Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_550 ID=scaffold_550-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: 6719
ACGTcount: A:0.26, C:0.14, G:0.15, T:0.30

Warning! 900 characters in sequence are not A, C, G, or T


Found at i:1999 original size:6 final size:6

Alignment explanation


    Indices: 1988--2053  Score: 50
    Period size: 6  Copynumber: 11.7  Consensus size: 6

       1978 GTGCGAGCGA

                               *     *                             
       1988 GAAAAT GAAAAT GAAAAA GAAATT G-AAA- GAAAA- GAAAAT GAAAA-
          1 GAAAAT GAAAAT GAAAAT GAAAAT GAAAAT GAAAAT GAAAAT GAAAAT

              * *       *     *      
       2032 GAGATT GAAAAA GAAATT GAAA
          1 GAAAAT GAAAAT GAAAAT GAAA

       2054 GAAAAGAAAA


Statistics
Matches: 46,  Mismatches: 11, Indels: 6
        0.73            0.17        0.10

Matches are distributed among these distances:
   4    1  0.02
   5   13  0.28
   6   32  0.70

ACGTcount: A:0.67, C:0.00, G:0.20, T:0.14


Consensus pattern (6 bp):   
GAAAAT

Found at i:2018 original size:10 final size:11

Alignment explanation


    Indices: 2016--2057  Score: 50
    Period size: 11  Copynumber: 3.8  Consensus size: 11

       2006 GAAATTGAAA

                     * 
       2016 GAAAAGAAAAT
          1 GAAAAGAAATT

                   *   
       2027 GAAAAGAGATT
          1 GAAAAGAAATT

                        
       2038 GAAAAAGAAATT
          1 G-AAAAGAAATT

                     
       2050 G-AAAGAAA
          1 GAAAAGAAA

       2058 AGAAAAAGAA


Statistics
Matches: 27,  Mismatches: 3, Indels: 3
        0.82            0.09        0.09

Matches are distributed among these distances:
  10    7  0.26
  11   10  0.37
  12   10  0.37

ACGTcount: A:0.67, C:0.00, G:0.21, T:0.12


Consensus pattern (11 bp):   
GAAAAGAAATT

Found at i:2047 original size:28 final size:28

Alignment explanation


    Indices: 1987--2041  Score: 87
    Period size: 26  Copynumber: 2.0  Consensus size: 28

       1977 AGTGCGAGCG

                                        
       1987 AGAAAATGAAAATGAAAAAGAAATTGAA
          1 AGAAAATGAAAATGAAAAAGAAATTGAA

                                 *      
       2015 AGAAAA-GAAAATG-AAAAGAGATTGAA
          1 AGAAAATGAAAATGAAAAAGAAATTGAA

             
       2041 A
          1 A

       2042 AAGAAATTGA


Statistics
Matches: 26,  Mismatches: 1, Indels: 2
        0.90            0.03        0.07

Matches are distributed among these distances:
  26   13  0.50
  27    7  0.27
  28    6  0.23

ACGTcount: A:0.67, C:0.00, G:0.20, T:0.13


Consensus pattern (28 bp):   
AGAAAATGAAAATGAAAAAGAAATTGAA
Done.