Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_568 ID=scaffold_568-JGI_221_v2.0

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: 7437
ACGTcount: A:0.24, C:0.14, G:0.16, T:0.21

Warning! 1816 characters in sequence are not A, C, G, or T


Found at i:110 original size:19 final size:18

Alignment explanation


    Indices: 86--131  Score: 56
    Period size: 19  Copynumber: 2.4  Consensus size: 18

         76 AACGTCTCTT

                        *      
         86 TTTGCATTCATTTCATGCA
          1 TTTGCATTCATTGCAT-CA

                               
        105 TTTGCATTTCATTGCATCA
          1 TTTGCA-TTCATTGCATCA

             *      
        124 TATGCATT
          1 TTTGCATT

        132 AAACACCTCT


Statistics
Matches: 24,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  18    2  0.08
  19   13  0.54
  20    9  0.38

ACGTcount: A:0.22, C:0.20, G:0.11, T:0.48


Consensus pattern (18 bp):   
TTTGCATTCATTGCATCA

Found at i:4271 original size:44 final size:44

Alignment explanation


    Indices: 4223--4419  Score: 135
    Period size: 44  Copynumber: 4.5  Consensus size: 44

       4213 TCAGATCTTG

                         *                              
       4223 CCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTA
          1 CCTCCCTAAGCAGCAGTGGAGCAGATCGAAGATGGCGGATTTTA

                       **    *    * *  *    ***  *    *  
       4267 CCTCCCTAAAGTTGCAGCGGAGTACATTGAAGCCAG-TGATTCTA
          1 CCTCCCT-AAGCAGCAGTGGAGCAGATCGAAGATGGCGGATTTTA

             *     **           **    *      ** *   *  *
       4311 CTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTG
          1 CCTCCCTAAGCAGCAGTGGAGCAGATCGAAGATGGCGGATTTTA

                         *                              
       4355 CCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTA
          1 CCTCCCTAAGCAGCAGTGGAGCAGATCGAAGATGGCGGATTTTA

                       **        
       4399 CCTCCCTGAAGTTGCAGTGGA
          1 CCTCCCT-AAGCAGCAGTGGA

       4420 NNNNNNNNNN


Statistics
Matches: 107,  Mismatches: 43, Indels: 5
        0.69            0.28        0.03

Matches are distributed among these distances:
  43   17  0.16
  44   62  0.58
  45   28  0.26

ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25


Consensus pattern (44 bp):   
CCTCCCTAAGCAGCAGTGGAGCAGATCGAAGATGGCGGATTTTA
Done.