Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002173.1 Kokia drynarioides strain JFW-HI SEQ_114136, 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: 15797
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.32

Warning! 347 characters in sequence are not A, C, G, or T


Found at i:5433 original size:12 final size:12

Alignment explanation


    Indices: 5416--5440  Score: 50
    Period size: 12  Copynumber: 2.1  Consensus size: 12

       5406 TAAAAAAGTT

                        
       5416 TTTTATTTTTTA
          1 TTTTATTTTTTA

                        
       5428 TTTTATTTTTTA
          1 TTTTATTTTTTA

             
       5440 T
          1 T

       5441 AATTGCAAAA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  12   13  1.00

ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84


Consensus pattern (12 bp):   
TTTTATTTTTTA

Found at i:12307 original size:51 final size:50

Alignment explanation


    Indices: 12178--12309  Score: 137
    Period size: 51  Copynumber: 2.6  Consensus size: 50

      12168 TAAACGAAAG

                                                       *   **   
      12178 GGTCCGATGACTA-AGTGTCATCGTGAGTAAATGAATTCATGATGGATTAAA
          1 GGTCCGATGACTATAGTGTCATCGTGAGT--ATGAATTCATGACGGAACAAA

                               *   *                             
      12229 GGTCCGATGACT-TAGTGTTATCTTGAGTATGAATTCTTAT-ACGGAACAAGA
          1 GGTCCGATGACTATAGTGTCATCGTGAGTATGAATTC--ATGACGGAACAA-A

                      *                    
      12280 GGTCCGATGAGTATA-TGTCATCGTGAGTAT
          1 GGTCCGATGACTATAGTGTCATCGTGAGTAT

      12310 TAAATAAAAT


Statistics
Matches: 68,  Mismatches: 8, Indels: 10
        0.79            0.09        0.12

Matches are distributed among these distances:
  49    8  0.12
  50    6  0.09
  51   52  0.76
  52    2  0.03

ACGTcount: A:0.30, C:0.13, G:0.26, T:0.32


Consensus pattern (50 bp):   
GGTCCGATGACTATAGTGTCATCGTGAGTATGAATTCATGACGGAACAAA

Found at i:15256 original size:9 final size:9

Alignment explanation


    Indices: 15175--15236  Score: 52
    Period size: 9  Copynumber: 6.7  Consensus size: 9

      15165 ATGTAGCAAA

                  *  
      15175 AAAAATAAT
          1 AAAAATTAT

                 **  
      15184 AAAAAAAAT
          1 AAAAATTAT

                *    
      15193 AAAAGTTAT
          1 AAAAATTAT

                     
      15202 AAAAATTAT
          1 AAAAATTAT

            *   *      
      15211 TAAATTTGAAT
          1 AAAAATT--AT

                     
      15222 AAAAATTAT
          1 AAAAATTAT

                  
      15231 AAAAAT
          1 AAAAAT

      15237 CGTAAAAAAA


Statistics
Matches: 42,  Mismatches: 9, Indels: 4
        0.76            0.16        0.07

Matches are distributed among these distances:
   9   35  0.83
  11    7  0.17

ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29


Consensus pattern (9 bp):   
AAAAATTAT
Done.