Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005854.1 Kokia drynarioides strain JFW-HI SEQ_120169, 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:0.16, T:0.31


Found at i:286 original size:30 final size:29

Alignment explanation


    Indices: 251--438  Score: 128
    Period size: 30  Copynumber: 6.3  Consensus size: 29

        241 AGATGTCAGC

                      *                   
        251 GTCAAAATGTGATTTTAGGAAAGTTTAAGG
          1 GTCAAAATGTAATTTT-GGAAAGTTTAAGG

                    *  **    **        *  
        281 GTCAAAATTTGCTTTTTTTAAAGTTTAGGG
          1 GTCAAAATGT-AATTTTGGAAAGTTTAAGG

                     *                   * 
        311 GTCAAAATGCAATTTTGGAAGAGTTTAGAAG
          1 GTCAAAATGTAATTTTGGAA-AGTTTA-AGG

            *     *                     *  
        342 CT-AAAGTGTAATTTTGGATAAGTTTGAGGG
          1 GTCAAAATGTAATTTTGGA-AAGTTT-AAGG

                   **                  *  
        372 GT-AAAAAATAATTTTGGAAAAGTTTAGGG
          1 GTCAAAATGTAATTTTGG-AAAGTTTAAGG

              *              **           
        401 GTTAAAATGTAATTTTTTTAAAGTTTAAGG
          1 GTCAAAATGTAA-TTTTGGAAAGTTTAAGG

                    
        431 GTCAAAAT
          1 GTCAAAAT

        439 ATGATTTTTA


Statistics
Matches: 121,  Mismatches: 29, Indels: 16
        0.73            0.17        0.10

Matches are distributed among these distances:
  29   12  0.10
  30   96  0.79
  31   13  0.11

ACGTcount: A:0.36, C:0.04, G:0.23, T:0.37


Consensus pattern (29 bp):   
GTCAAAATGTAATTTTGGAAAGTTTAAGG

Found at i:446 original size:30 final size:30

Alignment explanation


    Indices: 270--489  Score: 115
    Period size: 30  Copynumber: 7.4  Consensus size: 30

        260 TGATTTTAGG

                               * **     **
        270 AAAGTTTAAGGGTCAAAATTTGCTTTTTTT
          1 AAAGTTTAAGGGTCAAAATATAATTTTTAA

                    *          **      ** 
        300 AAAGTTTAGGGGTCAAAATGCAATTTTGGA
          1 AAAGTTTAAGGGTCAAAATATAATTTTTAA

             *        * *     * *       ** 
        330 AGAGTTTAGAAGCT-AAAGTGTAATTTTGGA
          1 AAAGTTTA-AGGGTCAAAATATAATTTTTAA

            *        *         *        ** 
        360 TAAGTTTGAGGGGT-AAAAAATAATTTTGGA
          1 AAAGTTT-AAGGGTCAAAATATAATTTTTAA

                    *    *     *        **
        390 AAAGTTTAGGGGTTAAAATGTAATTTTTTT
          1 AAAGTTTAAGGGTCAAAATATAATTTTTAA

                                 *        
        420 AAAGTTTAAGGGTCAAAATATGATTTTTAA
          1 AAAGTTTAAGGGTCAAAATATAATTTTTAA

                    *             *        
        450 AAAGTTT-CGGG-CTAAAATATTATTTTTAA
          1 AAAGTTTAAGGGTC-AAAATATAATTTTTAA

                       
        479 AAAGTTTAAGG
          1 AAAGTTTAAGG

        490 ACCTACTAGA


Statistics
Matches: 148,  Mismatches: 37, Indels: 10
        0.76            0.19        0.05

Matches are distributed among these distances:
  28    1  0.01
  29   31  0.21
  30  113  0.76
  31    3  0.02

ACGTcount: A:0.37, C:0.04, G:0.21, T:0.38


Consensus pattern (30 bp):   
AAAGTTTAAGGGTCAAAATATAATTTTTAA

Found at i:446 original size:60 final size:60

Alignment explanation


    Indices: 293--489  Score: 175
    Period size: 60  Copynumber: 3.3  Consensus size: 60

        283 CAAAATTTGC

                           *          **          *       **      *     
        293 TTTTTTTAAAGTTTAGGGGTCAAAATGCAATTTTGGAAGAGTTTAGAAGCTAAAGTGTAA
          1 TTTTTTTAAAGTTTAAGGGTCAAAATATAATTTTGGAAAAGTTTAGGGGCTAAAATGTAA

                 **          *         *                       *          
        353 -TTTTGGATAAGTTTGAGGGGT-AAAAAATAATTTTGGAAAAGTTTAGGGGTTAAAATGTAA
          1 TTTTTTTA-AAGTTT-AAGGGTCAAAATATAATTTTGGAAAAGTTTAGGGGCTAAAATGTAA

                                        *     **         *          * * 
        413 TTTTTTTAAAGTTTAAGGGTCAAAATATGATTTTTAAAAAGTTT-CGGGCTAAAATATTA
          1 TTTTTTTAAAGTTTAAGGGTCAAAATATAATTTTGGAAAAGTTTAGGGGCTAAAATGTAA

                 **           
        472 TTTTTAAAAAGTTTAAGG
          1 TTTTTTTAAAGTTTAAGG

        490 ACCTACTAGA


Statistics
Matches: 110,  Mismatches: 23, Indels: 9
        0.77            0.16        0.06

Matches are distributed among these distances:
  59   37  0.34
  60   62  0.56
  61   11  0.10

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


Consensus pattern (60 bp):   
TTTTTTTAAAGTTTAAGGGTCAAAATATAATTTTGGAAAAGTTTAGGGGCTAAAATGTAA
Done.