Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014404.1 Kokia drynarioides strain JFW-HI SEQ_129442, 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: 2371
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.34

Warning! 52 characters in sequence are not A, C, G, or T


Found at i:35 original size:23 final size:23

Alignment explanation


    Indices: 1--116  Score: 120
    Period size: 23  Copynumber: 5.3  Consensus size: 23

                                   
          1 CAGAGAGCACACAAAGTGCTAAA
          1 CAGAGAGCACACAAAGTGCTAAA

                   *               
         24 CAGAGAGTACACAAA--G-T--A
          1 CAGAGAGCACACAAAGTGCTAAA

               *              *   *
         42 C--TGAGCACACAAAGTGTTAAT
          1 CAGAGAGCACACAAAGTGCTAAA

                        *          
         63 CAGAGAGCACACGAAGTGCTAAA
          1 CAGAGAGCACACAAAGTGCTAAA

                         *        *
         86 CAGAGAGCACACACAGTGCTAAT
          1 CAGAGAGCACACAAAGTGCTAAA

                    
        109 CAGAGAGC
          1 CAGAGAGC

        117 GCCACTATTA


Statistics
Matches: 75,  Mismatches: 11, Indels: 14
        0.75            0.11        0.14

Matches are distributed among these distances:
  16   10  0.13
  18    3  0.04
  19    1  0.01
  20    1  0.01
  21    2  0.03
  23   58  0.77

ACGTcount: A:0.43, C:0.22, G:0.23, T:0.12


Consensus pattern (23 bp):   
CAGAGAGCACACAAAGTGCTAAA

Found at i:67 original size:39 final size:39

Alignment explanation


    Indices: 5--79  Score: 114
    Period size: 39  Copynumber: 1.9  Consensus size: 39

          1 CAGA

                                      *            
          5 GAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTACT
          1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT

                          *   *            *    
         44 GAGCACACAAAGTGTTAATCAGAGAGCACACGAAGT
          1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGT

         80 GCTAAACAGA


Statistics
Matches: 32,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  39   32  1.00

ACGTcount: A:0.44, C:0.20, G:0.23, T:0.13


Consensus pattern (39 bp):   
GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT

Done.