Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012976.1 Kokia drynarioides strain JFW-HI SEQ_127994, 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: 9216
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.33

Warning! 50 characters in sequence are not A, C, G, or T


Found at i:652 original size:39 final size:40

Alignment explanation


    Indices: 593--669  Score: 129
    Period size: 39  Copynumber: 1.9  Consensus size: 40

        583 GCACTCAATG

                                                    
        593 GACACCTTTTGAAGAGTCACAACCC-TTTCAAATTGGATA
          1 GACACCTTTTGAAGAGTCACAACCCTTTTCAAATTGGATA

                *                          *      
        632 GACATCTTTTGAAGAGTCACAACCCTTTTCATATTGGA
          1 GACACCTTTTGAAGAGTCACAACCCTTTTCAAATTGGA

        670 CATACCTCTT


Statistics
Matches: 35,  Mismatches: 2, Indels: 1
        0.92            0.05        0.03

Matches are distributed among these distances:
  39   24  0.69
  40   11  0.31

ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31


Consensus pattern (40 bp):   
GACACCTTTTGAAGAGTCACAACCCTTTTCAAATTGGATA

Found at i:685 original size:39 final size:39

Alignment explanation


    Indices: 593--686  Score: 109
    Period size: 39  Copynumber: 2.4  Consensus size: 39

        583 GCACTCAATG

                *    *                           * 
        593 GACACCTTTTGAAGAGTCACAACCCTTTCAAATTGGATA
          1 GACATCTTTGGAAGAGTCACAACCCTTTCAAATTGGACA

                     *                     *        
        632 GACATCTTTTGAAGAGTCACAACCCTTTTCATATTGGACA
          1 GACATCTTTGGAAGAGTCACAACCC-TTTCAAATTGGACA

            *  *            
        672 TACCTC-TTGGAAGAG
          1 GACATCTTTGGAAGAG

        687 ACTTGTCCCA


Statistics
Matches: 48,  Mismatches: 6, Indels: 2
        0.86            0.11        0.04

Matches are distributed among these distances:
  39   32  0.67
  40   16  0.33

ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30


Consensus pattern (39 bp):   
GACATCTTTGGAAGAGTCACAACCCTTTCAAATTGGACA

Found at i:2889 original size:18 final size:18

Alignment explanation


    Indices: 2862--2897  Score: 63
    Period size: 18  Copynumber: 2.0  Consensus size: 18

       2852 AATGCTAGAG

                              
       2862 ATTGTAAGGAAATGAAAT
          1 ATTGTAAGGAAATGAAAT

                 *            
       2880 ATTGTGAGGAAATGAAAT
          1 ATTGTAAGGAAATGAAAT

       2898 CAGGACCAAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.47, C:0.00, G:0.25, T:0.28


Consensus pattern (18 bp):   
ATTGTAAGGAAATGAAAT
Done.