Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013211.1 Kokia drynarioides strain JFW-HI SEQ_128230, 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: 13549
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.33


Found at i:4791 original size:30 final size:30

Alignment explanation


    Indices: 4745--4885  Score: 135
    Period size: 30  Copynumber: 4.7  Consensus size: 30

       4735 ATTAAAACCA

                      *        *          *
       4745 GGTCAAAATTTGAATTTTTAGAAAGTTCGAT
          1 GGTC-AAATTAGAATTTTTGGAAAGTTCGAG

            *                           *  
       4776 TGTCAAATTCA-AATTTTTGGAAAGTT-TAG
          1 GGTCAAATT-AGAATTTTTGGAAAGTTCGAG

                                           
       4805 GGTCAAATTAGAATTTTTGGAAAGTTC-AGG
          1 GGTCAAATTAGAATTTTTGGAAAGTTCGA-G

                     *  *     *       * * 
       4835 GGTCAAATTGGAGTTTTTAGAAAGTTTGGG
          1 GGTCAAATTAGAATTTTTGGAAAGTTCGAG

                     *           
       4865 GGTCAAATTGGAATTTTTGGA
          1 GGTCAAATTAGAATTTTTGGA

       4886 CAATTTACGG


Statistics
Matches: 92,  Mismatches: 13, Indels: 11
        0.79            0.11        0.09

Matches are distributed among these distances:
  28    1  0.01
  29   25  0.27
  30   63  0.68
  31    3  0.03

ACGTcount: A:0.32, C:0.06, G:0.25, T:0.38


Consensus pattern (30 bp):   
GGTCAAATTAGAATTTTTGGAAAGTTCGAG

Found at i:4898 original size:30 final size:30

Alignment explanation


    Indices: 4777--4901  Score: 155
    Period size: 30  Copynumber: 4.2  Consensus size: 30

       4767 AAGTTCGATT

                    **                    
       4777 GTCAAATTCAAATTTTTGGAAAGTTTA-GG
          1 GTCAAATTGGAATTTTTGGAAAGTTTAGGG

                    *                *    
       4806 GTCAAATTAGAATTTTTGGAAAGTTCAGGG
          1 GTCAAATTGGAATTTTTGGAAAGTTTAGGG

                       *     *        *   
       4836 GTCAAATTGGAGTTTTTAGAAAGTTTGGGG
          1 GTCAAATTGGAATTTTTGGAAAGTTTAGGG

                                        *  
       4866 GTCAAATTGGAATTTTTGGACAA-TTTACGG
          1 GTCAAATTGGAATTTTTGGA-AAGTTTAGGG

                  
       4896 GTCAAA
          1 GTCAAA

       4902 ACCTAATTTT


Statistics
Matches: 82,  Mismatches: 12, Indels: 3
        0.85            0.12        0.03

Matches are distributed among these distances:
  29   24  0.29
  30   56  0.68
  31    2  0.02

ACGTcount: A:0.32, C:0.07, G:0.26, T:0.35


Consensus pattern (30 bp):   
GTCAAATTGGAATTTTTGGAAAGTTTAGGG

Found at i:4898 original size:60 final size:59

Alignment explanation


    Indices: 4745--4901  Score: 156
    Period size: 59  Copynumber: 2.6  Consensus size: 59

       4735 ATTAAAACCA

                      *        *           **        ** *     *          
       4745 GGTCAAAATTTGAATTTTTAGAAAGTTCGA-TTGTCAAATTCAAATTTTTGGAAAGTTTAG
          1 GGTC-AAATTAGAATTTTTGGAAAGTTC-ACGGGTCAAATTGGAGTTTTTAGAAAGTTTAG

                                        *                             * 
       4805 GGTCAAATTAGAATTTTTGGAAAGTTCAGGGGTCAAATTGGAGTTTTTAGAAAGTTTGGG
          1 GGTCAAATTAGAATTTTTGGAAAGTTCACGGGTCAAATTGGAGTTTTTAGAAAGTTT-AG

                     *                 *          
       4865 GGTCAAATTGGAATTTTTGGACAA-TTTACGGGTCAAA
          1 GGTCAAATTAGAATTTTTGGA-AAGTTCACGGGTCAAA

       4902 ACCTAATTTT


Statistics
Matches: 82,  Mismatches: 12, Indels: 6
        0.82            0.12        0.06

Matches are distributed among these distances:
  58    1  0.01
  59   43  0.52
  60   36  0.44
  61    2  0.02

ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36


Consensus pattern (59 bp):   
GGTCAAATTAGAATTTTTGGAAAGTTCACGGGTCAAATTGGAGTTTTTAGAAAGTTTAG
Done.