Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010867.1 Kokia drynarioides strain JFW-HI SEQ_125835, 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: 19928
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35


Found at i:9056 original size:31 final size:31

Alignment explanation


    Indices: 9016--9078  Score: 117
    Period size: 31  Copynumber: 2.0  Consensus size: 31

       9006 TTATAATGGA

                *                          
       9016 ATCTGTTTGGCTTGCTTGTGTCCCTATCTGC
          1 ATCTATTTGGCTTGCTTGTGTCCCTATCTGC

                                           
       9047 ATCTATTTGGCTTGCTTGTGTCCCTATCTGC
          1 ATCTATTTGGCTTGCTTGTGTCCCTATCTGC

             
       9078 A
          1 A

       9079 CCTGTTTAGA


Statistics
Matches: 31,  Mismatches: 1, Indels: 0
        0.97            0.03        0.00

Matches are distributed among these distances:
  31   31  1.00

ACGTcount: A:0.10, C:0.25, G:0.21, T:0.44


Consensus pattern (31 bp):   
ATCTATTTGGCTTGCTTGTGTCCCTATCTGC

Found at i:12263 original size:20 final size:20

Alignment explanation


    Indices: 12238--12288  Score: 93
    Period size: 20  Copynumber: 2.5  Consensus size: 20

      12228 TACCTTGCAC

                                
      12238 TTCTACCGAAACACACATGG
          1 TTCTACCGAAACACACATGG

                   *            
      12258 TTCTACCAAAACACACATGG
          1 TTCTACCGAAACACACATGG

                       
      12278 TTCTACCGAAA
          1 TTCTACCGAAA

      12289 TAAGTAAGCT


Statistics
Matches: 29,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  20   29  1.00

ACGTcount: A:0.37, C:0.29, G:0.12, T:0.22


Consensus pattern (20 bp):   
TTCTACCGAAACACACATGG

Found at i:12858 original size:61 final size:61

Alignment explanation


    Indices: 12782--12907  Score: 216
    Period size: 61  Copynumber: 2.1  Consensus size: 61

      12772 TGTTTGCATT

                                *               *                        
      12782 GGAACTCATTTCATTTAATATTCACGATGACATATAGTCAACGGACCTCTTGTTCCGTATA
          1 GGAACTCATTTCATTTAATACTCACGATGACATATAATCAACGGACCTCTTGTTCCGTATA

                                                    *       *            
      12843 GGAACTCATTTCATTTAATACTCACGATGACATATAATCATCGGACCTTTTGTTCCGTATA
          1 GGAACTCATTTCATTTAATACTCACGATGACATATAATCAACGGACCTCTTGTTCCGTATA

                
      12904 GGAA
          1 GGAA

      12908 TTTATATACT


Statistics
Matches: 61,  Mismatches: 4, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  61   61  1.00

ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34


Consensus pattern (61 bp):   
GGAACTCATTTCATTTAATACTCACGATGACATATAATCAACGGACCTCTTGTTCCGTATA

Found at i:12974 original size:51 final size:51

Alignment explanation


    Indices: 12907--13038  Score: 167
    Period size: 51  Copynumber: 2.6  Consensus size: 51

      12897 CCGTATAGGA

                  *                     *  *               * *  
      12907 ATTTATATACTCACGATGACA-TTAAGTTATTGAAACTTTAATCCATCACGG
          1 ATTTATTTACTCACGATGACACTT-AGTCATCGAAACTTTAATCCATAAAGG

                                            * *         *      
      12958 ATTTATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGG
          1 ATTTATTTACTCACGATGACACTTAGTCATCGAAACTTTAATCCATAAAGG

               *                          
      13009 ATTCATTTACTCACGATGACACTTAGTCAT
          1 ATTTATTTACTCACGATGACACTTAGTCAT

      13039 TAGATCCTTT


Statistics
Matches: 71,  Mismatches: 9, Indels: 2
        0.87            0.11        0.02

Matches are distributed among these distances:
  51   69  0.97
  52    2  0.03

ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35


Consensus pattern (51 bp):   
ATTTATTTACTCACGATGACACTTAGTCATCGAAACTTTAATCCATAAAGG
Done.