Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012205.1 Kokia drynarioides strain JFW-HI SEQ_127206, 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: 3791
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31


Found at i:1938 original size:6 final size:6

Alignment explanation


    Indices: 1927--1961  Score: 70
    Period size: 6  Copynumber: 5.8  Consensus size: 6

       1917 ATAGGATCAC

                                                    
       1927 AAATGA AAATGA AAATGA AAATGA AAATGA AAATG
          1 AAATGA AAATGA AAATGA AAATGA AAATGA AAATG

       1962 GAGTCGCCAC


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

Matches are distributed among these distances:
   6   29  1.00

ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17


Consensus pattern (6 bp):   
AAATGA

Found at i:2567 original size:22 final size:21

Alignment explanation


    Indices: 2537--2587  Score: 57
    Period size: 22  Copynumber: 2.3  Consensus size: 21

       2527 AATTTACAAG

                                  
       2537 TATAAATAATAAGAAAATAATA
          1 TATAAATAA-AAGAAAATAATA

                *        *     * 
       2559 TATACATAAAAGACAATAAGA
          1 TATAAATAAAAGAAAATAATA

                    
       2580 TTATAAAT
          1 -TATAAAT

       2588 CGAGTAAATA


Statistics
Matches: 24,  Mismatches: 4, Indels: 2
        0.80            0.13        0.07

Matches are distributed among these distances:
  21   10  0.42
  22   14  0.58

ACGTcount: A:0.63, C:0.04, G:0.06, T:0.27


Consensus pattern (21 bp):   
TATAAATAAAAGAAAATAATA

Found at i:2792 original size:30 final size:30

Alignment explanation


    Indices: 2754--2926  Score: 163
    Period size: 30  Copynumber: 5.8  Consensus size: 30

       2744 CTTTAAAACC

                                        * 
       2754 GGGTCAAATTTGAATTTTTAGAAAGTTTAA
          1 GGGTCAAATTTGAATTTTTAGAAAGTTTGA

               *       *       *    *     
       2784 GGGCCAAATTTAAATTTTTGGAAAATTTGA
          1 GGGTCAAATTTGAATTTTTAGAAAGTTTGA

                * *    *             *     
       2814 GGGTTATA-TTCAATTTTTTAGAAAATTT-A
          1 GGGTCAAATTTGAA-TTTTTAGAAAGTTTGA

                 *   *          *       *  
       2843 GGGGTTAAAGTTGAATTTTTTG-AAGTTCGA
          1 -GGGTCAAATTTGAATTTTTAGAAAGTTTGA

                *              *         *
       2873 GGGTAAAATTTGAATTTTTGGAAAGTTTGG
          1 GGGTCAAATTTGAATTTTTAGAAAGTTTGA

                                    
       2903 GGGTCAAATTTGAATTTTTAGAAA
          1 GGGTCAAATTTGAATTTTTAGAAA

       2927 ACTTGGGGGT


Statistics
Matches: 116,  Mismatches: 22, Indels: 10
        0.78            0.15        0.07

Matches are distributed among these distances:
  29   27  0.23
  30   85  0.73
  31    4  0.03

ACGTcount: A:0.34, C:0.03, G:0.23, T:0.40


Consensus pattern (30 bp):   
GGGTCAAATTTGAATTTTTAGAAAGTTTGA

Done.