Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007979.1 Kokia drynarioides strain JFW-HI SEQ_122630, 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: 9836
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35


Found at i:2716 original size:11 final size:11

Alignment explanation


    Indices: 2689--2731  Score: 50
    Period size: 11  Copynumber: 3.9  Consensus size: 11

       2679 ACAATAACGA

                      *
       2689 CAAAATAATAA
          1 CAAAATAATAG

                       
       2700 CAAAATAATAG
          1 CAAAATAATAG

            **    *    
       2711 TGAAATGATAG
          1 CAAAATAATAG

                      
       2722 CAAAATAATA
          1 CAAAATAATA

       2732 TAAAAACAAC


Statistics
Matches: 25,  Mismatches: 7, Indels: 0
        0.78            0.22        0.00

Matches are distributed among these distances:
  11   25  1.00

ACGTcount: A:0.63, C:0.07, G:0.09, T:0.21


Consensus pattern (11 bp):   
CAAAATAATAG

Found at i:3828 original size:16 final size:17

Alignment explanation


    Indices: 3798--3830  Score: 50
    Period size: 18  Copynumber: 1.9  Consensus size: 17

       3788 AGTTAGAGAA

                              
       3798 GAAAAAAAAGGAAAATTT
          1 GAAAAAAAA-GAAAATTT

                            
       3816 GAAAAAAAA-AAAATT
          1 GAAAAAAAAGAAAATT

       3831 AAAATGTTTT


Statistics
Matches: 15,  Mismatches: 0, Indels: 2
        0.88            0.00        0.12

Matches are distributed among these distances:
  16    6  0.40
  18    9  0.60

ACGTcount: A:0.73, C:0.00, G:0.12, T:0.15


Consensus pattern (17 bp):   
GAAAAAAAAGAAAATTT

Found at i:9656 original size:22 final size:22

Alignment explanation


    Indices: 9615--9657  Score: 68
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       9605 AACTTTCTTT

                          *       
       9615 TTTTGTTGTCATTTTATTATTG
          1 TTTTGTTGTCATTTCATTATTG

                           *     
       9637 TTTTGTTGTCATTTCGTTATT
          1 TTTTGTTGTCATTTCATTATT

       9658 ATATTGTTAT


Statistics
Matches: 19,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  22   19  1.00

ACGTcount: A:0.12, C:0.07, G:0.14, T:0.67


Consensus pattern (22 bp):   
TTTTGTTGTCATTTCATTATTG

Found at i:9664 original size:22 final size:22

Alignment explanation


    Indices: 9617--9665  Score: 62
    Period size: 22  Copynumber: 2.2  Consensus size: 22

       9607 CTTTCTTTTT

                        *      * *
       9617 TTGTTGTCATTTTATTATTGTT
          1 TTGTTGTCATTTCATTATTATA

                         *        
       9639 TTGTTGTCATTTCGTTATTATA
          1 TTGTTGTCATTTCATTATTATA

                 
       9661 TTGTT
          1 TTGTT

       9666 ATTATTTTAT


Statistics
Matches: 23,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  22   23  1.00

ACGTcount: A:0.14, C:0.06, G:0.14, T:0.65


Consensus pattern (22 bp):   
TTGTTGTCATTTCATTATTATA
Done.