Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_420 ID=scaffold_420-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: 7301
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.35

Warning! 100 characters in sequence are not A, C, G, or T


Found at i:1981 original size:30 final size:29

Alignment explanation


    Indices: 1947--2013  Score: 89
    Period size: 29  Copynumber: 2.3  Consensus size: 29

       1937 ATTTACTTTT

                                    *     
       1947 TTTTTTGAATTTTTATAAACTTTTTATATA
          1 TTTTTTGAATTTTTA-AAACTTTTAATATA

                              *       *  
       1977 TTTTTTGAATTTTTAAAAGTTTTAATTTA
          1 TTTTTTGAATTTTTAAAACTTTTAATATA

               *    
       2006 TTTGTTGA
          1 TTTTTTGA

       2014 TGACACATAT


Statistics
Matches: 33,  Mismatches: 4, Indels: 1
        0.87            0.11        0.03

Matches are distributed among these distances:
  29   18  0.55
  30   15  0.45

ACGTcount: A:0.28, C:0.01, G:0.07, T:0.63


Consensus pattern (29 bp):   
TTTTTTGAATTTTTAAAACTTTTAATATA

Found at i:5343 original size:16 final size:17

Alignment explanation


    Indices: 5314--5348  Score: 54
    Period size: 16  Copynumber: 2.1  Consensus size: 17

       5304 TAAAATAATA

                             
       5314 TAATATATTAATTATAT
          1 TAATATATTAATTATAT

                     *       
       5331 TAATA-ATTTATTATAT
          1 TAATATATTAATTATAT

              
       5347 TA
          1 TA

       5349 TTAAATATAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 1
        0.89            0.05        0.05

Matches are distributed among these distances:
  16   12  0.71
  17    5  0.29

ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54


Consensus pattern (17 bp):   
TAATATATTAATTATAT

Found at i:5355 original size:20 final size:20

Alignment explanation


    Indices: 5308--5355  Score: 53
    Period size: 20  Copynumber: 2.4  Consensus size: 20

       5298 ATTTATTAAA

                                 
       5308 ATAATATAATATATTAATTAT
          1 ATAA-ATAATATATTAATTAT

              *      *           
       5329 ATTAATAATTTATTATATTAT
          1 ATAAATAATATATTA-ATTAT

                   
       5350 -TAAATA
          1 ATAAATA

       5356 TAAACAATTA


Statistics
Matches: 23,  Mismatches: 3, Indels: 3
        0.79            0.10        0.10

Matches are distributed among these distances:
  20   15  0.65
  21    8  0.35

ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50


Consensus pattern (20 bp):   
ATAAATAATATATTAATTAT
Done.