Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014422.1 Kokia drynarioides strain JFW-HI SEQ_129460, 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: 6097
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34


Found at i:2772 original size:2 final size:2

Alignment explanation


    Indices: 2765--2798  Score: 59
    Period size: 2  Copynumber: 17.0  Consensus size: 2

       2755 TGATGGTATT

                                                      *       
       2765 TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA
          1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA

       2799 GGTTTTGTTT


Statistics
Matches: 30,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
   2   30  1.00

ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47


Consensus pattern (2 bp):   
TA

Found at i:3676 original size:9 final size:9

Alignment explanation


    Indices: 3662--3695  Score: 54
    Period size: 9  Copynumber: 4.0  Consensus size: 9

       3652 ATGAAAAGTA

                     
       3662 TTTAAAATT
          1 TTTAAAATT

                     
       3671 TTTAAAA--
          1 TTTAAAATT

                     
       3678 TTTAAAATT
          1 TTTAAAATT

                     
       3687 TTTAAAATT
          1 TTTAAAATT

       3696 AAATTTATTG


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

Matches are distributed among these distances:
   7    7  0.30
   9   16  0.70

ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53


Consensus pattern (9 bp):   
TTTAAAATT

Found at i:3682 original size:16 final size:16

Alignment explanation


    Indices: 3661--3695  Score: 70
    Period size: 16  Copynumber: 2.2  Consensus size: 16

       3651 AATGAAAAGT

                            
       3661 ATTTAAAATTTTTAAA
          1 ATTTAAAATTTTTAAA

                            
       3677 ATTTAAAATTTTTAAA
          1 ATTTAAAATTTTTAAA

               
       3693 ATT
          1 ATT

       3696 AAATTTATTG


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  16   19  1.00

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


Consensus pattern (16 bp):   
ATTTAAAATTTTTAAA

Found at i:3712 original size:14 final size:14

Alignment explanation


    Indices: 3666--3701  Score: 54
    Period size: 16  Copynumber: 2.4  Consensus size: 14

       3656 AAAGTATTTA

                           
       3666 AAATTTTTAAAATTT
          1 AAATTTTTAAAA-TT

                           
       3681 AAAATTTTTAAAATT
          1 -AAATTTTTAAAATT

                  
       3696 AAATTT
          1 AAATTT

       3702 ATTGAAATAA


Statistics
Matches: 20,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  14    6  0.30
  15    2  0.10
  16   12  0.60

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


Consensus pattern (14 bp):   
AAATTTTTAAAATT
Done.