Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005855.1 Kokia drynarioides strain JFW-HI SEQ_120170, 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, 698

Length: 1164
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31


Found at i:316 original size:60 final size:59

Alignment explanation


    Indices: 251--486  Score: 190
    Period size: 60  Copynumber: 3.9  Consensus size: 59

        241 AGATGTCAGC

                    * *                           *  *          *       
        251 GTCAAAATGTGATTTTAGGAAAGTTTAGGGGTCAAAATGTGCTTTTTTAAAATTTTAGGG
          1 GTCAAAATATAATTTTA-GAAAGTTTAGGGGTCAAAATATGATTTTTTAAAAGTTTAGGG

                    **                  *        * * *     ** *           
        311 GTCAAAATGCAATTTTAGAAGAGTTTAGAGG-CTAAAGTGTAATTTTAGAGAAGTTTGAGGG
          1 GTCAAAATATAATTTTAGAA-AGTTTAGGGGTC-AAAATATGATTTTTTAAAAGTTT-AGGG

                   *        *               *       *                 * 
        372 GT-AAAAAATAATTTTGGAAAAGTTTAGGGGTTAAAATATAATTTTTTAAAAGTTTAGTG
          1 GTCAAAATATAATTTTAG-AAAGTTTAGGGGTCAAAATATGATTTTTTAAAAGTTTAGGG

                        *     *           *                *         
        431 GTCAAAATATGATTTTTAAAAAGTTTAGGGCT-AAAATATGATTTTTAAAAAGTTTA
          1 GTCAAAATAT-AATTTTAGAAAGTTTAGGGGTCAAAATATGATTTTTTAAAAGTTTA

        487 AGGACCTACT


Statistics
Matches: 140,  Mismatches: 29, Indels: 15
        0.76            0.16        0.08

Matches are distributed among these distances:
  59   31  0.22
  60   96  0.69
  61   13  0.09

ACGTcount: A:0.38, C:0.03, G:0.22, T:0.37


Consensus pattern (59 bp):   
GTCAAAATATAATTTTAGAAAGTTTAGGGGTCAAAATATGATTTTTTAAAAGTTTAGGG

Found at i:466 original size:29 final size:29

Alignment explanation


    Indices: 270--486  Score: 168
    Period size: 30  Copynumber: 7.3  Consensus size: 29

        260 TGATTTTAGG

                               *  *     * 
        270 AAAGTTTAGGGGTCAAAATGTGCTTTTTTA
          1 AAAGTTTAGGGGT-AAAATATGATTTTTAA

               *         *         *       
        300 AAATTTTAGGGGTCAAA-ATGCAATTTTAGA
          1 AAAGTTTAGGGGTAAAATATG-ATTTTTA-A

             *          *    * *   *       
        330 AGAGTTTAGAGGCTAAAGTGT-AATTTTAGA
          1 AAAGTTTAG-GGGTAAAATATGATTTTTA-A

            *                 *  *     ** 
        360 GAAGTTTGAGGGGTAAAAAATAATTTTGGA
          1 AAAGTTT-AGGGGTAAAATATGATTTTTAA

                                 *      * 
        390 AAAGTTTAGGGGTTAAAATATAATTTTTTA
          1 AAAGTTTAGGGG-TAAAATATGATTTTTAA

                     *                    
        420 AAAGTTTAGTGGTCAAAATATGATTTTTAA
          1 AAAGTTTAGGGGT-AAAATATGATTTTTAA

                       *                 
        450 AAAGTTTAGGGCTAAAATATGATTTTTAA
          1 AAAGTTTAGGGGTAAAATATGATTTTTAA

                    
        479 AAAGTTTA
          1 AAAGTTTA

        487 AGGACCTACT


Statistics
Matches: 149,  Mismatches: 30, Indels: 17
        0.76            0.15        0.09

Matches are distributed among these distances:
  28    2  0.01
  29   37  0.25
  30   98  0.66
  31   11  0.07
  32    1  0.01

ACGTcount: A:0.39, C:0.03, G:0.21, T:0.37


Consensus pattern (29 bp):   
AAAGTTTAGGGGTAAAATATGATTTTTAA
Done.