Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004323.1 Kokia drynarioides strain JFW-HI SEQ_117642, 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: 11109
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.37


Found at i:695 original size:16 final size:16

Alignment explanation


    Indices: 670--708  Score: 51
    Period size: 16  Copynumber: 2.4  Consensus size: 16

        660 TTTATAAGTC

                       **   
        670 TTTTTATTTTTTTATA
          1 TTTTTATTTTTAAATA

                 *          
        686 TTTTTGTTTTTAAATA
          1 TTTTTATTTTTAAATA

                   
        702 TTTTTAT
          1 TTTTTAT

        709 AAATTTTAAA


Statistics
Matches: 19,  Mismatches: 4, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  16   19  1.00

ACGTcount: A:0.21, C:0.00, G:0.03, T:0.77


Consensus pattern (16 bp):   
TTTTTATTTTTAAATA

Found at i:3494 original size:24 final size:24

Alignment explanation


    Indices: 3462--3510  Score: 89
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       3452 GATTTATATT

                *                   
       3462 AAAGGTTGGATAGAGCCATTTGTA
          1 AAAGCTTGGATAGAGCCATTTGTA

                                    
       3486 AAAGCTTGGATAGAGCCATTTGTA
          1 AAAGCTTGGATAGAGCCATTTGTA

             
       3510 A
          1 A

       3511 CGGAGCTTAG


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  24   24  1.00

ACGTcount: A:0.35, C:0.10, G:0.27, T:0.29


Consensus pattern (24 bp):   
AAAGCTTGGATAGAGCCATTTGTA

Found at i:8889 original size:17 final size:16

Alignment explanation


    Indices: 8862--8893  Score: 55
    Period size: 17  Copynumber: 1.9  Consensus size: 16

       8852 AAATTTATAT

                            
       8862 ATTTTAATTTTTAAAA
          1 ATTTTAATTTTTAAAA

                            
       8878 ATTTTCAATTTTTAAA
          1 ATTTT-AATTTTTAAA

       8894 TATAATTTTT


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  16    5  0.33
  17   10  0.67

ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56


Consensus pattern (16 bp):   
ATTTTAATTTTTAAAA
Done.