Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001593.1 Kokia drynarioides strain JFW-HI SEQ_113208, 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: 5030
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33


Found at i:1945 original size:15 final size:15

Alignment explanation


    Indices: 1927--1999  Score: 94
    Period size: 15  Copynumber: 4.9  Consensus size: 15

       1917 TGAGCACTAG

                           
       1927 TGTTGCGAACACTCA
          1 TGTTGCGAACACTCA

                           
       1942 TGTTGCGAACACTCA
          1 TGTTGCGAACACTCA

                 *         
       1957 TGTTGTGAACACT-A
          1 TGTTGCGAACACTCA

              *      *      
       1971 GTATTGCGAGCACTCA
          1 -TGTTGCGAACACTCA

                  *      
       1987 TGTTGCAAACACT
          1 TGTTGCGAACACT

       2000 AGAGCTGTGA


Statistics
Matches: 49,  Mismatches: 7, Indels: 4
        0.82            0.12        0.07

Matches are distributed among these distances:
  14    1  0.02
  15   47  0.96
  16    1  0.02

ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29


Consensus pattern (15 bp):   
TGTTGCGAACACTCA

Found at i:2009 original size:45 final size:45

Alignment explanation


    Indices: 1915--2014  Score: 130
    Period size: 45  Copynumber: 2.2  Consensus size: 45

       1905 GCTTGGAAGA

                         *                   *        * *
       1915 TGTGAGCACTAGTGTTGCGAACACTCATGTTGCGAACACTCATGT
          1 TGTGAGCACTAGTATTGCGAACACTCATGTTGCAAACACTCAAGC

                 *              *                         
       1960 TGTGAACACTAGTATTGCGAGCACTCATGTTGCAAACACT-AGAGC
          1 TGTGAGCACTAGTATTGCGAACACTCATGTTGCAAACACTCA-AGC

                      
       2005 TGTGAGCACT
          1 TGTGAGCACT

       2015 GATGTTGTCA


Statistics
Matches: 47,  Mismatches: 7, Indels: 2
        0.84            0.12        0.04

Matches are distributed among these distances:
  44    1  0.02
  45   46  0.98

ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27


Consensus pattern (45 bp):   
TGTGAGCACTAGTATTGCGAACACTCATGTTGCAAACACTCAAGC

Found at i:2042 original size:30 final size:30

Alignment explanation


    Indices: 1918--2042  Score: 112
    Period size: 30  Copynumber: 4.2  Consensus size: 30

       1908 TGGAAGATGT

                            *               
       1918 GAGCACT-AGTGTTGCGAACACTCA-TGTTGC
          1 GAGCACTCA-TGTTGCAAACACT-AGTGTTGC

              *           **         *    
       1948 GAACACTCATGTTGTGAACACTAGTATTGC
          1 GAGCACTCATGTTGCAAACACTAGTGTTGC

                                    * *  *
       1978 GAGCACTCATGTTGCAAACACTAGAGCTGT
          1 GAGCACTCATGTTGCAAACACTAGTGTTGC

                   *               *       
       2008 GAGCACTGATGTTGTC-AACACTCGTGTTGC
          1 GAGCACTCATGTTG-CAAACACTAGTGTTGC

                 
       2038 GAGCA
          1 GAGCA

       2043 TGGATGAAGG


Statistics
Matches: 77,  Mismatches: 15, Indels: 6
        0.79            0.15        0.06

Matches are distributed among these distances:
  29    1  0.01
  30   74  0.96
  31    2  0.03

ACGTcount: A:0.26, C:0.22, G:0.25, T:0.26


Consensus pattern (30 bp):   
GAGCACTCATGTTGCAAACACTAGTGTTGC
Done.