Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003476.1 Kokia drynarioides strain JFW-HI SEQ_116282, 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: 2206
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.40


Found at i:568 original size:31 final size:31

Alignment explanation


    Indices: 525--601  Score: 111
    Period size: 31  Copynumber: 2.5  Consensus size: 31

        515 GAACCCCAAA

                   *                       
        525 AAGTTTAAGTACCAACTTAAAAAAAAGTGCC
          1 AAGTTTAGGTACCAACTTAAAAAAAAGTGCC

                               **          
        556 AAGTTTAGGTACCAACTTAGGAAAAAGTGCC
          1 AAGTTTAGGTACCAACTTAAAAAAAAGTGCC

                            
        587 AAGTTT-GAGTACCAA
          1 AAGTTTAG-GTACCAA

        602 ATTTAACCAG


Statistics
Matches: 42,  Mismatches: 3, Indels: 2
        0.89            0.06        0.04

Matches are distributed among these distances:
  30    1  0.02
  31   41  0.98

ACGTcount: A:0.43, C:0.16, G:0.18, T:0.23


Consensus pattern (31 bp):   
AAGTTTAGGTACCAACTTAAAAAAAAGTGCC

Found at i:616 original size:90 final size:91

Alignment explanation


    Indices: 470--662  Score: 228
    Period size: 90  Copynumber: 2.1  Consensus size: 91

        460 TAAAAAAAGA

                                     *                          *            
        470 TTAGGTACCAAAATAGGAAAAAGAGTCAAGTTCAAGTACCAAATTGAACC-CCAAAAAGTTTAAG
          1 TTAGGTACCAAAATAGGAAAAAGAGCCAAGTTCAAGTACCAAATTGAACCACAAAAAAGTTTAAG

                  *                    
        534 TACCAACTTA-AAAAAAAGTGCCAAGT
         66 TACCAAATTAGAAAAAAA-TGCCAAGT

                       **          *        **           *     *           * 
        560 TTAGGTACCAACTTAGGAAAAAGTGCCAAGTTTGAGTACCAAATTTAACCAGAAAAAAGTTTAGG
          1 TTAGGTACCAAAATAGGAAAAAGAGCCAAGTTCAAGTACCAAATTGAACCACAAAAAAGTTTAAG

                       *        *     
        625 TACCAAATTAGGAAAAAATGTCAAGT
         66 TACCAAATTAGAAAAAAATGCCAAGT

             * *        
        651 TCAAGTACCAAA
          1 TTAGGTACCAAA

        663 TATTATATTA


Statistics
Matches: 85,  Mismatches: 16, Indels: 3
        0.82            0.15        0.03

Matches are distributed among these distances:
  90   43  0.51
  91   36  0.42
  92    6  0.07

ACGTcount: A:0.46, C:0.16, G:0.17, T:0.22


Consensus pattern (91 bp):   
TTAGGTACCAAAATAGGAAAAAGAGCCAAGTTCAAGTACCAAATTGAACCACAAAAAAGTTTAAG
TACCAAATTAGAAAAAAATGCCAAGT

Done.