Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold875

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: 4859
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36


Found at i:4552 original size:36 final size:35

Alignment explanation


    Indices: 4512--4592  Score: 117
    Period size: 36  Copynumber: 2.3  Consensus size: 35

       4502 AGCATGTTTA

                    *                           
       4512 ATAAATAATTTAAAGTTTGTTTATTGTTCCATTAGT
          1 ATAAATAAATT-AAGTTTGTTTATTGTTCCATTAGT

                         **                     
       4548 ATAAATAAAATTATTTTTGTTTATTGTTCCATTAGT
          1 ATAAAT-AAATTAAGTTTGTTTATTGTTCCATTAGT

                     
       4584 ATAAATAAA
          1 ATAAATAAA

       4593 ATTATTATGT


Statistics
Matches: 41,  Mismatches: 3, Indels: 3
        0.87            0.06        0.06

Matches are distributed among these distances:
  35    3  0.07
  36   34  0.83
  37    4  0.10

ACGTcount: A:0.38, C:0.05, G:0.09, T:0.48


Consensus pattern (35 bp):   
ATAAATAAATTAAGTTTGTTTATTGTTCCATTAGT

Found at i:4593 original size:36 final size:36

Alignment explanation


    Indices: 4527--4598  Score: 144
    Period size: 36  Copynumber: 2.0  Consensus size: 36

       4517 TAATTTAAAG

                                                
       4527 TTTGTTTATTGTTCCATTAGTATAAATAAAATTATT
          1 TTTGTTTATTGTTCCATTAGTATAAATAAAATTATT

                                                
       4563 TTTGTTTATTGTTCCATTAGTATAAATAAAATTATT
          1 TTTGTTTATTGTTCCATTAGTATAAATAAAATTATT

       4599 ATGTTTCATG


Statistics
Matches: 36,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  36   36  1.00

ACGTcount: A:0.33, C:0.06, G:0.08, T:0.53


Consensus pattern (36 bp):   
TTTGTTTATTGTTCCATTAGTATAAATAAAATTATT
Done.