Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009389.1 Kokia drynarioides strain JFW-HI SEQ_124096, 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: 9406
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31


Found at i:3915 original size:3 final size:3

Alignment explanation


    Indices: 3907--3938  Score: 64
    Period size: 3  Copynumber: 10.7  Consensus size: 3

       3897 ACACTGATAC

                                                      
       3907 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
          1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA

       3939 ACTCAGTCTC


Statistics
Matches: 29,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   29  1.00

ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00


Consensus pattern (3 bp):   
AAG

Found at i:5391 original size:25 final size:27

Alignment explanation


    Indices: 5363--5412  Score: 68
    Period size: 25  Copynumber: 1.9  Consensus size: 27

       5353 CAGTTTTGTA

                  *                    
       5363 TGATTTTATATAT-CAAATT-TTAATT
          1 TGATTTAATATATACAAATTATTAATT

                     *               
       5388 TGATTTAATTTATACAAATTATTAA
          1 TGATTTAATATATACAAATTATTAA

       5413 CAAAAATAAT


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  25   11  0.52
  26    6  0.29
  27    4  0.19

ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52


Consensus pattern (27 bp):   
TGATTTAATATATACAAATTATTAATT

Found at i:8876 original size:23 final size:23

Alignment explanation


    Indices: 8756--8882  Score: 96
    Period size: 23  Copynumber: 5.4  Consensus size: 23

       8746 AGTGCTGGGC

                     *     * * *   
       8756 AACAGAGAGTACACATAATACTA
          1 AACAGAGAGCACACACAGTGCTA

                     *     *   ** *
       8779 AACAGAGAGTACACAAAGTATTC
          1 AACAGAGAGCACACACAGTGCTA

             *                      
       8802 ATCAGAGAGCACACA-ATGTGCTA
          1 AACAGAGAGCACACACA-GTGCTA

             *                      
       8825 ATCAGAGAGCACACACAGTGCTAA
          1 AACAGAGAGCACACACAGTGCT-A

                           *         
       8849 TAACAGAGAGCACGAGAC-GTGCTA
          1 -AACAGAGAGCAC-ACACAGTGCTA

                      
       8873 AACAGAGAGC
          1 AACAGAGAGC

       8883 GCGCTAGTGT


Statistics
Matches: 88,  Mismatches: 11, Indels: 10
        0.81            0.10        0.09

Matches are distributed among these distances:
  22    1  0.01
  23   65  0.74
  24    3  0.03
  25   16  0.18
  26    3  0.03

ACGTcount: A:0.44, C:0.20, G:0.21, T:0.14


Consensus pattern (23 bp):   
AACAGAGAGCACACACAGTGCTA
Done.