Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004038.1 Kokia drynarioides strain JFW-HI SEQ_117176, 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: 3988
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33


Found at i:530 original size:29 final size:30

Alignment explanation


    Indices: 498--654  Score: 151
    Period size: 29  Copynumber: 5.3  Consensus size: 30

        488 AAAAATTCAA

                                          
        498 TTTTTACCCTCGAACTTCCAAAAA-CCCAT
          1 TTTTTACCCTCGAACTTCCAAAAATCCCAT

                *       *   *              
        527 TTTTAACCC-CAAAACATCCAAAAATCCCA-
          1 TTTTTACCCTC-GAACTTCCAAAAATCCCAT

                     *        *        *  
        556 TTTTTACCCCCGAACTTCTAAAAATCCAAT
          1 TTTTTACCCTCGAACTTCCAAAAATCCCAT

                *     **     *     * *    
        586 TTTTAACCCTAAAACTTTCAAAAGTTCCA-
          1 TTTTTACCCTCGAACTTCCAAAAATCCCAT

                           *              
        615 TTTTTACCCTCGAACCTCCAAAAATCCCAT
          1 TTTTTACCCTCGAACTTCCAAAAATCCCAT

                *     
        645 TTTTGACCCT
          1 TTTTTACCCT

        655 GAATTTTCCC


Statistics
Matches: 98,  Mismatches: 25, Indels: 9
        0.74            0.19        0.07

Matches are distributed among these distances:
  28    1  0.01
  29   63  0.64
  30   34  0.35

ACGTcount: A:0.34, C:0.32, G:0.03, T:0.31


Consensus pattern (30 bp):   
TTTTTACCCTCGAACTTCCAAAAATCCCAT

Found at i:616 original size:59 final size:59

Alignment explanation


    Indices: 485--654  Score: 234
    Period size: 59  Copynumber: 2.9  Consensus size: 59

        475 CACTAAATTG

                       *                                        *      
        485 TTCAAAAATTCAATTTTTACCCTCGAACTTCCAAAAA-CCCATTTTTAACCCCAAAACA
          1 TTCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCTAAAACA

             *       *            *        *        *                 *
        543 TCCAAAAATCCCATTTTTACCCCCGAACTTCTAAAAATCCAATTTTTAACCCTAAAACT
          1 TTCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCTAAAACA

                   *                    *                  *     
        602 TTCAAAAGTTCCATTTTTACCCTCGAACCTCCAAAAATCCCATTTTTGACCCT
          1 TTCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCT

        655 GAATTTTCCC


Statistics
Matches: 95,  Mismatches: 16, Indels: 1
        0.85            0.14        0.01

Matches are distributed among these distances:
  58   32  0.34
  59   63  0.66

ACGTcount: A:0.35, C:0.31, G:0.03, T:0.31


Consensus pattern (59 bp):   
TTCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCCTAAAACA
Done.