Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_356 ID=scaffold_356-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: 8174
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.35

Warning! 229 characters in sequence are not A, C, G, or T


Found at i:5094 original size:16 final size:18

Alignment explanation


    Indices: 5073--5106  Score: 54
    Period size: 18  Copynumber: 2.0  Consensus size: 18

       5063 TTAAACACAC

                              
       5073 AATTAA-AC-AAATTCAT
          1 AATTAACACTAAATTCAT

                              
       5089 AATTAACACTAAATTCAT
          1 AATTAACACTAAATTCAT

       5107 TCTATTAACA


Statistics
Matches: 16,  Mismatches: 0, Indels: 2
        0.89            0.00        0.11

Matches are distributed among these distances:
  16    6  0.38
  17    2  0.12
  18    8  0.50

ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32


Consensus pattern (18 bp):   
AATTAACACTAAATTCAT

Found at i:6180 original size:8 final size:8

Alignment explanation


    Indices: 6163--6199  Score: 65
    Period size: 8  Copynumber: 4.6  Consensus size: 8

       6153 TGTTGGTTGG

                    
       6163 ATCCGCAT
          1 ATCCGCAT

                 *  
       6171 ATCCGTAT
          1 ATCCGCAT

                    
       6179 ATCCGCAT
          1 ATCCGCAT

                    
       6187 ATCCGCAT
          1 ATCCGCAT

                 
       6195 ATCCG
          1 ATCCG

       6200 AGTCTGAGTT


Statistics
Matches: 27,  Mismatches: 2, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
   8   27  1.00

ACGTcount: A:0.24, C:0.35, G:0.14, T:0.27


Consensus pattern (8 bp):   
ATCCGCAT

Found at i:7772 original size:17 final size:17

Alignment explanation


    Indices: 7740--7772  Score: 50
    Period size: 17  Copynumber: 1.9  Consensus size: 17

       7730 CTTCCATTCT

                             
       7740 TTTAGATTTTAATTTAC
          1 TTTAGATTTTAATTTAC

                             
       7757 TTTAG-TTTTAACTTTA
          1 TTTAGATTTTAA-TTTA

       7773 GTTTCACCAC


Statistics
Matches: 15,  Mismatches: 0, Indels: 2
        0.88            0.00        0.12

Matches are distributed among these distances:
  16    6  0.40
  17    9  0.60

ACGTcount: A:0.27, C:0.06, G:0.06, T:0.61


Consensus pattern (17 bp):   
TTTAGATTTTAATTTAC
Done.