Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006941.1 Kokia drynarioides strain JFW-HI SEQ_121544, 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: 3126
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35


Found at i:2002 original size:12 final size:12

Alignment explanation


    Indices: 1986--2032  Score: 60
    Period size: 12  Copynumber: 4.0  Consensus size: 12

       1976 CTTGTTTAAA

                        
       1986 AGCTCATTTATT
          1 AGCTCATTTATT

            *          *
       1998 GGCTCATTTATA
          1 AGCTCATTTATT

                 *      
       2010 AGCTCGTTTA-T
          1 AGCTCATTTATT

                        
       2021 AGCTCATTTATT
          1 AGCTCATTTATT

       2033 TATTAATGAT


Statistics
Matches: 28,  Mismatches: 6, Indels: 2
        0.78            0.17        0.06

Matches are distributed among these distances:
  11    9  0.32
  12   19  0.68

ACGTcount: A:0.23, C:0.17, G:0.13, T:0.47


Consensus pattern (12 bp):   
AGCTCATTTATT

Found at i:2012 original size:24 final size:23

Alignment explanation


    Indices: 1980--2031  Score: 68
    Period size: 24  Copynumber: 2.2  Consensus size: 23

       1970 AACAAACTTG

                *             *     
       1980 TTTAAAAGCTCATTTATTGGCTCA
          1 TTTATAAGCTCATTTA-TAGCTCA

                       *           
       2004 TTTATAAGCTCGTTTATAGCTCA
          1 TTTATAAGCTCATTTATAGCTCA

                 
       2027 TTTAT
          1 TTTAT

       2032 TTATTAATGA


Statistics
Matches: 25,  Mismatches: 3, Indels: 1
        0.86            0.10        0.03

Matches are distributed among these distances:
  23   11  0.44
  24   14  0.56

ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46


Consensus pattern (23 bp):   
TTTATAAGCTCATTTATAGCTCA

Found at i:2900 original size:31 final size:30

Alignment explanation


    Indices: 2837--2901  Score: 78
    Period size: 31  Copynumber: 2.1  Consensus size: 30

       2827 GATTTTGAAA

                       *    *             
       2837 AGTTGAGTGATTAAATTGAAAAAAATTAAT
          1 AGTTGAGTGATAAAATAGAAAAAAATTAAT

                                 *          
       2867 AGTTGAGTGACTAAAATAGAACAAAA-TATAT
          1 AGTTGAGTGA-TAAAATAGAAAAAAATTA-AT

                
       2898 AGTT
          1 AGTT

       2902 AGATGATTAT


Statistics
Matches: 30,  Mismatches: 3, Indels: 3
        0.83            0.08        0.08

Matches are distributed among these distances:
  30   12  0.40
  31   18  0.60

ACGTcount: A:0.49, C:0.03, G:0.17, T:0.31


Consensus pattern (30 bp):   
AGTTGAGTGATAAAATAGAAAAAAATTAAT
Done.