Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2475

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: 13021
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31


Found at i:163 original size:29 final size:29

Alignment explanation


    Indices: 118--214  Score: 128
    Period size: 29  Copynumber: 3.4  Consensus size: 29

        108 CATGAAATTG

                                         
        118 GCACTAA--GTGCGGGTTCAAATTGTATA
          1 GCACTAAGTGTGCGGGTTCAAATTGTATA

                                 *       
        145 GCACTAAGTGTGCGGGTTCAAGTTGTATA
          1 GCACTAAGTGTGCGGGTTCAAATTGTATA

                          *     *   *    
        174 GCACTAAGTGTGCGAGTTC-GATTATATA
          1 GCACTAAGTGTGCGGGTTCAAATTGTATA

            *            
        202 ACACTAAGTGTGC
          1 GCACTAAGTGTGC

        215 AGACTTACTA


Statistics
Matches: 62,  Mismatches: 6, Indels: 3
        0.87            0.08        0.04

Matches are distributed among these distances:
  27    7  0.11
  28   18  0.29
  29   37  0.60

ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30


Consensus pattern (29 bp):   
GCACTAAGTGTGCGGGTTCAAATTGTATA

Found at i:1940 original size:21 final size:22

Alignment explanation


    Indices: 1892--1937  Score: 92
    Period size: 22  Copynumber: 2.1  Consensus size: 22

       1882 ACTTCTGACG

                                  
       1892 GTTAAAATTTTTGTTTTGATTA
          1 GTTAAAATTTTTGTTTTGATTA

                                  
       1914 GTTAAAATTTTTGTTTTGATTA
          1 GTTAAAATTTTTGTTTTGATTA

              
       1936 GT
          1 GT

       1938 AAATGAACCC


Statistics
Matches: 24,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   24  1.00

ACGTcount: A:0.26, C:0.00, G:0.15, T:0.59


Consensus pattern (22 bp):   
GTTAAAATTTTTGTTTTGATTA

Found at i:6621 original size:13 final size:14

Alignment explanation


    Indices: 6586--6621  Score: 56
    Period size: 14  Copynumber: 2.6  Consensus size: 14

       6576 TGTGGGGGAG

                         *
       6586 AGTTGTGACAGCCC
          1 AGTTGTGACAGCCA

                          
       6600 AGTTGTGACAGCCA
          1 AGTTGTGACAGCCA

                     
       6614 AG-TGTGAC
          1 AGTTGTGAC

       6622 CTTAGTCGGA


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

Matches are distributed among these distances:
  13    6  0.29
  14   15  0.71

ACGTcount: A:0.25, C:0.22, G:0.31, T:0.22


Consensus pattern (14 bp):   
AGTTGTGACAGCCA

Found at i:8064 original size:29 final size:29

Alignment explanation


    Indices: 8022--8122  Score: 150
    Period size: 29  Copynumber: 3.5  Consensus size: 29

       8012 CATGAAATTG

                                         
       8022 GCACTAAGTGTGCGGGTTCAAATTGTATA
          1 GCACTAAGTGTGCGGGTTCAAATTGTATA

                                 *       
       8051 GCACTAAGTGTGCGGGTTCAAGTTGTATA
          1 GCACTAAGTGTGCGGGTTCAAATTGTATA

                          *     *   *    
       8080 GCACTAAGTGTGCGAGTTC-GATTATATA
          1 GCACTAAGTGTGCGGGTTCAAATTGTATA

            *              
       8108 ACACTAAGTGTGCGG
          1 GCACTAAGTGTGCGG

       8123 ACTTACTATA


Statistics
Matches: 65,  Mismatches: 7, Indels: 1
        0.89            0.10        0.01

Matches are distributed among these distances:
  28   19  0.29
  29   46  0.71

ACGTcount: A:0.27, C:0.15, G:0.29, T:0.30


Consensus pattern (29 bp):   
GCACTAAGTGTGCGGGTTCAAATTGTATA

Done.