Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007633.1 Kokia drynarioides strain JFW-HI SEQ_122264, 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: 2228
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40


Found at i:1740 original size:24 final size:24

Alignment explanation


    Indices: 1713--1787  Score: 61
    Period size: 24  Copynumber: 3.2  Consensus size: 24

       1703 GGTTGGAATG

                                    
       1713 GAATGAGACCATTTATGGTCTCGT
          1 GAATGAGACCATTTATGGTCTCGT

                    **           *    
       1737 GAATG-G-GTA-TT-TGGT-TGGAAT
          1 GAATGAGACCATTTATGGTCTCG--T

                                     
       1758 GGAATGAGACCATTTATGGTCTCGT
          1 -GAATGAGACCATTTATGGTCTCGT

                 
       1783 GAATG
          1 GAATG

       1788 TGTTTGGGGA


Statistics
Matches: 37,  Mismatches: 6, Indels: 16
        0.63            0.10        0.27

Matches are distributed among these distances:
  19    2  0.05
  20    4  0.11
  21    3  0.08
  22    6  0.16
  23    2  0.05
  24   11  0.30
  25    3  0.08
  26    4  0.11
  27    2  0.05

ACGTcount: A:0.25, C:0.11, G:0.31, T:0.33


Consensus pattern (24 bp):   
GAATGAGACCATTTATGGTCTCGT

Found at i:1756 original size:46 final size:46

Alignment explanation


    Indices: 1689--1787  Score: 189
    Period size: 46  Copynumber: 2.2  Consensus size: 46

       1679 TTGCTGCCTT

                      *                                   
       1689 GTGAATGGGTGTTTGGTTGGAATGGAATGAGACCATTTATGGTCTC
          1 GTGAATGGGTATTTGGTTGGAATGGAATGAGACCATTTATGGTCTC

                                                          
       1735 GTGAATGGGTATTTGGTTGGAATGGAATGAGACCATTTATGGTCTC
          1 GTGAATGGGTATTTGGTTGGAATGGAATGAGACCATTTATGGTCTC

                   
       1781 GTGAATG
          1 GTGAATG

       1788 TGTTTGGGGA


Statistics
Matches: 52,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  46   52  1.00

ACGTcount: A:0.23, C:0.08, G:0.34, T:0.34


Consensus pattern (46 bp):   
GTGAATGGGTATTTGGTTGGAATGGAATGAGACCATTTATGGTCTC

Found at i:1994 original size:17 final size:18

Alignment explanation


    Indices: 1974--2013  Score: 57
    Period size: 16  Copynumber: 2.3  Consensus size: 18

       1964 TGTTTTTTTT

                              
       1974 ATTTTTATTTTTGATT-A
          1 ATTTTTATTTTTGATTGA

                 *            
       1991 A-TTTAATTTTTGATTGA
          1 ATTTTTATTTTTGATTGA

                  
       2008 ATTTTT
          1 ATTTTT

       2014 TATTAAATTA


Statistics
Matches: 19,  Mismatches: 2, Indels: 3
        0.79            0.08        0.12

Matches are distributed among these distances:
  16   13  0.68
  17    3  0.16
  18    3  0.16

ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68


Consensus pattern (18 bp):   
ATTTTTATTTTTGATTGA

Found at i:2122 original size:31 final size:31

Alignment explanation


    Indices: 2087--2165  Score: 88
    Period size: 31  Copynumber: 2.5  Consensus size: 31

       2077 GTTATGTTTA

                           *  *             
       2087 TTTTTATGTTTTTTTTATTATGTA-GGTTTTT
          1 TTTTTATGTTTTTTTGA-AATGTATGGTTTTT

                                      *     
       2118 TTTTTATGTTTTGTTTGAAATGTATGTTTTTT
          1 TTTTTATGTTTT-TTTGAAATGTATGGTTTTT

                            
       2150 TATTGTTATGTTTTTT
          1 T-TT-TTATGTTTTTT

       2166 AATATGCATA


Statistics
Matches: 41,  Mismatches: 3, Indels: 6
        0.82            0.06        0.12

Matches are distributed among these distances:
  31   17  0.41
  32   11  0.27
  33    4  0.10
  34    9  0.22

ACGTcount: A:0.14, C:0.00, G:0.14, T:0.72


Consensus pattern (31 bp):   
TTTTTATGTTTTTTTGAAATGTATGGTTTTT
Done.