Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007182.1 Kokia drynarioides strain JFW-HI SEQ_121795, 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: 7200
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35


Found at i:753 original size:55 final size:55

Alignment explanation


    Indices: 679--791  Score: 208
    Period size: 55  Copynumber: 2.1  Consensus size: 55

        669 AATAAGATTT

                                                                   
        679 AAACACAAGTTTTTCAACACTCCACCAATACTTATTATTGTTTAAATTTTAAAAG
          1 AAACACAAGTTTTTCAACACTCCACCAATACTTATTATTGTTTAAATTTTAAAAG

                          *                                    *   
        734 AAACACAAGTTTTTTAACACTCCACCAATACTTATTATTGTTTAAATTTTAGAAG
          1 AAACACAAGTTTTTCAACACTCCACCAATACTTATTATTGTTTAAATTTTAAAAG

               
        789 AAA
          1 AAA

        792 TATTTTTGAA


Statistics
Matches: 56,  Mismatches: 2, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  55   56  1.00

ACGTcount: A:0.41, C:0.17, G:0.06, T:0.36


Consensus pattern (55 bp):   
AAACACAAGTTTTTCAACACTCCACCAATACTTATTATTGTTTAAATTTTAAAAG

Found at i:2409 original size:105 final size:105

Alignment explanation


    Indices: 2221--2412  Score: 339
    Period size: 105  Copynumber: 1.8  Consensus size: 105

       2211 GTCAATATGG

                *     *   *                                                  
       2221 TTTGTATATTTTGGGTCATGCTACAAACATTATAATTCTTGAAGGATTTAAATGAAATTTAGTAA
          1 TTTGAATATTGTGGATCATGCTACAAACATTATAATTCTTGAAGGATTTAAATGAAATTTAGTAA

                         *                          
       2286 ATTAATGCTGTATTTGGTTTGTATATTTTAAGTTAAGGAT
         66 ATTAATGCTGTATATGGTTTGTATATTTTAAGTTAAGGAT

                                                                             
       2326 TTTGAATATTGTGGATCATGCTACAAACATTATAATTCTTGAAGGATTTAAATGAAATTTAGTAA
          1 TTTGAATATTGTGGATCATGCTACAAACATTATAATTCTTGAAGGATTTAAATGAAATTTAGTAA

                   *              
       2391 ATTAATGTTGTATATGGTTTGT
         66 ATTAATGCTGTATATGGTTTGT

       2413 GTAAGTGTTT


Statistics
Matches: 82,  Mismatches: 5, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
 105   82  1.00

ACGTcount: A:0.33, C:0.06, G:0.17, T:0.44


Consensus pattern (105 bp):   
TTTGAATATTGTGGATCATGCTACAAACATTATAATTCTTGAAGGATTTAAATGAAATTTAGTAA
ATTAATGCTGTATATGGTTTGTATATTTTAAGTTAAGGAT

Found at i:5870 original size:35 final size:32

Alignment explanation


    Indices: 5829--5897  Score: 93
    Period size: 32  Copynumber: 2.1  Consensus size: 32

       5819 GTTCGATTGC

                                               
       5829 AAAAATAAGATTCATCAACTCGACTAATTGCAATA
          1 AAAAATAAGA-T--TCAACTCGACTAATTGCAATA

                   *     *                  
       5864 AAAAATAGGATTCGACTCGACTAATTGCAATA
          1 AAAAATAAGATTCAACTCGACTAATTGCAATA

              
       5896 AA
          1 AA

       5898 GAAACCATTT


Statistics
Matches: 32,  Mismatches: 2, Indels: 3
        0.86            0.05        0.08

Matches are distributed among these distances:
  32   22  0.69
  34    1  0.03
  35    9  0.28

ACGTcount: A:0.48, C:0.16, G:0.12, T:0.25


Consensus pattern (32 bp):   
AAAAATAAGATTCAACTCGACTAATTGCAATA
Done.