Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_4289

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: 15252
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31


Found at i:639 original size:18 final size:19

Alignment explanation


    Indices: 596--639  Score: 54
    Period size: 18  Copynumber: 2.4  Consensus size: 19

        586 TAGTCGTTTC

                      *        
        596 CAGCTCACTCGACTCAAGT
          1 CAGCTCACTCAACTCAAGT

              *              * 
        615 CAACTCAC-CAACTCAATT
          1 CAGCTCACTCAACTCAAGT

                   
        633 CAGCTCA
          1 CAGCTCA

        640 ATCTTAACCC


Statistics
Matches: 21,  Mismatches: 4, Indels: 1
        0.81            0.15        0.04

Matches are distributed among these distances:
  18   14  0.67
  19    7  0.33

ACGTcount: A:0.32, C:0.39, G:0.09, T:0.20


Consensus pattern (19 bp):   
CAGCTCACTCAACTCAAGT

Found at i:3091 original size:47 final size:47

Alignment explanation


    Indices: 3000--3104  Score: 119
    Period size: 47  Copynumber: 2.2  Consensus size: 47

       2990 GAGTGTCATG

                                   *                        
       3000 GAAAAAGAAATTGAGATTGAAAAGGATGTGAAAAAGAGAA-AGAAATC
          1 GAAAAAGAAATTGAGATTGAAAAAGATGTGAAAAAGAGAAGA-AAATC

                                                              *
       3047 GAAAAAGAAATTGAGATTGAACAAA-AGTGTGAGGAAAA-AG-AGAAAATT
          1 GAAAAAGAAATTGAGATTGAA-AAAGA-TGTGA--AAAAGAGAAGAAAATC

                      
       3095 GAAAAAGAAA
          1 GAAAAAGAAA

       3105 GAAAAGACAA


Statistics
Matches: 51,  Mismatches: 2, Indels: 9
        0.82            0.03        0.15

Matches are distributed among these distances:
  47   22  0.43
  48   22  0.43
  49    3  0.06
  50    4  0.08

ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14


Consensus pattern (47 bp):   
GAAAAAGAAATTGAGATTGAAAAAGATGTGAAAAAGAGAAGAAAATC

Found at i:13357 original size:9 final size:10

Alignment explanation


    Indices: 13316--13360  Score: 56
    Period size: 10  Copynumber: 4.5  Consensus size: 10

      13306 AAAAAGGAAT

                      
      13316 GAGCTAAAAC
          1 GAGCTAAAAC

                     * 
      13326 GAGCTAAATTC
          1 GAGCTAAA-AC

                 *    
      13337 GAGCTCAAAC
          1 GAGCTAAAAC

                      
      13347 GAGCT-AAAC
          1 GAGCTAAAAC

                 
      13356 GAGCT
          1 GAGCT

      13361 CAAGTGAGCT


Statistics
Matches: 31,  Mismatches: 3, Indels: 3
        0.84            0.08        0.08

Matches are distributed among these distances:
   9    9  0.29
  10   14  0.45
  11    8  0.26

ACGTcount: A:0.40, C:0.22, G:0.22, T:0.16


Consensus pattern (10 bp):   
GAGCTAAAAC

Found at i:13370 original size:19 final size:20

Alignment explanation


    Indices: 13316--13363  Score: 71
    Period size: 21  Copynumber: 2.4  Consensus size: 20

      13306 AAAAAGGAAT

                 *               
      13316 GAGCTAAAACGAGCTAAATTC
          1 GAGCTCAAACGAGCTAAA-TC

                                
      13337 GAGCTCAAACGAGCTAAA-C
          1 GAGCTCAAACGAGCTAAATC

                    
      13356 GAGCTCAA
          1 GAGCTCAA

      13364 GTGAGCTGAT


Statistics
Matches: 26,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  19    9  0.35
  21   17  0.65

ACGTcount: A:0.42, C:0.23, G:0.21, T:0.15


Consensus pattern (20 bp):   
GAGCTCAAACGAGCTAAATC

Found at i:13842 original size:15 final size:15

Alignment explanation


    Indices: 13822--13869  Score: 53
    Period size: 15  Copynumber: 3.3  Consensus size: 15

      13812 TCAAAGATGG

                           
      13822 GTTTATGGATATGAA
          1 GTTTATGGATATGAA

                   * *    *
      13837 GTTTATGTAGATG-G
          1 GTTTATGGATATGAA

                        *  
      13851 GTTTATGGATATAAA
          1 GTTTATGGATATGAA

                
      13866 GTTT
          1 GTTT

      13870 TTGTAGGTTT


Statistics
Matches: 25,  Mismatches: 7, Indels: 2
        0.74            0.21        0.06

Matches are distributed among these distances:
  14   10  0.40
  15   15  0.60

ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44


Consensus pattern (15 bp):   
GTTTATGGATATGAA

Found at i:13849 original size:29 final size:29

Alignment explanation


    Indices: 13816--13875  Score: 102
    Period size: 29  Copynumber: 2.1  Consensus size: 29

      13806 AAGGATTCAA

                              *          
      13816 AGATGGGTTTATGGATATGAAGTTTATGT
          1 AGATGGGTTTATGGATATAAAGTTTATGT

                                     *   
      13845 AGATGGGTTTATGGATATAAAGTTTTTGT
          1 AGATGGGTTTATGGATATAAAGTTTATGT

              
      13874 AG
          1 AG

      13876 GTTTGGTATA


Statistics
Matches: 29,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  29   29  1.00

ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42


Consensus pattern (29 bp):   
AGATGGGTTTATGGATATAAAGTTTATGT

Found at i:13856 original size:14 final size:14

Alignment explanation


    Indices: 13816--13859  Score: 52
    Period size: 14  Copynumber: 3.1  Consensus size: 14

      13806 AAGGATTCAA

                          
      13816 AGATGGGTTTATGG
          1 AGATGGGTTTATGG

             *    *       *
      13830 ATATGAAGTTTATGT
          1 AGATG-GGTTTATGG

                          
      13845 AGATGGGTTTATGG
          1 AGATGGGTTTATGG

             
      13859 A
          1 A

      13860 TATAAAGTTT


Statistics
Matches: 23,  Mismatches: 6, Indels: 2
        0.74            0.19        0.06

Matches are distributed among these distances:
  14   12  0.52
  15   11  0.48

ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39


Consensus pattern (14 bp):   
AGATGGGTTTATGG
Done.