Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008341.1 Kokia drynarioides strain JFW-HI SEQ_123007, 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: 6608
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.37


Found at i:444 original size:25 final size:25

Alignment explanation


    Indices: 416--471  Score: 103
    Period size: 25  Copynumber: 2.2  Consensus size: 25

        406 CTCGTTTATT

                                     
        416 TATTAATGATATTTTCTTATAAAAA
          1 TATTAATGATATTTTCTTATAAAAA

                                  *  
        441 TATTAATGATATTTTCTTATAATAA
          1 TATTAATGATATTTTCTTATAAAAA

                  
        466 TATTAA
          1 TATTAA

        472 AATAATATTT


Statistics
Matches: 30,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  25   30  1.00

ACGTcount: A:0.43, C:0.04, G:0.04, T:0.50


Consensus pattern (25 bp):   
TATTAATGATATTTTCTTATAAAAA

Found at i:577 original size:23 final size:24

Alignment explanation


    Indices: 524--579  Score: 78
    Period size: 24  Copynumber: 2.4  Consensus size: 24

        514 TCATTAACAT

                *                   
        524 TGTTTGTGAACATGTTCAATTATA
          1 TGTTCGTGAACATGTTCAATTATA

                             **     
        548 TGTTCGTGAACATGTTCGTTTA-A
          1 TGTTCGTGAACATGTTCAATTATA

                     
        571 TGTTCGTGA
          1 TGTTCGTGA

        580 GTATATTCAA


Statistics
Matches: 29,  Mismatches: 3, Indels: 1
        0.88            0.09        0.03

Matches are distributed among these distances:
  23   10  0.34
  24   19  0.66

ACGTcount: A:0.23, C:0.11, G:0.21, T:0.45


Consensus pattern (24 bp):   
TGTTCGTGAACATGTTCAATTATA

Found at i:593 original size:23 final size:23

Alignment explanation


    Indices: 524--593  Score: 68
    Period size: 23  Copynumber: 3.0  Consensus size: 23

        514 TCATTAACAT

                *        *          
        524 TGTTTGTGAACATGTTCAATTATA
          1 TGTTCGTGAACATATTCAATTA-A

                         *   **    
        548 TGTTCGTGAACATGTTCGTTTAA
          1 TGTTCGTGAACATATTCAATTAA

                     **            
        571 TGTTCGTGAGTATATTCAATTAA
          1 TGTTCGTGAACATATTCAATTAA

        594 GTTAAATGAA


Statistics
Matches: 38,  Mismatches: 8, Indels: 1
        0.81            0.17        0.02

Matches are distributed among these distances:
  23   19  0.50
  24   19  0.50

ACGTcount: A:0.27, C:0.10, G:0.19, T:0.44


Consensus pattern (23 bp):   
TGTTCGTGAACATATTCAATTAA

Found at i:2907 original size:15 final size:16

Alignment explanation


    Indices: 2870--2916  Score: 51
    Period size: 15  Copynumber: 3.0  Consensus size: 16

       2860 TTTAAAACCT

                *           
       2870 TTGACCCAAATCCAAA
          1 TTGAACCAAATCCAAA

              *          *  
       2886 TTTAACCAAA-CCCAA
          1 TTGAACCAAATCCAAA

                     *      
       2901 TTGAACCAAGTCCAAA
          1 TTGAACCAAATCCAAA

       2917 CCCAAACCAA


Statistics
Matches: 24,  Mismatches: 6, Indels: 2
        0.75            0.19        0.06

Matches are distributed among these distances:
  15   12  0.50
  16   12  0.50

ACGTcount: A:0.45, C:0.30, G:0.06, T:0.19


Consensus pattern (16 bp):   
TTGAACCAAATCCAAA
Done.