Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold2198

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: 12660
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35


Found at i:3437 original size:20 final size:20

Alignment explanation


    Indices: 3358--3443  Score: 65
    Period size: 20  Copynumber: 4.5  Consensus size: 20

       3348 AAGTATTTAG

                    *           
       3358 ATTTTTAATTTAA-AA-ATT
          1 ATTTTTAAATTAATAATATT

               *        *       
       3376 -TTATTAAA-TATTAATATT
          1 ATTTTTAAATTAATAATATT

                 *       *     * 
       3394 ATTTTCAAATTAAAAATACAT
          1 ATTTTTAAATTAATAATA-TT

                                 
       3415 ATTTTTAAATT-ATAATATTT
          1 ATTTTTAAATTAATAATA-TT

                     
       3435 ATTTTTAAA
          1 ATTTTTAAA

       3444 AAATATTTGA


Statistics
Matches: 51,  Mismatches: 12, Indels: 8
        0.72            0.17        0.11

Matches are distributed among these distances:
  16    2  0.04
  17    8  0.16
  18    3  0.06
  19    6  0.12
  20   21  0.41
  21   11  0.22

ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52


Consensus pattern (20 bp):   
ATTTTTAAATTAATAATATT

Found at i:3793 original size:16 final size:16

Alignment explanation


    Indices: 3761--3814  Score: 54
    Period size: 16  Copynumber: 3.2  Consensus size: 16

       3751 ATTTATATTT

                              
       3761 ATATAAATATAAAATATA
          1 ATATAAAT-T-AAATATA

                           *
       3779 ATATAAATTAAATATT
          1 ATATAAATTAAATATA

              **       *    
       3795 ATCGAAATTAACTATA
          1 ATATAAATTAAATATA

                
       3811 ATAT
          1 ATAT

       3815 TTTATATTTA


Statistics
Matches: 29,  Mismatches: 7, Indels: 2
        0.76            0.18        0.05

Matches are distributed among these distances:
  16   20  0.69
  17    1  0.03
  18    8  0.28

ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37


Consensus pattern (16 bp):   
ATATAAATTAAATATA

Found at i:3854 original size:18 final size:17

Alignment explanation


    Indices: 3824--3862  Score: 60
    Period size: 18  Copynumber: 2.2  Consensus size: 17

       3814 TTTTATATTT

                             
       3824 ATTATATATATATAATA
          1 ATTATATATATATAATA

                          *   
       3841 ATTATATCATATATCATA
          1 ATTATAT-ATATATAATA

                
       3859 ATTA
          1 ATTA

       3863 AATTATGGTA


Statistics
Matches: 20,  Mismatches: 1, Indels: 1
        0.91            0.05        0.05

Matches are distributed among these distances:
  17    7  0.35
  18   13  0.65

ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46


Consensus pattern (17 bp):   
ATTATATATATATAATA

Found at i:5149 original size:21 final size:22

Alignment explanation


    Indices: 5116--5158  Score: 61
    Period size: 21  Copynumber: 2.0  Consensus size: 22

       5106 TTTTTATAAA

                                  
       5116 AAAAAAATATATTAAATTTTAT
          1 AAAAAAATATATTAAATTTTAT

                         * *      
       5138 AAAAAAAT-TATTTATTTTTAT
          1 AAAAAAATATATTAAATTTTAT

       5159 TTATTTTATT


Statistics
Matches: 19,  Mismatches: 2, Indels: 1
        0.86            0.09        0.05

Matches are distributed among these distances:
  21   11  0.58
  22    8  0.42

ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47


Consensus pattern (22 bp):   
AAAAAAATATATTAAATTTTAT
Done.