Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold841

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: 13771
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32


Found at i:4739 original size:20 final size:19

Alignment explanation


    Indices: 4701--4738  Score: 51
    Period size: 19  Copynumber: 2.0  Consensus size: 19

       4691 TTACCTCTTA

                               
       4701 CTTTTCCAACTTTTCTTTT
          1 CTTTTCCAACTTTTCTTTT

                 *              
       4720 CTTTTTCAATCTTTT-TTTT
          1 CTTTTCCAA-CTTTTCTTTT

       4739 TTTCTTTTGC


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  19   12  0.71
  20    5  0.29

ACGTcount: A:0.11, C:0.21, G:0.00, T:0.68


Consensus pattern (19 bp):   
CTTTTCCAACTTTTCTTTT

Found at i:4940 original size:21 final size:21

Alignment explanation


    Indices: 4897--4942  Score: 65
    Period size: 21  Copynumber: 2.2  Consensus size: 21

       4887 TTGACCCAAG

                          * * *  
       4897 AGAATTGACCCAAATAGATAA
          1 AGAATTGACCCAAAGAAACAA

                                 
       4918 AGAATTGACCCAAAGAAACAA
          1 AGAATTGACCCAAAGAAACAA

                
       4939 AGAA
          1 AGAA

       4943 ATAAAATTGA


Statistics
Matches: 22,  Mismatches: 3, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
  21   22  1.00

ACGTcount: A:0.57, C:0.15, G:0.15, T:0.13


Consensus pattern (21 bp):   
AGAATTGACCCAAAGAAACAA

Found at i:12914 original size:11 final size:12

Alignment explanation


    Indices: 12885--12918  Score: 52
    Period size: 12  Copynumber: 2.9  Consensus size: 12

      12875 TATGTAAAGT

                    *   
      12885 TTTTATTTTTTA
          1 TTTTATTTATTA

                        
      12897 TTTTATTTATTA
          1 TTTTATTTATTA

                       
      12909 -TTTATTTATT
          1 TTTTATTTATT

      12919 TACTTACGTT


Statistics
Matches: 21,  Mismatches: 1, Indels: 1
        0.91            0.04        0.04

Matches are distributed among these distances:
  11   10  0.48
  12   11  0.52

ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79


Consensus pattern (12 bp):   
TTTTATTTATTA
Done.