 final size:20

Alignment explanation


    Indices: 6842--6879  Score: 60
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       6832 CAGTCTGGGA

                                 
       6842 TTTTATTA-ATTTTCTACTAC
          1 TTTTATTATATTTT-TACTAC

                              
       6862 TTTTATTATATTTTTACT
          1 TTTTATTATATTTTTACT

       6880 TAAAACTAGT


Statistics
Matches: 17,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  20   12  0.71
  21    5  0.29

ACGTcount: A:0.24, C:0.11, G:0.00, T:0.66


Consensus pattern (20 bp):   
TTTTATTATATTTTTACTAC

Found at i:22922 original size:15 final size:15

Alignment explanation


    Indices: 22902--22936  Score: 61
    Period size: 15  Copynumber: 2.3  Consensus size: 15

      22892 ATTAATTTTA

                           
      22902 AAAGGGATAAATCTC
          1 AAAGGGATAAATCTC

                        *  
      22917 AAAGGGATAAATTTC
          1 AAAGGGATAAATCTC

                 
      22932 AAAGG
          1 AAAGG

      22937 TATACATAAA


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  15   19  1.00

ACGTcount: A:0.49, C:0.09, G:0.23, T:0.20


Consensus pattern (15 bp):   
AAAGGGATAAATCTC

Found at i:22996 original size:29 final size:30

Alignment explanation


    Indices: 22937--23015  Score: 88
    Period size: 31  Copynumber: 2.6  Consensus size: 30

      22927 ATTTCAAAGG

                      *   *                
      22937 TATACATAAATTTTGATTTAATGCGTAATTA
          1 TATACATAAACTTTAATTTAATGCG-AATTA

                               *          
      22968 TATACATAAACTTTAATTTGATGC-AATTA
          1 TATACATAAACTTTAATTTAATGCGAATTA

              * *              
      22997 TACATATGAAACTTTAATT
          1 TATACAT-AAACTTTAATT

      23016 ATAGTTCAAA


Statistics
Matches: 42,  Mismatches: 5, Indels: 3
        0.84            0.10        0.06

Matches are distributed among these distances:
  29   10  0.24
  30   11  0.26
  31   21  0.50

ACGTcount: A:0.41, C:0.09, G:0.08, T:0.43


Consensus pattern (30 bp):   
TATACATAAACTTTAATTTAATGCGAATTA
Done.