Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2201

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: 3119
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.29


Found at i:1868 original size:20 final size:19

Alignment explanation


    Indices: 1825--1925  Score: 67
    Period size: 20  Copynumber: 5.5  Consensus size: 19

       1815 AAAATGCTTG

                          *     
       1825 AATGTATCGATACATTGTAA
          1 AATGTATCGATACAATG-AA

                               *
       1845 AATGTATCGATACAATGAGC
          1 AATGTATCGATACAATGA-A

                                
       1865 AATGCT-T-GATAC------
          1 AATG-TATCGATACAATGAA

                               *
       1877 AATGTATCGATACAA-GAGC
          1 AATGTATCGATACAATGA-A

                                
       1896 AATGTATCGATACAATGCAA
          1 AATGTATCGATACAATG-AA

                      
       1916 AATGTATCGA
          1 AATGTATCGA

       1926 CACATCTGGG


Statistics
Matches: 66,  Mismatches: 3, Indels: 24
        0.71            0.03        0.26

Matches are distributed among these distances:
  11    1  0.02
  12    5  0.08
  13    5  0.08
  19   21  0.32
  20   32  0.48
  21    2  0.03

ACGTcount: A:0.41, C:0.14, G:0.18, T:0.28


Consensus pattern (19 bp):   
AATGTATCGATACAATGAA

Found at i:1886 original size:32 final size:32

Alignment explanation


    Indices: 1845--1912  Score: 104
    Period size: 32  Copynumber: 2.1  Consensus size: 32

       1835 TACATTGTAA

                                              
       1845 AATGTATCGATACAATGAGCAATGCT-T-GATAC
          1 AATGTATCGATACAA-GAGCAATG-TATCGATAC

                                            
       1877 AATGTATCGATACAAGAGCAATGTATCGATAC
          1 AATGTATCGATACAAGAGCAATGTATCGATAC

                
       1909 AATG
          1 AATG

       1913 CAAAATGTAT


Statistics
Matches: 34,  Mismatches: 0, Indels: 4
        0.89            0.00        0.11

Matches are distributed among these distances:
  30    1  0.03
  31    9  0.26
  32   24  0.71

ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26


Consensus pattern (32 bp):   
AATGTATCGATACAAGAGCAATGTATCGATAC
Done.