Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000692.1 Kokia drynarioides strain JFW-HI SEQ_111692, 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, 729

Length: 1216
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.36


Found at i:171 original size:23 final size:23

Alignment explanation


    Indices: 137--262  Score: 130
    Period size: 23  Copynumber: 5.4  Consensus size: 23

        127 AAGTGCTGGG

                                   
        137 TAAT-AGAGAGCACACAAAGTGC
          1 TAATCAGAGAGCACACAAAGTGC

                            *      
        159 TAATCAGAGAGCACACGAAGTGC
          1 TAATCAGAGAGCACACAAAGTGC

                               * *    
        182 TAATAACAGAGAGCACGA-GACGTGC
          1 TAAT--CAGAGAGCAC-ACAAAGTGC

               *     *       *     
        207 TAAACAGAGGGCACACACAGTGC
          1 TAATCAGAGAGCACACAAAGTGC

               *             **    
        230 TAAACAGAGAGCACACACGGTGC
          1 TAATCAGAGAGCACACAAAGTGC

                      
        253 TAATCAGAGA
          1 TAATCAGAGA

        263 ACGCGCTAGT


Statistics
Matches: 89,  Mismatches: 10, Indels: 9
        0.82            0.09        0.08

Matches are distributed among these distances:
  22    5  0.06
  23   64  0.72
  25   19  0.21
  26    1  0.01

ACGTcount: A:0.41, C:0.21, G:0.25, T:0.12


Consensus pattern (23 bp):   
TAATCAGAGAGCACACAAAGTGC

Found at i:193 original size:48 final size:46

Alignment explanation


    Indices: 115--262  Score: 147
    Period size: 48  Copynumber: 3.1  Consensus size: 46

        105 AAGTATTAAA

                       *         *   *                      
        115 CAGAGAGCACATAAGTGCTGGGTAATAGAGAGCACACAAAGTGCTAAT
          1 CAGAGAGCACACAAGTGCT--ATAACAGAGAGCACACAAAGTGCTAAT

                                                  * *       *
        163 CAGAGAGCACACGAAGTGCTAATAACAGAGAGCACGA-GACGTGCTAAA
          1 CAGAGAGCACAC-AAGTGCT-ATAACAGAGAGCAC-ACAAAGTGCTAAT

                 *                               **        
        211 CAGAGGGCACACACAGTGCTA-AACAGAGAGCACACACGGTGCTAAT
          1 CAGAGAGCACACA-AGTGCTATAACAGAGAGCACACAAAGTGCTAAT

                  
        257 CAGAGA
          1 CAGAGA

        263 ACGCGCTAGT


Statistics
Matches: 83,  Mismatches: 13, Indels: 10
        0.78            0.12        0.09

Matches are distributed among these distances:
  45    1  0.01
  46   24  0.29
  47    2  0.02
  48   48  0.58
  49    8  0.10

ACGTcount: A:0.40, C:0.21, G:0.27, T:0.12


Consensus pattern (46 bp):   
CAGAGAGCACACAAGTGCTATAACAGAGAGCACACAAAGTGCTAAT
Done.