Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001276.1 Kokia drynarioides strain JFW-HI SEQ_112663, 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, 720

Length: 1201
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39


Found at i:707 original size:29 final size:29

Alignment explanation


    Indices: 637--766  Score: 129
    Period size: 29  Copynumber: 4.4  Consensus size: 29

        627 GTTACATGGC

                           *       *     
        637 CGAACTTCCAAAAATCCCATTTTGACCCT
          1 CGAACTTCCAAAAATTCCATTTTTACCCT

                  *  *       **           
        666 -GAAACATCAAAAAATTTTATTTTTACCCT
          1 CG-AACTTCCAAAAATTCCATTTTTACCCT

                           *             *
        695 CGAACTTCCAAAAATGCCATTTTTGACCCC
          1 CGAACTTCCAAAAATTCCATTTTT-ACCCT

              *                      *    
        725 CAAAACTTCCAAAAATTCCA-TTTTGCCCT
          1 C-GAACTTCCAAAAATTCCATTTTTACCCT

                         
        754 CGAACTTCCAAAA
          1 CGAACTTCCAAAA

        767 TCTTCATATT


Statistics
Matches: 80,  Mismatches: 17, Indels: 9
        0.75            0.16        0.08

Matches are distributed among these distances:
  28   12  0.15
  29   42  0.52
  30   10  0.12
  31   16  0.20

ACGTcount: A:0.35, C:0.29, G:0.06, T:0.29


Consensus pattern (29 bp):   
CGAACTTCCAAAAATTCCATTTTTACCCT

Found at i:707 original size:58 final size:59

Alignment explanation


    Indices: 637--766  Score: 165
    Period size: 59  Copynumber: 2.2  Consensus size: 59

        627 GTTACATGGC

                                          **               **           
        637 CGAACTTCCAAAAATCCCA-TTTTGA-CCCTGAAACATCAAAAAATTTTATTTTTACCCT
          1 CGAACTTCCAAAAATCCCATTTTTGACCCCCAAAACATCAAAAAATTCCA-TTTTACCCT

                           *                    *  *              *    
        695 CGAACTTCCAAAAATGCCATTTTTGACCCCCAAAACTTCCAAAAATTCCATTTTGCCCT
          1 CGAACTTCCAAAAATCCCATTTTTGACCCCCAAAACATCAAAAAATTCCATTTTACCCT

                         
        754 CGAACTTCCAAAA
          1 CGAACTTCCAAAA

        767 TCTTCATATT


Statistics
Matches: 62,  Mismatches: 8, Indels: 3
        0.85            0.11        0.04

Matches are distributed among these distances:
  58   18  0.29
  59   27  0.44
  60   17  0.27

ACGTcount: A:0.35, C:0.29, G:0.06, T:0.29


Consensus pattern (59 bp):   
CGAACTTCCAAAAATCCCATTTTTGACCCCCAAAACATCAAAAAATTCCATTTTACCCT

Found at i:983 original size:15 final size:17

Alignment explanation


    Indices: 963--994  Score: 50
    Period size: 16  Copynumber: 2.0  Consensus size: 17

        953 TGCACTCGTA

                             
        963 TTTTG-CATTTT-TTTT
          1 TTTTGCCATTTTATTTT

                             
        978 TTTTGCCATTTTATTTT
          1 TTTTGCCATTTTATTTT

        995 CTTATTTATC


Statistics
Matches: 15,  Mismatches: 0, Indels: 2
        0.88            0.00        0.12

Matches are distributed among these distances:
  15    5  0.33
  16    6  0.40
  17    4  0.27

ACGTcount: A:0.09, C:0.09, G:0.06, T:0.75


Consensus pattern (17 bp):   
TTTTGCCATTTTATTTT
Done.