Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004339.1 Kokia drynarioides strain JFW-HI SEQ_117672, whole genome shotgun sequence

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: 37428
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:2048 original size:6 final size:6

Alignment explanation


    Indices: 2037--2075  Score: 51
    Period size: 6  Copynumber: 6.5  Consensus size: 6

       2027 TGATCAAAAT

                                      *   *  *           
       2037 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
          1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA

       2076 TATGAATTGT


Statistics
Matches: 29,  Mismatches: 4, Indels: 0
        0.88            0.12        0.00

Matches are distributed among these distances:
   6   29  1.00

ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23


Consensus pattern (6 bp):   
TGAAAG

Found at i:9688 original size:11 final size:11

Alignment explanation


    Indices: 9672--9702  Score: 53
    Period size: 11  Copynumber: 2.8  Consensus size: 11

       9662 TTCAGTCCTT

                    *  
       9672 TGCTTGAATTC
          1 TGCTTGAACTC

                       
       9683 TGCTTGAACTC
          1 TGCTTGAACTC

                     
       9694 TGCTTGAAC
          1 TGCTTGAAC

       9703 CGTCTTCTGT


Statistics
Matches: 19,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  11   19  1.00

ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39


Consensus pattern (11 bp):   
TGCTTGAACTC

Found at i:17136 original size:53 final size:53

Alignment explanation


    Indices: 17008--17309  Score: 408
    Period size: 53  Copynumber: 5.7  Consensus size: 53

      16998 TTCACATTTG

                              *                                * 
      17008 ATAACTCACGATGACACAAAGTCATCGGACCTTTAATCCATGAT-GGATTCGT
          1 ATAACTCACGATGACACATAGTCATCGGACCTTTAATCCATGATAGGATTCAT

               *              *        *   *       * *         **
      17060 ATATCTCACGATGACACAAAGTCATCGAACCCTTAATCCGTAATAGGATTCGC
          1 ATAACTCACGATGACACATAGTCATCGGACCTTTAATCCATGATAGGATTCAT

                                    *  *                         
      17113 ATAACTCACGATGACACATAGTCAACGAACCTTTAATCCATGATAGGATTCAT
          1 ATAACTCACGATGACACATAGTCATCGGACCTTTAATCCATGATAGGATTCAT

                    *           *          *         *        *  
      17166 ATAACTCATGATGACACATAATCATCGGACCCTTAATCCATAATAGGATTTAT
          1 ATAACTCACGATGACACATAGTCATCGGACCTTTAATCCATGATAGGATTCAT

                     *    *                                      
      17219 ATAACTCACAATGAGACATAGTCATCGGACCTTTAATCCATGATAGGATTCAT
          1 ATAACTCACGATGACACATAGTCATCGGACCTTTAATCCATGATAGGATTCAT

                          *          *            
      17272 ATAACTCACGATGAGACATAGTCATTGGACCTTTAATC
          1 ATAACTCACGATGACACATAGTCATCGGACCTTTAATC

      17310 TTTGGCATAA


Statistics
Matches: 219,  Mismatches: 30, Indels: 1
        0.88            0.12        0.00

Matches are distributed among these distances:
  52   39  0.18
  53  180  0.82

ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27


Consensus pattern (53 bp):   
ATAACTCACGATGACACATAGTCATCGGACCTTTAATCCATGATAGGATTCAT

Found at i:21810 original size:17 final size:17

Alignment explanation


    Indices: 21768--21818  Score: 75
    Period size: 17  Copynumber: 2.9  Consensus size: 17

      21758 GCAATAAGAT

                    * *      
      21768 AAGAAAAAATGCAAAAG
          1 AAGAAAAACTACAAAAG

                             
      21785 AAGAAAAACTACAAAAG
          1 AAGAAAAACTACAAAAG

                             
      21802 AAGAAAAACTACCAAAA
          1 AAGAAAAACTA-CAAAA

      21819 CAAGGCAACA


Statistics
Matches: 31,  Mismatches: 2, Indels: 1
        0.91            0.06        0.03

Matches are distributed among these distances:
  17   26  0.84
  18    5  0.16

ACGTcount: A:0.71, C:0.12, G:0.12, T:0.06


Consensus pattern (17 bp):   
AAGAAAAACTACAAAAG
Done.