Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002394.1 Kokia drynarioides strain JFW-HI SEQ_114480, 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, 825

Length: 1376
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30


Found at i:525 original size:30 final size:30

Alignment explanation


    Indices: 491--795  Score: 306
    Period size: 30  Copynumber: 10.3  Consensus size: 30

        481 CGGGAGTGGA

                            *           * 
        491 ATTTTTGGAAGTTTTGGGGTCAAAAATGAG
          1 ATTTTTGGAAGTTTTGAGGTCAAAAATGGG

                            *   *         
        521 ATTTTTGGAAGTTTTGGGGTTAAAAATGGG
          1 ATTTTTGGAAGTTTTGAGGTCAAAAATGGG

                                     *  * 
        551 ATTTTTGGAAG-TTTGAGGTCAAAATTGAG
          1 ATTTTTGGAAGTTTTGAGGTCAAAAATGGG

                            *          *  
        580 ATTTTTGGAAGTTTTGTGGTC-AAAATAGG
          1 ATTTTTGGAAGTTTTGAGGTCAAAAATGGG

                       *  *               *
        609 ATTTTTGGAA-ATTCGAGG-CTAAAAATGGA
          1 ATTTTTGGAAGTTTTGAGGTC-AAAAATGGG

                     *    *               
        638 ATTTTTGGAGGTTTCGAGGTCAAAAATGGG
          1 ATTTTTGGAAGTTTTGAGGTCAAAAATGGG

                       *  *                
        668 ATTTTTGGAA-ATTCGAGG-CTAAAAA-GGG
          1 ATTTTTGGAAGTTTTGAGGTC-AAAAATGGG

                             *             
        696 AATTTTTGGAAGTTTTGGGGTCAAAAATGGG
          1 -ATTTTTGGAAGTTTTGAGGTCAAAAATGGG

                          *               **
        727 ATTTTTGGAAG-TTCGAGGGGT-AAAAATGAA
          1 ATTTTTGGAAGTTTTGA--GGTCAAAAATGGG

                           *              
        757 ATTTTTGGAAG-TTTCAGGTCAAAAATGGG
          1 ATTTTTGGAAGTTTTGAGGTCAAAAATGGG

                 *    
        786 ATTTTGGGAA
          1 ATTTTTGGAA

        796 ATTCGAGGCT


Statistics
Matches: 230,  Mismatches: 32, Indels: 27
        0.80            0.11        0.09

Matches are distributed among these distances:
  27    1  0.00
  28   12  0.05
  29   96  0.42
  30  113  0.49
  31    8  0.03

ACGTcount: A:0.31, C:0.04, G:0.30, T:0.35


Consensus pattern (30 bp):   
ATTTTTGGAAGTTTTGAGGTCAAAAATGGG

Found at i:581 original size:59 final size:58

Alignment explanation


    Indices: 491--829  Score: 355
    Period size: 59  Copynumber: 5.7  Consensus size: 58

        481 CGGGAGTGGA

                          * *   *                         *   *         
        491 ATTTTTGGAAGTTTTGGGGTCAAAAATGAGATTTTTGGAAGTTTTGGGGTTAAAAATGGG
          1 ATTTTTGGAAG-TTCGAGGTAAAAAATGA-ATTTTTGGAAGTTTTGAGGTCAAAAATGGG

                         *     *    *                    *          *  
        551 ATTTTTGGAAGTTTGAGGTCAAAATTGAGATTTTTGGAAGTTTTGTGGTC-AAAATAGG
          1 ATTTTTGGAAGTTCGAGGTAAAAAATGA-ATTTTTGGAAGTTTTGAGGTCAAAAATGGG

                      *                            *    *               
        609 ATTTTTGGAAATTCGAGGCT-AAAAATGGAATTTTTGGAGGTTTCGAGGTCAAAAATGGG
          1 ATTTTTGGAAGTTCGAGG-TAAAAAAT-GAATTTTTGGAAGTTTTGAGGTCAAAAATGGG

                      *              **                  *             
        668 ATTTTTGGAAATTCGAGGCTAAAAAGGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGG
          1 ATTTTTGGAAGTTCGAGG-TAAAAAATGAATTTTTGGAAGTTTTGAGGTCAAAAATGGG

                                                          *              
        727 ATTTTTGGAAGTTCGAGGGGT-AAAAATGAAATTTTTGGAAG-TTTCAGGTCAAAAATGGG
          1 ATTTTTGGAAGTTCGA--GGTAAAAAATG-AATTTTTGGAAGTTTTGAGGTCAAAAATGGG

                 *    *                                  
        786 ATTTTGGGAAATTCGAGGCTAAAAACAT-AATTTTTGGATAGTTT
          1 ATTTTTGGAAGTTCGAGG-TAAAAA-ATGAATTTTTGGA-AGTTT

        830 AGGGACCTTC


Statistics
Matches: 243,  Mismatches: 24, Indels: 24
        0.84            0.08        0.08

Matches are distributed among these distances:
  57    2  0.01
  58   57  0.23
  59  150  0.62
  60   32  0.13
  61    2  0.01

ACGTcount: A:0.32, C:0.05, G:0.28, T:0.35


Consensus pattern (58 bp):   
ATTTTTGGAAGTTCGAGGTAAAAAATGAATTTTTGGAAGTTTTGAGGTCAAAAATGGG
Done.