Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011829.1 Kokia drynarioides strain JFW-HI SEQ_126825, 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: 2098
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.34


Found at i:1981 original size:47 final size:47

Alignment explanation


    Indices: 1902--2000  Score: 128
    Period size: 47  Copynumber: 2.1  Consensus size: 47

       1892 CGAAGTACTT

                   *    *              *            *      
       1902 AACAGAAGCACATAAGTGCTGGGGAAATAGAAGCACACACGGTGCTA
          1 AACAGAACCACACAAGTGCTGGGGAAACAGAAGCACACACAGTGCTA

                                     *                     *
       1949 AACAGAACCACACACAGTGCT-GGGTAACAGAAGCACACACAGTGCTG
          1 AACAGAACCACACA-AGTGCTGGGGAAACAGAAGCACACACAGTGCTA

                 
       1996 AACAG
          1 AACAG

       2001 TAAGCGCACT


Statistics
Matches: 45,  Mismatches: 6, Indels: 2
        0.85            0.11        0.04

Matches are distributed among these distances:
  47   39  0.87
  48    6  0.13

ACGTcount: A:0.40, C:0.23, G:0.25, T:0.11


Consensus pattern (47 bp):   
AACAGAACCACACAAGTGCTGGGGAAACAGAAGCACACACAGTGCTA

Found at i:1985 original size:25 final size:25

Alignment explanation


    Indices: 1902--1995  Score: 106
    Period size: 25  Copynumber: 3.9  Consensus size: 25

       1892 CGAAGTACTT

                        *             
       1902 AACAGAAGCACATA-AGTGCTGGGGA
          1 AACAGAAGCACACACAGTGCT-GGGA

              *            *         
       1927 AATAGAAGCACACACGGTGCT---A
          1 AACAGAAGCACACACAGTGCTGGGA

                   *                *
       1949 AACAGAACCACACACAGTGCTGGGT
          1 AACAGAAGCACACACAGTGCTGGGA

                                  
       1974 AACAGAAGCACACACAGTGCTG
          1 AACAGAAGCACACACAGTGCTG

       1996 AACAGTAAGC


Statistics
Matches: 57,  Mismatches: 8, Indels: 8
        0.78            0.11        0.11

Matches are distributed among these distances:
  22   19  0.33
  25   33  0.58
  26    5  0.09

ACGTcount: A:0.39, C:0.23, G:0.26, T:0.12


Consensus pattern (25 bp):   
AACAGAAGCACACACAGTGCTGGGA

Found at i:2009 original size:25 final size:23

Alignment explanation


    Indices: 1930--2009  Score: 76
    Period size: 25  Copynumber: 3.4  Consensus size: 23

       1920 CTGGGGAAAT

                         *     *   
       1930 AGAA-GCACACACGGTGCTAAAC
          1 AGAACGCACACACAGTGCTGAAC

                                      
       1952 AGAAC-CACACACAGTGCTGGGTAAC
          1 AGAACGCACACACAGTGCT--G-AAC

                                   
       1977 AGAA-GCACACACAGTGCTGAAC
          1 AGAACGCACACACAGTGCTGAAC

                       
       1999 AGTAAGCGCAC
          1 AG-AA-CGCAC

       2010 TAGCGTTCCT


Statistics
Matches: 48,  Mismatches: 2, Indels: 13
        0.76            0.03        0.21

Matches are distributed among these distances:
  22   21  0.44
  23    3  0.06
  25   24  0.50

ACGTcount: A:0.39, C:0.28, G:0.24, T:0.10


Consensus pattern (23 bp):   
AGAACGCACACACAGTGCTGAAC
Done.