Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003296.1 Kokia drynarioides strain JFW-HI SEQ_115975, 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: 3868
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.33


Found at i:395 original size:20 final size:20

Alignment explanation


    Indices: 370--414  Score: 56
    Period size: 20  Copynumber: 2.2  Consensus size: 20

        360 CATGATTTGT

                           *     
        370 ATTAAGAGTAAATA-TGATTA
          1 ATTAAGAGTAAA-AGAGATTA

                   *            
        390 ATTAAGATTAAAAGAGATTA
          1 ATTAAGAGTAAAAGAGATTA

                 
        410 ATTAA
          1 ATTAA

        415 AGCTTAATAA


Statistics
Matches: 22,  Mismatches: 2, Indels: 2
        0.85            0.08        0.08

Matches are distributed among these distances:
  19    1  0.05
  20   21  0.95

ACGTcount: A:0.53, C:0.00, G:0.13, T:0.33


Consensus pattern (20 bp):   
ATTAAGAGTAAAAGAGATTA

Found at i:2617 original size:83 final size:83

Alignment explanation


    Indices: 2464--2618  Score: 188
    Period size: 83  Copynumber: 1.9  Consensus size: 83

       2454 ATTACGTAAG

                                               *         * *            *    
       2464 GATGAACAATGATAAATGAATAGTAAGACACCAGAGCCCTAATAGGCGATGATTTTCAAGTTTTG
          1 GATGAACAATGATAAATGAATAGTAAGACACCAGAACCCTAATAGACAATGATTTTCAAGATTTG

            *                 
       2529 GGTGTTATATTTAGTCAA
         66 AGTGTTATATTTAGTCAA

                    *        *              *    *         *                 
       2547 GATGAACAGTGATAAATTAATAGTAAGACACCGGAACTCTAACT-GATAATGATTTTCGAA-ATT
          1 GATGAACAATGATAAATGAATAGTAAGACACCAGAACCCTAA-TAGACAATGATTTTC-AAGATT

                     
       2610 TGAGTGTTA
         64 TGAGTGTTA

       2619 CATTCCTGGT


Statistics
Matches: 60,  Mismatches: 10, Indels: 4
        0.81            0.14        0.05

Matches are distributed among these distances:
  83   57  0.95
  84    3  0.05

ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30


Consensus pattern (83 bp):   
GATGAACAATGATAAATGAATAGTAAGACACCAGAACCCTAATAGACAATGATTTTCAAGATTTG
AGTGTTATATTTAGTCAA
Done.