Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012814.1 Kokia drynarioides strain JFW-HI SEQ_127827, 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: 2086
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.25

Warning! 61 characters in sequence are not A, C, G, or T


Found at i:215 original size:27 final size:27

Alignment explanation


    Indices: 179--238  Score: 84
    Period size: 27  Copynumber: 2.2  Consensus size: 27

        169 AATTTTCAAC

                                 *      
        179 TAATGATTGTTTCCTTTGATCTTCCTTT
          1 TAAT-ATTGTTTCCTTTGATCCTCCTTT

                       *           *   
        207 TAATATTGTTTTCTTTGATCCTCTTTT
          1 TAATATTGTTTCCTTTGATCCTCCTTT

                 
        234 TAATA
          1 TAATA

        239 GAATTTCTGA


Statistics
Matches: 29,  Mismatches: 3, Indels: 1
        0.88            0.09        0.03

Matches are distributed among these distances:
  27   25  0.86
  28    4  0.14

ACGTcount: A:0.18, C:0.15, G:0.08, T:0.58


Consensus pattern (27 bp):   
TAATATTGTTTCCTTTGATCCTCCTTT

Found at i:1908 original size:17 final size:17

Alignment explanation


    Indices: 1857--1948  Score: 75
    Period size: 17  Copynumber: 5.4  Consensus size: 17

       1847 TTCATTTTGG

                        *     
       1857 GTTTAAATTTAATTTAAA
          1 GTTTAAATTTAAATT-AA

                        **    
       1875 GTTTAAACTTT-TCTTAA
          1 GTTTAAA-TTTAAATTAA

                             
       1892 GTTTAAATTTAAATTAA
          1 GTTTAAATTTAAATTAA

                   *    *     
       1909 GTTTAAAATTAATTTGAA
          1 GTTTAAATTTAAATT-AA

                              
       1927 -TTTAAAATTT-AATTAA
          1 GTTT-AAATTTAAATTAA

                   
       1943 -TTTAAA
          1 GTTTAAA

       1949 AAAAGAAGTC


Statistics
Matches: 62,  Mismatches: 8, Indels: 11
        0.77            0.10        0.14

Matches are distributed among these distances:
  15    3  0.05
  16    8  0.13
  17   32  0.52
  18   16  0.26
  19    3  0.05

ACGTcount: A:0.43, C:0.02, G:0.05, T:0.49


Consensus pattern (17 bp):   
GTTTAAATTTAAATTAA

Found at i:1931 original size:34 final size:34

Alignment explanation


    Indices: 1857--1949  Score: 95
    Period size: 35  Copynumber: 2.7  Consensus size: 34

       1847 TTCATTTTGG

                        *            *      *  
       1857 GTTTAAATTTAATTTAAAGTTTAAACTTTTCTTAA
          1 GTTTAAATTTAAATT-AAGTTTAAAATTTTCTGAA

                                                
       1892 GTTTAAATTTAAATTAAGTTTAAAATTAATT-TGAA
          1 GTTTAAATTTAAATTAAGTTTAAAATT--TTCTGAA

                                      
       1927 -TTTAAAATTT-AATTAA-TTTAAAA
          1 GTTT-AAATTTAAATTAAGTTTAAAA

       1950 AAAGAAGTCC


Statistics
Matches: 52,  Mismatches: 3, Indels: 8
        0.83            0.05        0.13

Matches are distributed among these distances:
  33    7  0.13
  34   20  0.38
  35   23  0.44
  36    2  0.04

ACGTcount: A:0.44, C:0.02, G:0.05, T:0.48


Consensus pattern (34 bp):   
GTTTAAATTTAAATTAAGTTTAAAATTTTCTGAA

Found at i:2033 original size:16 final size:16

Alignment explanation


    Indices: 2012--2051  Score: 55
    Period size: 15  Copynumber: 2.6  Consensus size: 16

       2002 ACTAACCTAA

                            
       2012 GCCCAAATTCTAAAAG
          1 GCCCAAATTCTAAAAG

                    *     * 
       2028 GCCCAAA-CCTAAATG
          1 GCCCAAATTCTAAAAG

                     
       2043 GCCCAAATT
          1 GCCCAAATT

       2052 GGCCCAAACC


Statistics
Matches: 20,  Mismatches: 3, Indels: 2
        0.80            0.12        0.08

Matches are distributed among these distances:
  15   13  0.65
  16    7  0.35

ACGTcount: A:0.40, C:0.30, G:0.12, T:0.17


Consensus pattern (16 bp):   
GCCCAAATTCTAAAAG
Done.