Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007128.1 Kokia drynarioides strain JFW-HI SEQ_121740, 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: 4058
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.37


Found at i:2895 original size:63 final size:60

Alignment explanation


    Indices: 2828--3014  Score: 223
    Period size: 63  Copynumber: 3.0  Consensus size: 60

       2818 AATTCTCTTA

                                                                           
       2828 TTATTATTATTTTTATTCATTTATTTATTATTTTTATGAATATAAATAAATATAAAATAATAT
          1 TTATT-TTA-TTTTATT-ATTTATTTATTATTTTTATGAATATAAATAAATATAAAATAATAT

                                  *                                          
       2891 TTATTTTATTTTATTATTTATTCATTTATTATTGTATGAATATAAATAAATAAATGTAAAATAAT
          1 TTATTTTATTTTATTATTTATTTA-TTATT-TT-TATGAATATAAATAAAT--A--TAAAATAAT

              
       2956 AT
         59 AT

             *     *                                 *       *        
       2958 TAATTTTGTTTTATTATTTATTTATTA-TTTTATGAATATAGATAAATAAATAAATAA
          1 TTATTTTATTTTATTATTTATTTATTATTTTTATGAATATAAATAAATATA-AAATAA

       3015 CAAACCCAAA


Statistics
Matches: 110,  Mismatches: 6, Indels: 19
        0.81            0.04        0.14

Matches are distributed among these distances:
  59    1  0.01
  60   14  0.13
  61   13  0.12
  62    5  0.05
  63   38  0.35
  64    2  0.02
  65    2  0.02
  66    3  0.03
  67   32  0.29

ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53


Consensus pattern (60 bp):   
TTATTTTATTTTATTATTTATTTATTATTTTTATGAATATAAATAAATATAAAATAATAT

Found at i:3009 original size:67 final size:67

Alignment explanation


    Indices: 2869--3013  Score: 195
    Period size: 67  Copynumber: 2.2  Consensus size: 67

       2859 TTTTATGAAT

                                   *                                *     *  
       2869 ATAAATAAATATAAAATAATATTTATTTTATTTTATTATTTATTCATTTATTATTGTATGAATAT
          1 ATAAATAAATATAAAATAATATTAATTTTATTTTATTATTTATTCATTTATTATTGAATGAAGAT

              
       2934 AA
         66 AA

                      *                  *              *       *            
       2936 ATAAATAAATGTAAAATAATATTAATTTTGTTTTATTATTTATTTA-TTATTTTATGAAT-ATAG
          1 ATAAATAAATATAAAATAATATTAATTTTATTTTATTATTTATTCATTTATTAT-TGAATGA-AG

                
       2999 ATAA
         64 ATAA

                       
       3003 ATAAATAAATA
          1 ATAAATAAATA

       3014 ACAAACCCAA


Statistics
Matches: 68,  Mismatches: 8, Indels: 4
        0.85            0.10        0.05

Matches are distributed among these distances:
  66    7  0.10
  67   61  0.90

ACGTcount: A:0.46, C:0.01, G:0.04, T:0.50


Consensus pattern (67 bp):   
ATAAATAAATATAAAATAATATTAATTTTATTTTATTATTTATTCATTTATTATTGAATGAAGAT
AA
Done.