Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000953.1 Kokia drynarioides strain JFW-HI SEQ_112126, 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: 3390
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34


Found at i:2836 original size:30 final size:29

Alignment explanation


    Indices: 2802--3034  Score: 210
    Period size: 30  Copynumber: 7.9  Consensus size: 29

       2792 ATTCAAGGTC

                                         *
       2802 AAAATGTAATTTTGGAAAAGTTTAGGTGTA
          1 AAAATGTAATTTTGGAAAAGTTTAGG-GTT

                                          
       2832 AAAATGTAATTTTAGG-AAAGTTT-GGGTT
          1 AAAATGTAATTTT-GGAAAAGTTTAGGGTT

                   *       **     *      
       2860 AAAATGTGATTTTGGTGAAGTTCAGGGTT
          1 AAAATGTAATTTTGGAAAAGTTTAGGGTT

                           * *            *
       2889 AAAATGCT-ATTTTGTAGAAGTTTAAGGGTC
          1 AAAATG-TAATTTTGGAAAAGTTT-AGGGTT

                  *                       
       2919 AAAATGCAATTTTGGAAAAGTTTAGAGGTT
          1 AAAATGTAATTTTGGAAAAGTTTAG-GGTT

                                         *
       2949 AAAATGTAA-TTTGGAAAAGTTTAAGGGTC
          1 AAAATGTAATTTTGGAAAAGTTT-AGGGTT

                                            
       2978 AAAATGTAATTTT--AAAGTAGTTTGAGGGTT
          1 AAAATGTAATTTTGGAAA--AGTTT-AGGGTT

                 *   *    *             
       3008 AAAATATGATTTTTTG-AAAGTTTAGGG
          1 AAAATGT-AATTTTGGAAAAGTTTAGGG

       3035 ACCTTTTGGG


Statistics
Matches: 171,  Mismatches: 18, Indels: 29
        0.78            0.08        0.13

Matches are distributed among these distances:
  27    2  0.01
  28   22  0.13
  29   56  0.33
  30   82  0.48
  31    7  0.04
  32    2  0.01

ACGTcount: A:0.36, C:0.02, G:0.24, T:0.37


Consensus pattern (29 bp):   
AAAATGTAATTTTGGAAAAGTTTAGGGTT

Found at i:2940 original size:59 final size:58

Alignment explanation


    Indices: 2798--3012  Score: 233
    Period size: 59  Copynumber: 3.7  Consensus size: 58

       2788 GAGAATTCAA

                                             *                           
       2798 GGTCAAAATGTAATTTTGGAAAAGTTTAGGTGTAAAAATGTAATTT-TAGGAAAGTTT--G
          1 GGTCAAAATGTAATTTTGGAAAAGTTTAGG-GTTAAAATGTAATTTGTA-G-AAGTTTAAG

               *       *       **     *               *                
       2856 GGTTAAAATGTGATTTTGGTGAAGTTCAGGGTTAAAATGCTATTTTGTAGAAGTTTAAG
          1 GGTCAAAATGTAATTTTGGAAAAGTTTAGGGTTAAAATG-TAATTTGTAGAAGTTTAAG

                      *                                    * *         
       2915 GGTCAAAATGCAATTTTGGAAAAGTTTAGAGGTTAAAATGTAATTTGGAAAAGTTTAAG
          1 GGTCAAAATGTAATTTTGGAAAAGTTTAG-GGTTAAAATGTAATTTGTAGAAGTTTAAG

                                                     
       2974 GGTCAAAATGTAATTTT--AAAGTAGTTTGAGGGTTAAAAT
          1 GGTCAAAATGTAATTTTGGAAA--AGTTT-AGGGTTAAAAT

       3013 ATGATTTTTT


Statistics
Matches: 132,  Mismatches: 17, Indels: 15
        0.80            0.10        0.09

Matches are distributed among these distances:
  57   17  0.13
  58   31  0.23
  59   72  0.55
  60   12  0.09

ACGTcount: A:0.37, C:0.03, G:0.25, T:0.36


Consensus pattern (58 bp):   
GGTCAAAATGTAATTTTGGAAAAGTTTAGGGTTAAAATGTAATTTGTAGAAGTTTAAG
Done.