Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010630.1 Kokia drynarioides strain JFW-HI SEQ_125566, 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: 2804
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37


Found at i:718 original size:30 final size:29

Alignment explanation


    Indices: 658--957  Score: 279
    Period size: 30  Copynumber: 10.3  Consensus size: 29

        648 CCTAAACTGC

                                    *     
        658 CCAAAAAT-TCCATTTTTACCCCCGAACTT
          1 CCAAAAATCT-CATTTTTACCCCCAAACTT

                                          
        687 CCAAAAATCTCATTTTTACCCCCAAAACTT
          1 CCAAAAATCTCATTTTTACCCCC-AAACTT

                      *            *      
        717 CCAAAAATCTAATTTTTTACCCCAAAACTT
          1 CCAAAAATCTCA-TTTTTACCCCCAAACTT

            ***     *              *     
        747 TTGAAAATTTCATTTTTACCCCCGAACTT
          1 CCAAAAATCTCATTTTTACCCCCAAACTT

                  *  *             *      
        776 CCAAAACTCCCATTTTTTACCCCAAAACTT
          1 CCAAAAATCTCA-TTTTTACCCCCAAACTT

                                 **       
        806 CCAAAAAT-TCCATTTTTACCATCAAACTT
          1 CCAAAAATCT-CATTTTTACCCCCAAACTT

                     *             *      
        835 CCAAAAATCCCATTTTTGACCCCGAAACTT
          1 CCAAAAATCTCATTTTT-ACCCCCAAACTT

                                    *     
        865 CCAAAAAT-TCCATTTTT-CCCCCGAACTT
          1 CCAAAAATCT-CATTTTTACCCCCAAACTT

                     *       *  *  *      
        893 CC--AAATCCCATTTTAAACACCAAAACTT
          1 CCAAAAATCTCATTTT-TACCCCCAAACTT

             *       *            *      
        921 CTAAAAATCCCATTTTTACCCCTAAACTT
          1 CCAAAAATCTCATTTTTACCCCCAAACTT

                    
        950 CCAAAAAT
          1 CCAAAAAT

        958 AATTGAATAC


Statistics
Matches: 218,  Mismatches: 40, Indels: 26
        0.77            0.14        0.09

Matches are distributed among these distances:
  26   10  0.05
  28   20  0.09
  29   88  0.40
  30   90  0.41
  31   10  0.05

ACGTcount: A:0.35, C:0.31, G:0.02, T:0.31


Consensus pattern (29 bp):   
CCAAAAATCTCATTTTTACCCCCAAACTT

Found at i:775 original size:59 final size:59

Alignment explanation


    Indices: 658--957  Score: 349
    Period size: 59  Copynumber: 5.1  Consensus size: 59

        648 CCTAAACTGC

                    *              **                                    
        658 CCAAAAATTCCA-TTTTTACCCCCGAACTTCCAAAAA-TCTCATTTTTACCCCCAAAACTT
          1 CCAAAAATCCCATTTTTTACCCCAAAACTTCCAAAAATTC-CATTTTTACCCCC-AAACTT

                     **                   ***      *             *     
        717 CCAAAAATCTAATTTTTTACCCCAAAACTTTTGAAAATTTCATTTTTACCCCCGAACTT
          1 CCAAAAATCCCATTTTTTACCCCAAAACTTCCAAAAATTCCATTTTTACCCCCAAACTT

                  *                                           **       
        776 CCAAAACTCCCATTTTTTACCCCAAAACTTCCAAAAATTCCATTTTTACCATCAAACTT
          1 CCAAAAATCCCATTTTTTACCCCAAAACTTCCAAAAATTCCATTTTTACCCCCAAACTT

                             *     *                             *     
        835 CCAAAAATCCCATTTTTGACCCCGAAACTTCCAAAAATTCCATTTTT-CCCCCGAACTT
          1 CCAAAAATCCCATTTTTTACCCCAAAACTTCCAAAAATTCCATTTTTACCCCCAAACTT

                            **  *          *      *             *      
        893 CC--AAATCCCATTTTAAACACCAAAACTTCTAAAAATCCCATTTTTACCCCTAAACTT
          1 CCAAAAATCCCATTTTTTACCCCAAAACTTCCAAAAATTCCATTTTTACCCCCAAACTT

                    
        950 CCAAAAAT
          1 CCAAAAAT

        958 AATTGAATAC


Statistics
Matches: 202,  Mismatches: 34, Indels: 10
        0.82            0.14        0.04

Matches are distributed among these distances:
  56   37  0.18
  57   11  0.05
  58   10  0.05
  59  111  0.55
  60   32  0.16
  61    1  0.00

ACGTcount: A:0.35, C:0.31, G:0.02, T:0.31


Consensus pattern (59 bp):   
CCAAAAATCCCATTTTTTACCCCAAAACTTCCAAAAATTCCATTTTTACCCCCAAACTT
Done.