Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004186.1 Kokia drynarioides strain JFW-HI SEQ_117419, 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: 24256
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35


Found at i:5598 original size:16 final size:16

Alignment explanation


    Indices: 5579--5617  Score: 51
    Period size: 16  Copynumber: 2.4  Consensus size: 16

       5569 ATTTTTTCTT

                            
       5579 ATTATGGCATCAATTA
          1 ATTATGGCATCAATTA

                *      *    
       5595 ATTAGGGCATCCATTA
          1 ATTATGGCATCAATTA

              *    
       5611 ATAATGG
          1 ATTATGG

       5618 TACTCAGAGG


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:0.36, C:0.13, G:0.18, T:0.33


Consensus pattern (16 bp):   
ATTATGGCATCAATTA

Found at i:14411 original size:22 final size:20

Alignment explanation


    Indices: 14372--14411  Score: 53
    Period size: 20  Copynumber: 1.9  Consensus size: 20

      14362 ATTCTTTTAT

                     *          
      14372 TTATATAAATAAATTAATCA
          1 TTATATAAAAAAATTAATCA

                                
      14392 TTATATAATAAAAATATAAT
          1 TTATATAA-AAAAAT-TAAT

      14412 TTTTATATTT


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  20    8  0.47
  21    5  0.29
  22    4  0.24

ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40


Consensus pattern (20 bp):   
TTATATAAAAAAATTAATCA

Found at i:14417 original size:22 final size:20

Alignment explanation


    Indices: 14371--14419  Score: 53
    Period size: 22  Copynumber: 2.4  Consensus size: 20

      14361 AATTCTTTTA

                      *         
      14371 TTTATATAAATAAATTAATC
          1 TTTATATAAAAAAATTAATC

            *                    *
      14391 ATTATATAATAAAAATATAATT
          1 TTTATATAA-AAAAAT-TAATC

                   
      14413 TTTATAT
          1 TTTATAT

      14420 TTATCATTAT


Statistics
Matches: 23,  Mismatches: 4, Indels: 2
        0.79            0.14        0.07

Matches are distributed among these distances:
  20    8  0.35
  21    5  0.22
  22   10  0.43

ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47


Consensus pattern (20 bp):   
TTTATATAAAAAAATTAATC

Found at i:14822 original size:20 final size:19

Alignment explanation


    Indices: 14786--14837  Score: 54
    Period size: 19  Copynumber: 2.8  Consensus size: 19

      14776 ATTGAAAAAT

                          *    
      14786 AAATA-TTAC-AAATATAA
          1 AAATATTTACAAAAAATAA

                                
      14803 AAATTATTTACAAAAAATAA
          1 AAA-TATTTACAAAAAATAA

            **             
      14823 TGATATTTACAAAAA
          1 AAATATTTACAAAAA

      14838 TTATTTGATT


Statistics
Matches: 29,  Mismatches: 3, Indels: 4
        0.81            0.08        0.11

Matches are distributed among these distances:
  17    3  0.10
  18    2  0.07
  19   16  0.55
  20    8  0.28

ACGTcount: A:0.62, C:0.06, G:0.02, T:0.31


Consensus pattern (19 bp):   
AAATATTTACAAAAAATAA
Done.