Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_586 ID=scaffold_586-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: 7348
ACGTcount: A:0.23, C:0.14, G:0.13, T:0.24

Warning! 1886 characters in sequence are not A, C, G, or T


Found at i:2159 original size:54 final size:55

Alignment explanation


    Indices: 2096--2213  Score: 143
    Period size: 55  Copynumber: 2.2  Consensus size: 55

       2086 TTCCTTTACA

                                                   *         *       
       2096 GAAAACTCTGAAAAGAATA-ACCTTTAT-GTCAAACT-TGAAAGAAATGTCTTTGTG
          1 GAAAACTCTGAAAA-AATATACCTTTATGGTC-AACTCTAAAAGAAATGCCTTTGTG

                               *     *                *            
       2150 GAAAACTCTGAAAAAATATCCCTTTGTGGTCAACTCTAAAAGGAATGCCTTTGTG
          1 GAAAACTCTGAAAAAATATACCTTTATGGTCAACTCTAAAAGAAATGCCTTTGTG

             *       
       2205 GGAAACTCT
          1 GAAAACTCT

       2214 AAATGGAATG


Statistics
Matches: 55,  Mismatches: 6, Indels: 5
        0.83            0.09        0.08

Matches are distributed among these distances:
  53    4  0.07
  54   24  0.44
  55   27  0.49

ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29


Consensus pattern (55 bp):   
GAAAACTCTGAAAAAATATACCTTTATGGTCAACTCTAAAAGAAATGCCTTTGTG

Found at i:2214 original size:27 final size:27

Alignment explanation


    Indices: 2133--2227  Score: 93
    Period size: 27  Copynumber: 3.5  Consensus size: 27

       2123 GTCAAACTTG

                     *                  
       2133 AAAGAAATGTCTTTGTGGAAAACTCTGA
          1 AAAGAAATGCCTTTGTGGAAAACTCT-A

                     *         **       
       2161 AAA-AATATCCCTTTGTGGTCAACTCTA
          1 AAAGAA-ATGCCTTTGTGGAAAACTCTA

                *             *        
       2188 AAAGGAATGCCTTTGTGGGAAACTCTA
          1 AAAGAAATGCCTTTGTGGAAAACTCTA

              * *        
       2215 AATGGAATGCCTT
          1 AAAGAAATGCCTT

       2228 GATGGCACGT


Statistics
Matches: 56,  Mismatches: 9, Indels: 5
        0.80            0.13        0.07

Matches are distributed among these distances:
  27   36  0.64
  28   20  0.36

ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29


Consensus pattern (27 bp):   
AAAGAAATGCCTTTGTGGAAAACTCTA
Done.