Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012556.1 Kokia drynarioides strain JFW-HI SEQ_127565, 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: 9426
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30


Found at i:419 original size:23 final size:23

Alignment explanation


    Indices: 345--510  Score: 116
    Period size: 23  Copynumber: 7.5  Consensus size: 23

        335 TGAACGGAAC

                      *    *    *  
        345 AAACAGAGAGTAC-CGAAGTACT
          1 AAACAGAGAGCACACAAAGTGCT

                           *       
        367 AAACAGAGAGCACA-TAAGTGCT
          1 AAACAGAGAGCACACAAAGTGCT

               *                      
        389 GGGCAACAGAGAGCACACAAAGTGCT
          1 ---AAACAGAGAGCACACAAAGTGCT

                      *            
        415 AAACAGAGAGTACACAAA--G-T
          1 AAACAGAGAGCACACAAAGTGCT

                  *                
        435 --AC--TGAGCACACAAAGTGCT
          1 AAACAGAGAGCACACAAAGTGCT

              *            *       
        454 AATCAGAGAGCACACGAAGTGCT
          1 AAACAGAGAGCACACAAAGTGCT

              *  *          *      
        477 AATCAAAGAGCACACACAGTGCT
          1 AAACAGAGAGCACACAAAGTGCT

            * *        
        500 GACCAGAGAGC
          1 AAACAGAGAGC

        511 GCACTAGTGT


Statistics
Matches: 114,  Mismatches: 18, Indels: 23
        0.74            0.12        0.15

Matches are distributed among these distances:
  16   10  0.09
  18    3  0.03
  19    1  0.01
  20    1  0.01
  21    2  0.02
  22   18  0.16
  23   59  0.52
  25   13  0.11
  26    7  0.06

ACGTcount: A:0.43, C:0.22, G:0.24, T:0.11


Consensus pattern (23 bp):   
AAACAGAGAGCACACAAAGTGCT

Found at i:453 original size:39 final size:39

Alignment explanation


    Indices: 399--473  Score: 123
    Period size: 39  Copynumber: 1.9  Consensus size: 39

        389 GGGCAACAGA

                                      *            
        399 GAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTACT
          1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT

                              *            *    
        438 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGT
          1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGT

        474 GCTAATCAAA


Statistics
Matches: 33,  Mismatches: 3, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  39   33  1.00

ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12


Consensus pattern (39 bp):   
GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT

Found at i:611 original size:24 final size:26

Alignment explanation


    Indices: 573--620  Score: 66
    Period size: 24  Copynumber: 1.9  Consensus size: 26

        563 TCTACATGGG

                                       
        573 CATAATCTCTCATAT-TCATCATTTCT
          1 CATAATCTCTCATATGTCA-CATTTCT

                                    
        599 CATAAT-T-TCATATGTCACATTT
          1 CATAATCTCTCATATGTCACATTT

        621 ACATTTCTCT


Statistics
Matches: 21,  Mismatches: 0, Indels: 4
        0.84            0.00        0.16

Matches are distributed among these distances:
  24   11  0.52
  25    4  0.19
  26    6  0.29

ACGTcount: A:0.29, C:0.23, G:0.02, T:0.46


Consensus pattern (26 bp):   
CATAATCTCTCATATGTCACATTTCT
Done.