Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005588.1 Kokia drynarioides strain JFW-HI SEQ_119711, 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, 891

Length: 1486
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32


Found at i:149 original size:20 final size:20

Alignment explanation


    Indices: 124--216  Score: 59
    Period size: 20  Copynumber: 4.7  Consensus size: 20

        114 AAAGAGGGTT

                                
        124 TCGATATTTTTCAAATATTA
          1 TCGATATTTTTCAAATATTA

                    *              
        144 TCGATA--CTT-AAATATGGGTA
          1 TCGATATTTTTCAAATAT---TA

             *        *         
        164 TTGATATTTTCCAAATATTA
          1 TCGATATTTTTCAAATATTA

                  **    *     *  
        184 TCGATACCTTT-GAATGAGTA
          1 TCGATATTTTTCAAAT-ATTA

                         
        204 TCGATATTTTTCA
          1 TCGATATTTTTCA

        217 GACGTTTCAA


Statistics
Matches: 52,  Mismatches: 13, Indels: 15
        0.65            0.16        0.19

Matches are distributed among these distances:
  17    6  0.12
  18    2  0.04
  19    3  0.06
  20   34  0.65
  22    1  0.02
  23    6  0.12

ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44


Consensus pattern (20 bp):   
TCGATATTTTTCAAATATTA

Found at i:170 original size:40 final size:40

Alignment explanation


    Indices: 124--216  Score: 125
    Period size: 40  Copynumber: 2.3  Consensus size: 40

        114 AAAGAGGGTT

                                                 *   
        124 TCGATATTTTTCAAATATTATCGATA-CTTAAATATGGGTA
          1 TCGATATTTTTCAAATATTATCGATACCTTAAA-ATGAGTA

             *        *                   **        
        164 TTGATATTTTCCAAATATTATCGATACCTTTGAATGAGTA
          1 TCGATATTTTTCAAATATTATCGATACCTTAAAATGAGTA

                         
        204 TCGATATTTTTCA
          1 TCGATATTTTTCA

        217 GACGTTTCAA


Statistics
Matches: 45,  Mismatches: 7, Indels: 2
        0.83            0.13        0.04

Matches are distributed among these distances:
  40   41  0.91
  41    4  0.09

ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44


Consensus pattern (40 bp):   
TCGATATTTTTCAAATATTATCGATACCTTAAAATGAGTA
Done.