Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006193.1 Kokia drynarioides strain JFW-HI SEQ_120762, 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: 1724
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.27


Found at i:134 original size:41 final size:41

Alignment explanation


    Indices: 89--228  Score: 111
    Period size: 41  Copynumber: 3.3  Consensus size: 41

         79 TTCGTGTGTC

                                                     
         89 AGCCCGTGTGCCTCCAAATAGTATACACACACCCTGACACA
          1 AGCCCGTGTGCCTCCAAATAGTATACACACACCCTGACACA

                 *              * *   *            *  ***  
        130 AGCCCATGTGCCTCCAAACACAATCCTTGACACACATCCGTGTGTC-
          1 AGCCCGTGTGCCTCC-AA-ATAGT--AT-ACACACA-CCCTGACACA

              *           *                  *       
        176 AGTCCGTGTGCCTCGAAATAGTATACACACACCTTGACACA
          1 AGCCCGTGTGCCTCCAAATAGTATACACACACCCTGACACA

            *           
        217 CGCCCGTGTGCC
          1 AGCCCGTGTGCC

        229 AACTCGTGTG


Statistics
Matches: 72,  Mismatches: 20, Indels: 14
        0.68            0.19        0.13

Matches are distributed among these distances:
  40    5  0.07
  41   31  0.43
  42    3  0.04
  43    3  0.04
  44    3  0.04
  45    3  0.04
  46   19  0.26
  47    5  0.07

ACGTcount: A:0.27, C:0.36, G:0.17, T:0.20


Consensus pattern (41 bp):   
AGCCCGTGTGCCTCCAAATAGTATACACACACCCTGACACA

Found at i:212 original size:53 final size:53

Alignment explanation


    Indices: 154--260  Score: 153
    Period size: 53  Copynumber: 2.0  Consensus size: 53

        144 CAAACACAAT

                        *       *   *            *                
        154 CCTTGACACACATCCGTGTGTC-AGTCCGTGTGCCTCGAAATAGTATACACACA
          1 CCTTGACACACACCCGTGTGCCAACT-CGTGTGCCTCCAAATAGTATACACACA

                       *                                         
        207 CCTTGACACACGCCCGTGTGCCAACTCGTGTGCCTCCAAATAGTATACACACA
          1 CCTTGACACACACCCGTGTGCCAACTCGTGTGCCTCCAAATAGTATACACACA

             
        260 C
          1 C

        261 ACACCTTGAC


Statistics
Matches: 48,  Mismatches: 5, Indels: 2
        0.87            0.09        0.04

Matches are distributed among these distances:
  53   46  0.96
  54    2  0.04

ACGTcount: A:0.26, C:0.34, G:0.18, T:0.22


Consensus pattern (53 bp):   
CCTTGACACACACCCGTGTGCCAACTCGTGTGCCTCCAAATAGTATACACACA
Done.