Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011615.1 Kokia drynarioides strain JFW-HI SEQ_126605, 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: 3791
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.32

Warning! 100 characters in sequence are not A, C, G, or T


Found at i:2041 original size:39 final size:39

Alignment explanation


    Indices: 1997--2085  Score: 94
    Period size: 39  Copynumber: 2.3  Consensus size: 39

       1987 TGGGACAAGT

                     *      **                      
       1997 CTCTTCCAAGAG-GTATGTCCAATATGAAAAGGGTTGTGA
          1 CTCTTCCAAAAGTGTACATCCAATATG-AAAGGGTTGTGA

                            *        *              
       2036 CTCTT-CAAAAGTTGTCCATCCAATTTGAAAGGGTTGTGA
          1 CTCTTCCAAAAG-TGTACATCCAATATGAAAGGGTTGTGA

                        
       2075 CTCTT-CAAAAG
          1 CTCTTCCAAAAG

       2086 GTGTCCATTG


Statistics
Matches: 43,  Mismatches: 5, Indels: 4
        0.83            0.10        0.08

Matches are distributed among these distances:
  38    5  0.12
  39   28  0.65
  40   10  0.23

ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30


Consensus pattern (39 bp):   
CTCTTCCAAAAGTGTACATCCAATATGAAAGGGTTGTGA

Found at i:2091 original size:39 final size:40

Alignment explanation


    Indices: 2014--2093  Score: 135
    Period size: 39  Copynumber: 2.0  Consensus size: 40

       2004 AAGAGGTATG

                                             *      
       2014 TCCAATATGAAAAGGGTTGTGACTCTTCAAAAGTTGTCCA
          1 TCCAATATGAAAAGGGTTGTGACTCTTCAAAAGGTGTCCA

                  *                                 
       2054 TCCAATTTG-AAAGGGTTGTGACTCTTCAAAAGGTGTCCA
          1 TCCAATATGAAAAGGGTTGTGACTCTTCAAAAGGTGTCCA

             
       2093 T
          1 T

       2094 TGAGTGCATA


Statistics
Matches: 38,  Mismatches: 2, Indels: 1
        0.93            0.05        0.02

Matches are distributed among these distances:
  39   30  0.79
  40    8  0.21

ACGTcount: A:0.30, C:0.17, G:0.21, T:0.31


Consensus pattern (40 bp):   
TCCAATATGAAAAGGGTTGTGACTCTTCAAAAGGTGTCCA

Found at i:2340 original size:39 final size:39

Alignment explanation


    Indices: 2296--2384  Score: 94
    Period size: 39  Copynumber: 2.3  Consensus size: 39

       2286 TGGGACAAGT

                     *      **                      
       2296 CTCTTCCAAGAG-GTATGTCCAATATGAAAAGGGTTGTGA
          1 CTCTTCCAAAAGCGTACATCCAATATG-AAAGGGTTGTGA

                            *        *              
       2335 CTCTT-CAAAAGCTGTCCATCCAATTTGAAAGGGTTGTGA
          1 CTCTTCCAAAAGC-GTACATCCAATATGAAAGGGTTGTGA

                        
       2374 CTCTT-CAAAAG
          1 CTCTTCCAAAAG

       2385 GTGTCCATTG


Statistics
Matches: 43,  Mismatches: 5, Indels: 4
        0.83            0.10        0.08

Matches are distributed among these distances:
  38    5  0.12
  39   28  0.65
  40   10  0.23

ACGTcount: A:0.30, C:0.19, G:0.21, T:0.29


Consensus pattern (39 bp):   
CTCTTCCAAAAGCGTACATCCAATATGAAAGGGTTGTGA

Found at i:2390 original size:39 final size:40

Alignment explanation


    Indices: 2313--2392  Score: 135
    Period size: 39  Copynumber: 2.0  Consensus size: 40

       2303 AAGAGGTATG

                                                    
       2313 TCCAATATGAAAAGGGTTGTGACTCTTCAAAAGCTGTCCA
          1 TCCAATATGAAAAGGGTTGTGACTCTTCAAAAGCTGTCCA

                  *                          *      
       2353 TCCAATTTG-AAAGGGTTGTGACTCTTCAAAAGGTGTCCA
          1 TCCAATATGAAAAGGGTTGTGACTCTTCAAAAGCTGTCCA

             
       2392 T
          1 T

       2393 TGAGTAAATA


Statistics
Matches: 38,  Mismatches: 2, Indels: 1
        0.93            0.05        0.02

Matches are distributed among these distances:
  39   30  0.79
  40    8  0.21

ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30


Consensus pattern (40 bp):   
TCCAATATGAAAAGGGTTGTGACTCTTCAAAAGCTGTCCA
Done.