Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010936.1 Kokia drynarioides strain JFW-HI SEQ_125904, 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: 5962
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:795 original size:29 final size:30

Alignment explanation


    Indices: 773--927  Score: 210
    Period size: 29  Copynumber: 5.3  Consensus size: 30

        763 CCAAAATTTT

                                          
        773 CATTTTTACCCTCG-AACTTCCAAAAATCC
          1 CATTTTTACCCTCGAAACTTCCAAAAATCC

                    *                   * 
        802 CATTTTTAACCTCGAAACTTCCAAAAATTC
          1 CATTTTTACCCTCGAAACTTCCAAAAATCC

                       *                  
        832 CATTTTTACCCCCG-AACTTCCAAAAATCC
          1 CATTTTTACCCTCGAAACTTCCAAAAATCC

                                      *    
        861 CATTTTTGACCC-CGAAACTTCCAAATATCC
          1 CATTTTT-ACCCTCGAAACTTCCAAAAATCC

                         *      **        
        891 CATTTTTACCC-CTAAACTTTTAAAAATCC
          1 CATTTTTACCCTCGAAACTTCCAAAAATCC

                    
        920 CATTTTTA
          1 CATTTTTA

        928 ACTTGAATTT


Statistics
Matches: 113,  Mismatches: 10, Indels: 6
        0.88            0.08        0.05

Matches are distributed among these distances:
  29   62  0.55
  30   51  0.45

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


Consensus pattern (30 bp):   
CATTTTTACCCTCGAAACTTCCAAAAATCC

Found at i:849 original size:59 final size:59

Alignment explanation


    Indices: 756--929  Score: 240
    Period size: 59  Copynumber: 2.9  Consensus size: 59

        746 GGAGATCCCT

                         *  *           *                            *  
        756 AAACTGTCCAAAATTTTCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTAACCTCG
          1 AAACT-TCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCG

                                                                *      
        816 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG
          1 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCG

                       *  *             **     **                  
        875 AAACTTCCAAATATCCCATTTTTACCCCTAAACTTTTAAAAATCCCATTTTTAAC
          1 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAAC

        930 TTGAATTTTC


Statistics
Matches: 102,  Mismatches: 12, Indels: 1
        0.89            0.10        0.01

Matches are distributed among these distances:
  59   97  0.95
  60    5  0.05

ACGTcount: A:0.33, C:0.30, G:0.03, T:0.33


Consensus pattern (59 bp):   
AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCCG

Found at i:974 original size:27 final size:25

Alignment explanation


    Indices: 943--994  Score: 77
    Period size: 25  Copynumber: 2.0  Consensus size: 25

        933 AATTTTCACA

                                       
        943 AAATTATCGTTTCGCCCCCGAGAATCC
          1 AAATTAT--TTTCGCCCCCGAGAATCC

                      *              
        970 AAATTATTTTTGCCCCCGAGAATCC
          1 AAATTATTTTCGCCCCCGAGAATCC

        995 GAAAAGTCTT


Statistics
Matches: 24,  Mismatches: 1, Indels: 2
        0.89            0.04        0.07

Matches are distributed among these distances:
  25   17  0.71
  27    7  0.29

ACGTcount: A:0.27, C:0.31, G:0.13, T:0.29


Consensus pattern (25 bp):   
AAATTATTTTCGCCCCCGAGAATCC
Done.