Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012208.1 Kokia drynarioides strain JFW-HI SEQ_127209, 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: 20735
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33

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


Found at i:5512 original size:9 final size:9

Alignment explanation


    Indices: 5500--5526  Score: 54
    Period size: 9  Copynumber: 3.0  Consensus size: 9

       5490 AAAATTATCT

                     
       5500 ATAATTATA
          1 ATAATTATA

                     
       5509 ATAATTATA
          1 ATAATTATA

                     
       5518 ATAATTATA
          1 ATAATTATA

       5527 TTAAACCTAA


Statistics
Matches: 18,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   9   18  1.00

ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44


Consensus pattern (9 bp):   
ATAATTATA

Found at i:8969 original size:71 final size:72

Alignment explanation


    Indices: 8862--9000  Score: 217
    Period size: 71  Copynumber: 1.9  Consensus size: 72

       8852 TTGGCAAATA

                     *                  *                                    
       8862 ATAAAAAACGTTTAATATATCTCCAAAATCAACCAAACATAAACATTTATTATAAA-TTTAATGT
          1 ATAAAAAACATTTAATATATCTCCAAAACCAACCAAACATAAACATTTATTATAAATTTTAATGT

                   
       8926 CTATACG
         66 CTATACG

                 *                         *           **                    
       8933 ATAAAGAACATTTAATATATCTCCAAAACCAGCCAAACATAAAGGTTTATTATAAATTTTAATGT
          1 ATAAAAAACATTTAATATATCTCCAAAACCAACCAAACATAAACATTTATTATAAATTTTAATGT

               
       8998 CTA
         66 CTA

       9001 AATAAAGAAT


Statistics
Matches: 61,  Mismatches: 6, Indels: 1
        0.90            0.09        0.01

Matches are distributed among these distances:
  71   50  0.82
  72   11  0.18

ACGTcount: A:0.47, C:0.15, G:0.06, T:0.32


Consensus pattern (72 bp):   
ATAAAAAACATTTAATATATCTCCAAAACCAACCAAACATAAACATTTATTATAAATTTTAATGT
CTATACG

Found at i:9699 original size:41 final size:42

Alignment explanation


    Indices: 9638--9750  Score: 129
    Period size: 42  Copynumber: 2.7  Consensus size: 42

       9628 GAAAAAAAAT

                  *   *  *            *           *   
       9638 GTCCAATTAGACGCGCTTTCTGCACAGTTGT-AGAAAAGCTC
          1 GTCCAACTAGGCGAGCTTTCTGCACAATTGTCAGAAAAACTC

                 *         *        *                 
       9679 GTCCAGCTAGGCGAGTTTTCTGCATAATTGTCAGAAAAACTC
          1 GTCCAACTAGGCGAGCTTTCTGCACAATTGTCAGAAAAACTC

                  * *                     
       9721 GTCCAATTGGGCGAGCTTTCTGCACAATTG
          1 GTCCAACTAGGCGAGCTTTCTGCACAATTG

       9751 GCAGGAAAGT


Statistics
Matches: 58,  Mismatches: 13, Indels: 1
        0.81            0.18        0.01

Matches are distributed among these distances:
  41   24  0.41
  42   34  0.59

ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28


Consensus pattern (42 bp):   
GTCCAACTAGGCGAGCTTTCTGCACAATTGTCAGAAAAACTC

Found at i:12883 original size:21 final size:21

Alignment explanation


    Indices: 12857--12902  Score: 83
    Period size: 21  Copynumber: 2.2  Consensus size: 21

      12847 TTAAATATTT

                         *       
      12857 TAATATAATTTAATATAAAAA
          1 TAATATAATTTAACATAAAAA

                                 
      12878 TAATATAATTTAACATAAAAA
          1 TAATATAATTTAACATAAAAA

                
      12899 TAAT
          1 TAAT

      12903 TATATTAAGA


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  21   24  1.00

ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37


Consensus pattern (21 bp):   
TAATATAATTTAACATAAAAA

Found at i:12930 original size:24 final size:24

Alignment explanation


    Indices: 12903--12957  Score: 67
    Period size: 24  Copynumber: 2.3  Consensus size: 24

      12893 TAAAAATAAT

                                    
      12903 TATATTAAGAATGTTATTAAATTA
          1 TATATTAAGAATGTTATTAAATTA

                   ** * *           
      12927 TATATTATTATTTTTATTAAATTA
          1 TATATTAAGAATGTTATTAAATTA

                    
      12951 TAT-TTAA
          1 TATATTAA

      12958 TAATAATTCT


Statistics
Matches: 26,  Mismatches: 5, Indels: 1
        0.81            0.16        0.03

Matches are distributed among these distances:
  23    3  0.12
  24   23  0.88

ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55


Consensus pattern (24 bp):   
TATATTAAGAATGTTATTAAATTA
Done.