Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_210 ID=scaffold_210-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: 9907
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.32

Warning! 607 characters in sequence are not A, C, G, or T


Found at i:7155 original size:61 final size:61

Alignment explanation


    Indices: 7001--7157  Score: 178
    Period size: 60  Copynumber: 2.6  Consensus size: 61

       6991 TTTATGAATT

                                     *    *                  *        *  
       7001 ATATAAATATGTTAGCCGAATGTATATTTTAAGTTTGATATGTTGAAACTAATTGTATGAA
          1 ATATAAATATGTTAGCCGAATGTATGTTTTGAGTTTGATATGTTGAAACAAATTGTATAAA

            *                                                  *     *      
       7062 TTATAAATATGTTAG-C-AAGTGTATGTTTTGAGTTCT-ATGA-GTTGAAAGAAATTTTATAAA
          1 ATATAAATATGTTAGCCGAA-TGTATGTTTTGAGTT-TGAT-ATGTTGAAACAAATTGTATAAA

                 *  *                           
       7122 ATATATATCTGTTAGCCGAATGTATGTTTTGAGTTT
          1 ATATAAATATGTTAGCCGAATGTATGTTTTGAGTTT

       7158 TATAAGCTGA


Statistics
Matches: 81,  Mismatches: 10, Indels: 11
        0.79            0.10        0.11

Matches are distributed among these distances:
  59    2  0.02
  60   45  0.56
  61   32  0.40
  62    2  0.02

ACGTcount: A:0.34, C:0.05, G:0.18, T:0.43


Consensus pattern (61 bp):   
ATATAAATATGTTAGCCGAATGTATGTTTTGAGTTTGATATGTTGAAACAAATTGTATAAA

Found at i:7188 original size:61 final size:61

Alignment explanation


    Indices: 6974--7192  Score: 226
    Period size: 61  Copynumber: 3.6  Consensus size: 61

       6964 ATATATGTTC

                       *      *                                 *    *     
       6974 TATAAGCTGAATTTAATTTTATGAATTATATAAATATGTTAGCCGAATGTATATTTTAAGTTT
          1 TATAAGCTGAAATTAATTGTATGAATTATAT--ATATGTTAGCCGAATGTATGTTTTGAGTTT

            *   * *     *                 *                              *
       7037 GATATGTTGAAACTAATTGTATGAATTATAAATATGTTAG-C-AAGTGTATGTTTTGAGTTC
          1 TATAAGCTGAAATTAATTGTATGAATTATATATATGTTAGCCGAA-TGTATGTTTTGAGTTT

               *  *     **    *   *  *       *                           
       7097 TATGAGTTGAAAGAAATTTTATAAAATATATATCTGTTAGCCGAATGTATGTTTTGAGTTT
          1 TATAAGCTGAAATTAATTGTATGAATTATATATATGTTAGCCGAATGTATGTTTTGAGTTT

                       *                       
       7158 TATAAGCTGAATTTAATTGTATGAATTATATATAT
          1 TATAAGCTGAAATTAATTGTATGAATTATATATAT

       7193 ATATATCTTA


Statistics
Matches: 123,  Mismatches: 30, Indels: 8
        0.76            0.19        0.05

Matches are distributed among these distances:
  59    2  0.02
  60   44  0.36
  61   51  0.41
  62    2  0.02
  63   24  0.20

ACGTcount: A:0.36, C:0.05, G:0.16, T:0.44


Consensus pattern (61 bp):   
TATAAGCTGAAATTAATTGTATGAATTATATATATGTTAGCCGAATGTATGTTTTGAGTTT
Done.