Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_745 ID=scaffold_745-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: 4272
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.34

Warning! 176 characters in sequence are not A, C, G, or T


Found at i:2027 original size:84 final size:84

Alignment explanation


    Indices: 1886--2082  Score: 304
    Period size: 84  Copynumber: 2.3  Consensus size: 84

       1876 TAAACTTTTG

                 *      **             *   *              *                  
       1886 GTGGCATTTTTAGGAAAACGCCACAAATAATGCAATTCCAGACCACGAAAACGGTGTCGTTTCTG
          1 GTGGCGTTTTTACAAAAACGCCACAAAAAATACAATTCCAGACCACCAAAACGGTGTCGTTTCTG

                               
       1951 TTCACAGCTGTAAGATTTA
         66 TTCACAGCTGTAAGATTTA

                        *                                                    
       1970 GTGGCGTTTTTATAAAAACGCCACAAAAAATACAATTCCAGACCACCAAAACGGTGTCGTTTCTG
          1 GTGGCGTTTTTACAAAAACGCCACAAAAAATACAATTCCAGACCACCAAAACGGTGTCGTTTCTG

                         *     
       2035 TTCACAGCTGTAATATTTA
         66 TTCACAGCTGTAAGATTTA

                               *         
       2054 GTGGCGTTTTTACCAAAAATGCCACAAAA
          1 GTGGCGTTTTTA-CAAAAACGCCACAAAA

       2083 CGGTGTTAAT


Statistics
Matches: 103,  Mismatches: 9, Indels: 1
        0.91            0.08        0.01

Matches are distributed among these distances:
  84   89  0.86
  85   14  0.14

ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27


Consensus pattern (84 bp):   
GTGGCGTTTTTACAAAAACGCCACAAAAAATACAATTCCAGACCACCAAAACGGTGTCGTTTCTG
TTCACAGCTGTAAGATTTA

Found at i:3306 original size:11 final size:11

Alignment explanation


    Indices: 3286--3325  Score: 73
    Period size: 11  Copynumber: 3.7  Consensus size: 11

       3276 GAATATCTCA

                       
       3286 AACT-ATGGGT
          1 AACTAATGGGT

                       
       3296 AACTAATGGGT
          1 AACTAATGGGT

                       
       3307 AACTAATGGGT
          1 AACTAATGGGT

                    
       3318 AACTAATG
          1 AACTAATG

       3326 TATTATCATC


Statistics
Matches: 29,  Mismatches: 0, Indels: 1
        0.97            0.00        0.03

Matches are distributed among these distances:
  10    4  0.14
  11   25  0.86

ACGTcount: A:0.38, C:0.10, G:0.25, T:0.28


Consensus pattern (11 bp):   
AACTAATGGGT
Done.