Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008274.1 Kokia drynarioides strain JFW-HI SEQ_122939, 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: 19549
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35


Found at i:3046 original size:17 final size:17

Alignment explanation


    Indices: 3010--3050  Score: 57
    Period size: 17  Copynumber: 2.4  Consensus size: 17

       3000 GCAAAATCAA

                   *         
       3010 AATTTTTCTTTTCACTT
          1 AATTTTTATTTTCACTT

                              
       3027 AATATTTTATTTTC-CTT
          1 AAT-TTTTATTTTCACTT

                   
       3044 AATTTTT
          1 AATTTTT

       3051 TCGTTGACTG


Statistics
Matches: 22,  Mismatches: 1, Indels: 3
        0.85            0.04        0.12

Matches are distributed among these distances:
  16    4  0.18
  17    9  0.41
  18    9  0.41

ACGTcount: A:0.22, C:0.12, G:0.00, T:0.66


Consensus pattern (17 bp):   
AATTTTTATTTTCACTT

Found at i:5752 original size:22 final size:22

Alignment explanation


    Indices: 5727--5770  Score: 88
    Period size: 22  Copynumber: 2.0  Consensus size: 22

       5717 GTAAAGAATG

                                  
       5727 GTTAACCTTCATGTCTTTATGT
          1 GTTAACCTTCATGTCTTTATGT

                                  
       5749 GTTAACCTTCATGTCTTTATGT
          1 GTTAACCTTCATGTCTTTATGT

       5771 ATTTTTATAC


Statistics
Matches: 22,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  22   22  1.00

ACGTcount: A:0.18, C:0.18, G:0.14, T:0.50


Consensus pattern (22 bp):   
GTTAACCTTCATGTCTTTATGT

Found at i:6505 original size:19 final size:19

Alignment explanation


    Indices: 6481--6522  Score: 57
    Period size: 19  Copynumber: 2.2  Consensus size: 19

       6471 TTTCTTTTTC

                               
       6481 AAATATTTTAAAAAATTTA
          1 AAATATTTTAAAAAATTTA

                     *  *     *
       6500 AAATATTTTTAACAATTTT
          1 AAATATTTTAAAAAATTTA

                
       6519 AAAT
          1 AAAT

       6523 TCTAAAGTAA


Statistics
Matches: 20,  Mismatches: 3, Indels: 0
        0.87            0.13        0.00

Matches are distributed among these distances:
  19   20  1.00

ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45


Consensus pattern (19 bp):   
AAATATTTTAAAAAATTTA

Found at i:12838 original size:35 final size:35

Alignment explanation


    Indices: 12792--12864  Score: 146
    Period size: 35  Copynumber: 2.1  Consensus size: 35

      12782 CTCTCAAATG

                                               
      12792 TCATTAAAAGCAAATAATGATATAGAACCAAAACT
          1 TCATTAAAAGCAAATAATGATATAGAACCAAAACT

                                               
      12827 TCATTAAAAGCAAATAATGATATAGAACCAAAACT
          1 TCATTAAAAGCAAATAATGATATAGAACCAAAACT

               
      12862 TCA
          1 TCA

      12865 ACATGTTGAA


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  35   38  1.00

ACGTcount: A:0.53, C:0.15, G:0.08, T:0.23


Consensus pattern (35 bp):   
TCATTAAAAGCAAATAATGATATAGAACCAAAACT

Found at i:14188 original size:36 final size:36

Alignment explanation


    Indices: 14148--14218  Score: 106
    Period size: 36  Copynumber: 2.0  Consensus size: 36

      14138 TGCCCACCAC

                      *           *       *     
      14148 GCGTGAAAAAGTAAAATAAAAAGGAAATTATTTAAT
          1 GCGTGAAAAAATAAAATAAAAAAGAAATTACTTAAT

                          *                    
      14184 GCGTGAAAAAATAATATAAAAAAGAAATTACTTAA
          1 GCGTGAAAAAATAAAATAAAAAAGAAATTACTTAA

      14219 CATAATGTTT


Statistics
Matches: 31,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  36   31  1.00

ACGTcount: A:0.58, C:0.04, G:0.14, T:0.24


Consensus pattern (36 bp):   
GCGTGAAAAAATAAAATAAAAAAGAAATTACTTAAT
Done.