Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_656 ID=scaffold_656-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: 4900
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34


Found at i:2947 original size:21 final size:21

Alignment explanation


    Indices: 2923--2981  Score: 57
    Period size: 21  Copynumber: 2.8  Consensus size: 21

       2913 TGAAGAGTGT

                 *               
       2923 TGTGGCTGCATCTGAGTATGG
          1 TGTGGATGCATCTGAGTATGG

                 *          * *  *
       2944 TGTGGGTGCATAC-GACTTTGT
          1 TGTGGATGCAT-CTGAGTATGG

                             
       2965 TGTGGATGCATCTGAGT
          1 TGTGGATGCATCTGAGT

       2982 GTGCTAATTA


Statistics
Matches: 30,  Mismatches: 6, Indels: 4
        0.75            0.15        0.10

Matches are distributed among these distances:
  20    1  0.03
  21   28  0.93
  22    1  0.03

ACGTcount: A:0.15, C:0.14, G:0.36, T:0.36


Consensus pattern (21 bp):   
TGTGGATGCATCTGAGTATGG

Found at i:4816 original size:24 final size:24

Alignment explanation


    Indices: 4753--4825  Score: 85
    Period size: 24  Copynumber: 3.0  Consensus size: 24

       4743 GGTAAGACAT

                  *        *     *  
       4753 TTTCCACAGCTCCTCCCTTCAACC
          1 TTTCCATAGCTCCTCTCTTCACCC

                      *              
       4777 TTTCCACT-GTTCCTCTCTTCACCC
          1 TTTCCA-TAGCTCCTCTCTTCACCC

                            *       
       4801 TTTCCATAGCTCCTCTATTCACCC
          1 TTTCCATAGCTCCTCTCTTCACCC

             
       4825 T
          1 T

       4826 ATCGATTGCA


Statistics
Matches: 41,  Mismatches: 6, Indels: 4
        0.80            0.12        0.08

Matches are distributed among these distances:
  23    1  0.02
  24   40  0.98

ACGTcount: A:0.14, C:0.45, G:0.04, T:0.37


Consensus pattern (24 bp):   
TTTCCATAGCTCCTCTCTTCACCC
Done.