Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000999.1 Kokia drynarioides strain JFW-HI SEQ_112202, 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: 5006
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.35

Warning! 5 characters in sequence are not A, C, G, or T


Found at i:2699 original size:39 final size:39

Alignment explanation


    Indices: 2645--2721  Score: 111
    Period size: 39  Copynumber: 2.0  Consensus size: 39

       2635 AATGGATGAG

                            *                      
       2645 ATTACCTACTTCACTGGGCAACTTCCACCCTCTAAAAGA
          1 ATTACCTACTTCACTGCGCAACTTCCACCCTCTAAAAGA

                               *            *      
       2684 ATTACCTA-TATCACTGCGTAACTTCCACCCTGTAAAAG
          1 ATTACCTACT-TCACTGCGCAACTTCCACCCTCTAAAAG

       2722 GAAAATATAC


Statistics
Matches: 34,  Mismatches: 3, Indels: 2
        0.87            0.08        0.05

Matches are distributed among these distances:
  38    1  0.03
  39   33  0.97

ACGTcount: A:0.31, C:0.31, G:0.10, T:0.27


Consensus pattern (39 bp):   
ATTACCTACTTCACTGCGCAACTTCCACCCTCTAAAAGA

Found at i:4116 original size:31 final size:31

Alignment explanation


    Indices: 4048--4116  Score: 77
    Period size: 31  Copynumber: 2.2  Consensus size: 31

       4038 TTTTTCCAAC

                    *  *                   
       4048 TAAATTTGGCCCTCAACCTTTTAAAAAAAGT
          1 TAAATTTGACCATCAACCTTTTAAAAAAAGT

            **                           *  
       4079 CGAATTTGACCATCAACC-TTTAAAAAAGTGT
          1 TAAATTTGACCATCAACCTTTTAAAAAA-AGT

                   
       4110 TAAATTT
          1 TAAATTT

       4117 TTATTTTTTA


Statistics
Matches: 30,  Mismatches: 7, Indels: 2
        0.77            0.18        0.05

Matches are distributed among these distances:
  30    9  0.30
  31   21  0.70

ACGTcount: A:0.39, C:0.17, G:0.10, T:0.33


Consensus pattern (31 bp):   
TAAATTTGACCATCAACCTTTTAAAAAAAGT

Found at i:4891 original size:21 final size:20

Alignment explanation


    Indices: 4866--4906  Score: 64
    Period size: 21  Copynumber: 2.0  Consensus size: 20

       4856 TATTTTAAAC

                  *              
       4866 AATTTTTTTATTGTGTTTTAT
          1 AATTTTATTATTGT-TTTTAT

                                
       4887 AATTTTATTATTGTTTTTAT
          1 AATTTTATTATTGTTTTTAT

       4907 TGCGTTTTAA


Statistics
Matches: 19,  Mismatches: 1, Indels: 1
        0.90            0.05        0.05

Matches are distributed among these distances:
  20    6  0.32
  21   13  0.68

ACGTcount: A:0.22, C:0.00, G:0.07, T:0.71


Consensus pattern (20 bp):   
AATTTTATTATTGTTTTTAT
Done.