Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003456.1 Kokia drynarioides strain JFW-HI SEQ_116252, 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: 6006
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.35


Found at i:982 original size:22 final size:23

Alignment explanation


    Indices: 941--986  Score: 76
    Period size: 22  Copynumber: 2.0  Consensus size: 23

        931 TCAGCAAATG

                        *          
        941 ATTTTAAAATTATTAAAATTATT
          1 ATTTTAAAATTAATAAAATTATT

                                   
        964 ATTTTAAAA-TAATAAAATTATT
          1 ATTTTAAAATTAATAAAATTATT

             
        986 A
          1 A

        987 AATAATTTTA


Statistics
Matches: 22,  Mismatches: 1, Indels: 1
        0.92            0.04        0.04

Matches are distributed among these distances:
  22   13  0.59
  23    9  0.41

ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48


Consensus pattern (23 bp):   
ATTTTAAAATTAATAAAATTATT

Found at i:1969 original size:31 final size:29

Alignment explanation


    Indices: 1934--1998  Score: 85
    Period size: 29  Copynumber: 2.2  Consensus size: 29

       1924 ATTAAAATTA

                    *                      
       1934 TTTAATAATTTTATTATTTCAAAAAACTAAT
          1 TTTAATAAATTTA-TATTT-AAAAAACTAAT

                                    * *  
       1965 TTTAATAAATTTATATTTAAAAAATTTAT
          1 TTTAATAAATTTATATTTAAAAAACTAAT

                 
       1994 TTTAA
          1 TTTAA

       1999 AATCATTTGC


Statistics
Matches: 31,  Mismatches: 3, Indels: 2
        0.86            0.08        0.06

Matches are distributed among these distances:
  29   14  0.45
  30    5  0.16
  31   12  0.39

ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51


Consensus pattern (29 bp):   
TTTAATAAATTTATATTTAAAAAACTAAT

Found at i:1999 original size:14 final size:14

Alignment explanation


    Indices: 1947--2000  Score: 63
    Period size: 14  Copynumber: 3.8  Consensus size: 14

       1937 AATAATTTTA

                  *      *
       1947 TTATTTCAAAAAAC
          1 TTATTTTAAAAAAT

             *       *    
       1961 TAATTTTAATAAAT
          1 TTATTTTAAAAAAT

                           
       1975 TTATATTTAAAAAAT
          1 TTAT-TTTAAAAAAT

                       
       1990 TTATTTTAAAA
          1 TTATTTTAAAA

       2001 TCATTTGCTG


Statistics
Matches: 33,  Mismatches: 6, Indels: 2
        0.80            0.15        0.05

Matches are distributed among these distances:
  14   20  0.61
  15   13  0.39

ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46


Consensus pattern (14 bp):   
TTATTTTAAAAAAT

Found at i:2006 original size:15 final size:15

Alignment explanation


    Indices: 1932--2000  Score: 61
    Period size: 15  Copynumber: 4.6  Consensus size: 15

       1922 AAATTAAAAT

                   *  *    
       1932 TATTTAATAATTTTA
          1 TATTTAAAAAATTTA

                         * * 
       1947 TTATTTCAAAAAACTAA
          1 -TATTT-AAAAAATTTA

                   *       
       1964 T-TTTAATAAATTTA
          1 TATTTAAAAAATTTA

                           
       1978 TATTTAAAAAATTTA
          1 TATTTAAAAAATTTA

                     
       1993 T-TTTAAAA
          1 TATTTAAAA

       2001 TCATTTGCTG


Statistics
Matches: 43,  Mismatches: 8, Indels: 6
        0.75            0.14        0.11

Matches are distributed among these distances:
  14   15  0.35
  15   16  0.37
  16    6  0.14
  17    6  0.14

ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49


Consensus pattern (15 bp):   
TATTTAAAAAATTTA

Found at i:5969 original size:2 final size:2

Alignment explanation


    Indices: 5962--6006  Score: 90
    Period size: 2  Copynumber: 22.5  Consensus size: 2

       5952 TTTTAAGTCT

                                                                          
       5962 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

                
       6004 TA T
          1 TA T


Statistics
Matches: 43,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   43  1.00

ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51


Consensus pattern (2 bp):   
TA

Done.