Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1595

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: 11443
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35


Found at i:3463 original size:13 final size:13

Alignment explanation


    Indices: 3445--3469  Score: 50
    Period size: 13  Copynumber: 1.9  Consensus size: 13

       3435 TTTTACAATT

                         
       3445 TGTATCGATACAA
          1 TGTATCGATACAA

                        
       3458 TGTATCGATACA
          1 TGTATCGATACA

       3470 TAAGTTTTGT


Statistics
Matches: 12,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   12  1.00

ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32


Consensus pattern (13 bp):   
TGTATCGATACAA

Found at i:4474 original size:19 final size:20

Alignment explanation


    Indices: 4442--4496  Score: 94
    Period size: 19  Copynumber: 2.8  Consensus size: 20

       4432 TTATCAGCCC

                                
       4442 ATGTTCATGCATTTTGAGCT
          1 ATGTTCATGCATTTTGAGCT

                                
       4462 ATGTTCA-GCATTTTGAGCT
          1 ATGTTCATGCATTTTGAGCT

                            
       4481 ATGTTTCATGCATTTT
          1 ATG-TTCATGCATTTT

       4497 TAGTATGTCC


Statistics
Matches: 33,  Mismatches: 0, Indels: 3
        0.92            0.00        0.08

Matches are distributed among these distances:
  19   15  0.45
  20   11  0.33
  21    7  0.21

ACGTcount: A:0.20, C:0.15, G:0.18, T:0.47


Consensus pattern (20 bp):   
ATGTTCATGCATTTTGAGCT

Found at i:4503 original size:20 final size:21

Alignment explanation


    Indices: 4445--4504  Score: 90
    Period size: 19  Copynumber: 3.0  Consensus size: 21

       4435 TCAGCCCATG

                                 
       4445 TTCATGCATTTTGAGCTATG-
          1 TTCATGCATTTTGAGCTATGT

                                 
       4465 TTCA-GCATTTTGAGCTATGT
          1 TTCATGCATTTTGAGCTATGT

                        *        
       4485 TTCATGCATTTTTAG-TATGT
          1 TTCATGCATTTTGAGCTATGT

       4505 CCAATGCCTC


Statistics
Matches: 37,  Mismatches: 1, Indels: 4
        0.88            0.02        0.10

Matches are distributed among these distances:
  19   15  0.41
  20   13  0.35
  21    9  0.24

ACGTcount: A:0.20, C:0.13, G:0.18, T:0.48


Consensus pattern (21 bp):   
TTCATGCATTTTGAGCTATGT
Done.