Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006187.1 Kokia drynarioides strain JFW-HI SEQ_120756, 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: 1759
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32


Found at i:294 original size:22 final size:21

Alignment explanation


    Indices: 264--314  Score: 57
    Period size: 22  Copynumber: 2.3  Consensus size: 21

        254 AATTTACAAG

                                  
        264 TATAAATAATAAGAAAATAATA
          1 TATAAATAA-AAGAAAATAATA

                *        *     * 
        286 TATACATAAAAGACAATAAGA
          1 TATAAATAAAAGAAAATAATA

                    
        307 TTATAAAT
          1 -TATAAAT

        315 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:519 original size:30 final size:30

Alignment explanation


    Indices: 481--653  Score: 172
    Period size: 30  Copynumber: 5.8  Consensus size: 30

        471 CATTAAAACC

                                        * 
        481 GGGTCAAATTTGAATTTTTAGAAAGTTTAA
          1 GGGTCAAATTTGAATTTTTAGAAAGTTTGA

               *       *       *    *     
        511 GGGCCAAATTTAAATTTTTGGAAAATTTGA
          1 GGGTCAAATTTGAATTTTTAGAAAGTTTGA

                *      *             *     
        541 GGGTTAAA-TTCAATTTTTTAGAAAATTT-A
          1 GGGTCAAATTTGAA-TTTTTAGAAAGTTTGA

                 *   *          *       *  
        570 GGGGTTAAAGTTGAATTTTTTG-AAGTTCGA
          1 -GGGTCAAATTTGAATTTTTAGAAAGTTTGA

                *              *         *
        600 GGGTAAAATTTGAATTTTTGGAAAGTTTGG
          1 GGGTCAAATTTGAATTTTTAGAAAGTTTGA

                                    
        630 GGGTCAAATTTGAATTTTTAGAAA
          1 GGGTCAAATTTGAATTTTTAGAAA

        654 ACTTGGGGGT


Statistics
Matches: 118,  Mismatches: 20, Indels: 10
        0.80            0.14        0.07

Matches are distributed among these distances:
  29   27  0.23
  30   87  0.74
  31    4  0.03

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


Consensus pattern (30 bp):   
GGGTCAAATTTGAATTTTTAGAAAGTTTGA

Found at i:633 original size:59 final size:60

Alignment explanation


    Indices: 481--667  Score: 191
    Period size: 60  Copynumber: 3.1  Consensus size: 60

        471 CATTAAAACC

                *                        *   *       *               *  
        481 GGGTCAAATTTGAATTTTTAGAAAGTTTAAGGGCCAAATTTAAATTTTTGGAAAATTTGA
          1 GGGTAAAATTTGAATTTTTAGAAAGTTTAGGGGTCAAATTTGAATTTTTGGAAAATTCGA

                *      *             *         *   *          *    *     
        541 GGGTTAAA-TTCAATTTTTTAGAAAATTTAGGGGTTAAAGTTGAATTTTTTG-AAGTTCGA
          1 GGGTAAAATTTGAA-TTTTTAGAAAGTTTAGGGGTCAAATTTGAATTTTTGGAAAATTCGA

                               *        *                    *          *
        600 GGGTAAAATTTGAATTTTTGGAAAGTTTGGGGGTCAAATTTGAATTTTTAGAAAACTT-GG
          1 GGGTAAAATTTGAATTTTTAGAAAGTTTAGGGGTCAAATTTGAATTTTTGGAAAA-TTCGA

                    
        660 GGGTAAAA
          1 GGGTAAAA

        668 CATAATTTTA


Statistics
Matches: 102,  Mismatches: 21, Indels: 8
        0.78            0.16        0.06

Matches are distributed among these distances:
  59   48  0.47
  60   52  0.51
  61    2  0.02

ACGTcount: A:0.34, C:0.04, G:0.24, T:0.39


Consensus pattern (60 bp):   
GGGTAAAATTTGAATTTTTAGAAAGTTTAGGGGTCAAATTTGAATTTTTGGAAAATTCGA

Done.