Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold_138 ID=scaffold_138-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: 11416
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.30

Warning! 240 characters in sequence are not A, C, G, or T


Found at i:3931 original size:26 final size:26

Alignment explanation


    Indices: 3902--4083  Score: 87
    Period size: 26  Copynumber: 7.2  Consensus size: 26

       3892 TTCTCTCTCA

                                      
       3902 AGCCATATAACAGGAAGCTCACAAAG
          1 AGCCATATAACAGGAAGCTCACAAAG

                       **              
       3928 AGCCAT-TAATTGGGAAGCTCACAAAG
          1 AGCCATATAA-CAGGAAGCTCACAAAG

                       * *     *     * 
       3954 AGCC-TAT--CTGAAAGCTTATC--CG
          1 AGCCATATAACAGGAAGCTCA-CAAAG

            *  *                   *  
       3976 GGCTATATAACAGGAA-CTCACACAG
          1 AGCCATATAACAGGAAGCTCACAAAG

                     *       *        
       4001 AGCCATA-ATCAGGAAGTTCACAAAG
          1 AGCCATATAACAGGAAGCTCACAAAG

              * * *                *   
       4026 A-ACTTTTAATCAGGAAGCTCACGAAG
          1 AGCCATATAA-CAGGAAGCTCACAAAG

                  *     *    *     *   
       4052 AGCC-TTTAAACGGGAAACTCACGAAG
          1 AGCCATAT-AACAGGAAGCTCACAAAG

                  
       4078 AGCCAT
          1 AGCCAT

       4084 TAATTAGGAG


Statistics
Matches: 115,  Mismatches: 27, Indels: 27
        0.68            0.16        0.16

Matches are distributed among these distances:
  22    3  0.03
  23   11  0.10
  24   13  0.11
  25   23  0.20
  26   61  0.53
  27    4  0.03

ACGTcount: A:0.39, C:0.23, G:0.20, T:0.18


Consensus pattern (26 bp):   
AGCCATATAACAGGAAGCTCACAAAG

Found at i:4244 original size:63 final size:65

Alignment explanation


    Indices: 4135--4257  Score: 169
    Period size: 63  Copynumber: 1.9  Consensus size: 65

       4125 CGAGCCATAT

                           *  *     *      *      *                          
       4135 CAGGACACTCACAAAGAGTTGCGTTTGTGTCTGCAACATATGCAGGATCACAACCGATCATAAAA
          1 CAGGACACTCACAAAAAGCTGCGTGTGTGTCCGCAACACATGCAGGATCACAACCGATCATAAAA

                  *                                            *        
       4200 CAGGACGCTCACAAAAAGCTGCG-GTG-GTCCGCAACACATGCAGGATCACTACCGATCA
          1 CAGGACACTCACAAAAAGCTGCGTGTGTGTCCGCAACACATGCAGGATCACAACCGATCA

       4258 GGATGCTTGC


Statistics
Matches: 51,  Mismatches: 7, Indels: 2
        0.85            0.12        0.03

Matches are distributed among these distances:
  63   29  0.57
  64    2  0.04
  65   20  0.39

ACGTcount: A:0.33, C:0.27, G:0.22, T:0.18


Consensus pattern (65 bp):   
CAGGACACTCACAAAAAGCTGCGTGTGTGTCCGCAACACATGCAGGATCACAACCGATCATAAAA

Found at i:10169 original size:45 final size:44

Alignment explanation


    Indices: 10087--10187  Score: 141
    Period size: 45  Copynumber: 2.3  Consensus size: 44

      10077 NNNNNNNNNN

                              *       **             *   
      10087 AAGTGATAAGTGGTAGCTTTAGCTACTTTTATCTGATCAAGTGAC
          1 AAGTGATAAGTGGTAGCTCTAGCTACACTTATCTGATC-AGGGAC

                                                         
      10132 AAAGTGATAAGTGGTAGC-CTAGCTACACTTATCTGATCAGGGAC
          1 -AAGTGATAAGTGGTAGCTCTAGCTACACTTATCTGATCAGGGAC

                        
      10176 AAGTGATAAGTG
          1 AAGTGATAAGTG

      10188 ATCATACGTA


Statistics
Matches: 51,  Mismatches: 4, Indels: 3
        0.88            0.07        0.05

Matches are distributed among these distances:
  43   12  0.24
  44    5  0.10
  45   17  0.33
  46   17  0.33

ACGTcount: A:0.32, C:0.14, G:0.25, T:0.30


Consensus pattern (44 bp):   
AAGTGATAAGTGGTAGCTCTAGCTACACTTATCTGATCAGGGAC
Done.