Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_142 ID=scaffold_142-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: 11292
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.32

Warning! 200 characters in sequence are not A, C, G, or T


Found at i:240 original size:23 final size:23

Alignment explanation


    Indices: 214--331  Score: 173
    Period size: 23  Copynumber: 5.1  Consensus size: 23

        204 TTATTGATCG

                            ** **  
        214 GTGGTAGCTTCGGCTATGTTTCA
          1 GTGGTAGCTTCGGCTACATAACA

                                   
        237 GTGGTAGCTTCGGCTACATAACA
          1 GTGGTAGCTTCGGCTACATAACA

                               **  
        260 GTGGTAGCTTCGGCTACATTTCA
          1 GTGGTAGCTTCGGCTACATAACA

                                   
        283 GTGGTAGCTTCGGCTACATAACA
          1 GTGGTAGCTTCGGCTACATAACA

                                *  
        306 GTGGTAGCTTCGGCTACATATCA
          1 GTGGTAGCTTCGGCTACATAACA

               
        329 GTG
          1 GTG

        332 TTGCACTTAT


Statistics
Matches: 86,  Mismatches: 9, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  23   86  1.00

ACGTcount: A:0.20, C:0.20, G:0.28, T:0.31


Consensus pattern (23 bp):   
GTGGTAGCTTCGGCTACATAACA

Found at i:267 original size:46 final size:46

Alignment explanation


    Indices: 214--331  Score: 209
    Period size: 46  Copynumber: 2.6  Consensus size: 46

        204 TTATTGATCG

                            **                            
        214 GTGGTAGCTTCGGCTATGTTTCAGTGGTAGCTTCGGCTACATAACA
          1 GTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTCGGCTACATAACA

                                                          
        260 GTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTCGGCTACATAACA
          1 GTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTCGGCTACATAACA

                               *      
        306 GTGGTAGCTTCGGCTACATATCAGTG
          1 GTGGTAGCTTCGGCTACATTTCAGTG

        332 TTGCACTTAT


Statistics
Matches: 69,  Mismatches: 3, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  46   69  1.00

ACGTcount: A:0.20, C:0.20, G:0.28, T:0.31


Consensus pattern (46 bp):   
GTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTCGGCTACATAACA
Done.