Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold1246

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: 6765
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29


Found at i:2856 original size:32 final size:33

Alignment explanation


    Indices: 2820--2883  Score: 121
    Period size: 33  Copynumber: 2.0  Consensus size: 33

       2810 GAATGCCACG

                                             
       2820 AACA-TTTTATATCTTCATTCAGCCCATCCTCA
          1 AACATTTTTATATCTTCATTCAGCCCATCCTCA

                                            
       2852 AACATTTTTATATCTTCATTCAGCCCATCCTC
          1 AACATTTTTATATCTTCATTCAGCCCATCCTC

       2884 GAAGTGTTTA


Statistics
Matches: 31,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  32    4  0.13
  33   27  0.87

ACGTcount: A:0.27, C:0.31, G:0.03, T:0.39


Consensus pattern (33 bp):   
AACATTTTTATATCTTCATTCAGCCCATCCTCA

Found at i:5129 original size:79 final size:82

Alignment explanation


    Indices: 5018--5202  Score: 229
    Period size: 79  Copynumber: 2.3  Consensus size: 82

       5008 GCTACTCGTT

                            *         *                 *                    
       5018 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
          1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC

                *         *   
       5081 GGATTTAGTAAC-TCGCA
         65 GGATATAGTAACTTAGCA

                                              *                         **   
       5098 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
          1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG

                 *  *        
       5161 GATATGGTCACTTAGCA
         66 GATATAGTAACTTAGCA

                                      
       5178 CAAA-GCCTTCGGGACTTAGCCCGGA
          1 CAAATGCCTTCGGGACTTAGCCCGGA

       5203 CATCATTCAA


Statistics
Matches: 91,  Mismatches: 10, Indels: 8
        0.83            0.09        0.07

Matches are distributed among these distances:
  78    3  0.03
  79   54  0.59
  80   34  0.37

ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25


Consensus pattern (82 bp):   
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA

Found at i:5202 original size:40 final size:40

Alignment explanation


    Indices: 4999--5202  Score: 229
    Period size: 40  Copynumber: 5.1  Consensus size: 40

       4989 CGGAATTTAA

                              **                *    
       4999 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
          1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC

                *                 *               * 
       5039 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTAAC
          1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC

                  *                                 
       5079 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
          1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC

                         *                           *
       5118 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
          1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC

                    *  *    *                        
       5158 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
          1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC

                 
       5198 CCGGA
          1 CCGGA

       5203 CATCATTCAA


Statistics
Matches: 139,  Mismatches: 18, Indels: 14
        0.81            0.11        0.08

Matches are distributed among these distances:
  38    2  0.01
  39   33  0.24
  40   92  0.66
  41   12  0.09

ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25


Consensus pattern (40 bp):   
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Done.