Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_460 ID=scaffold_460-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: 6763
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.36


Found at i:329 original size:27 final size:30

Alignment explanation


    Indices: 298--355  Score: 77
    Period size: 27  Copynumber: 2.0  Consensus size: 30

        288 TAAAAGTGAT

                     *                    
        298 TCATTATAATA-TCTTTT-AAAT-ATTTTA
          1 TCATTATAAAATTCTTTTAAAATAATTTTA

                 *                        
        325 TCATTTTAAAATTCTTTTAAAATAATTTTA
          1 TCATTATAAAATTCTTTTAAAATAATTTTA

             
        355 T
          1 T

        356 AAAGTATTTA


Statistics
Matches: 26,  Mismatches: 2, Indels: 3
        0.84            0.06        0.10

Matches are distributed among these distances:
  27    9  0.35
  28    6  0.23
  29    4  0.15
  30    7  0.27

ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55


Consensus pattern (30 bp):   
TCATTATAAAATTCTTTTAAAATAATTTTA

Found at i:6558 original size:9 final size:9

Alignment explanation


    Indices: 6541--6577  Score: 65
    Period size: 9  Copynumber: 4.1  Consensus size: 9

       6531 TGAGTTTTTA

                     
       6541 AATTCGAAT
          1 AATTCGAAT

              *      
       6550 AACTCGAAT
          1 AATTCGAAT

                     
       6559 AATTCGAAT
          1 AATTCGAAT

                     
       6568 AATTCGAAT
          1 AATTCGAAT

             
       6577 A
          1 A

       6578 TCAAACTATA


Statistics
Matches: 26,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   9   26  1.00

ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30


Consensus pattern (9 bp):   
AATTCGAAT

Done.