Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold3979

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, 367

Length: 613
ACGTcount: A:0.27, C:0.02, G:0.29, T:0.42


Found at i:108 original size:14 final size:14

Alignment explanation


    Indices: 83--125  Score: 59
    Period size: 14  Copynumber: 3.0  Consensus size: 14

         73 AGTTTTATAT

                           
         83 ATTATGGGATTAGGG
          1 ATTAT-GGATTAGGG

                          
         98 ATTATGGATTAGGG
          1 ATTATGGATTAGGG

            *  *          
        112 GTTCTGGATTAGGG
          1 ATTATGGATTAGGG

        126 GTTCTGGTTT


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

Matches are distributed among these distances:
  14   21  0.81
  15    5  0.19

ACGTcount: A:0.23, C:0.02, G:0.40, T:0.35


Consensus pattern (14 bp):   
ATTATGGATTAGGG

Found at i:126 original size:14 final size:14

Alignment explanation


    Indices: 89--156  Score: 75
    Period size: 14  Copynumber: 4.9  Consensus size: 14

         79 ATATATTATG

                     *  * 
         89 GGATTAGGGATTAT
          1 GGATTAGGGGTTCT

                          
        103 GGATTAGGGGTTCT
          1 GGATTAGGGGTTCT

                          
        117 GGATTAGGGGTTCT
          1 GGATTAGGGGTTCT

              *   *     * 
        131 GGTTTAAGGGTTGT
          1 GGATTAGGGGTTCT

                         
        145 -GATTTAGGGGTT
          1 GGA-TTAGGGGTT

        157 AGGGTTAGAG


Statistics
Matches: 46,  Mismatches: 7, Indels: 2
        0.84            0.13        0.04

Matches are distributed among these distances:
  13    1  0.02
  14   45  0.98

ACGTcount: A:0.18, C:0.03, G:0.41, T:0.38


Consensus pattern (14 bp):   
GGATTAGGGGTTCT

Found at i:373 original size:21 final size:21

Alignment explanation


    Indices: 349--416  Score: 66
    Period size: 21  Copynumber: 3.2  Consensus size: 21

        339 TAAATAAGGT

                                 
        349 TTAGGGGTTAGTAGTTAGGGG
          1 TTAGGGGTTAGTAGTTAGGGG

                               *  
        370 TTAGGGGTTAG-AGCTTAGAGG
          1 TTAGGGGTTAGTAG-TTAGGGG

               * *        *      *
        391 TTAAGAGTTAGTGATTTAGGGT
          1 TTAGGGGTTAGT-AGTTAGGGG

                
        413 TTAG
          1 TTAG

        417 AGATTCGGGG


Statistics
Matches: 37,  Mismatches: 7, Indels: 5
        0.76            0.14        0.10

Matches are distributed among these distances:
  20    2  0.05
  21   26  0.70
  22    8  0.22
  23    1  0.03

ACGTcount: A:0.24, C:0.01, G:0.40, T:0.35


Consensus pattern (21 bp):   
TTAGGGGTTAGTAGTTAGGGG
Done.