Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_606 ID=scaffold_606-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: 5312
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.31


Found at i:472 original size:20 final size:20

Alignment explanation


    Indices: 449--494  Score: 76
    Period size: 20  Copynumber: 2.3  Consensus size: 20

        439 TGTTAATATT

                                 
        449 TTGTTA-TTATTTCAAATAGG
          1 TTGTTACTTATTT-AAATAGG

                                
        469 TTGTTACTTATTTAAATAGG
          1 TTGTTACTTATTTAAATAGG

                  
        489 TTGTTA
          1 TTGTTA

        495 AGATTTACTA


Statistics
Matches: 25,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
  20   19  0.76
  21    6  0.24

ACGTcount: A:0.28, C:0.04, G:0.15, T:0.52


Consensus pattern (20 bp):   
TTGTTACTTATTTAAATAGG

Found at i:5031 original size:20 final size:20

Alignment explanation


    Indices: 5006--5051  Score: 58
    Period size: 20  Copynumber: 2.3  Consensus size: 20

       4996 TGTTAACATT

                                 
       5006 TTGTTA-TTAATTCAAATAGG
          1 TTGTTACTT-ATTCAAATAGG

                     *  *       
       5026 TTGTTACTTGTTTAAATAGG
          1 TTGTTACTTATTCAAATAGG

                  
       5046 TTGTTA
          1 TTGTTA

       5052 AGATTTACTA


Statistics
Matches: 23,  Mismatches: 2, Indels: 2
        0.85            0.07        0.07

Matches are distributed among these distances:
  20   21  0.91
  21    2  0.09

ACGTcount: A:0.28, C:0.04, G:0.17, T:0.50


Consensus pattern (20 bp):   
TTGTTACTTATTCAAATAGG
Done.