Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012349.1 Kokia drynarioides strain JFW-HI SEQ_127351, 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: 3107
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33


Found at i:907 original size:24 final size:24

Alignment explanation


    Indices: 875--921  Score: 85
    Period size: 24  Copynumber: 2.0  Consensus size: 24

        865 TTTTCATTTA

                        *           
        875 TTATTCAATTACTTGTTTGTGAAT
          1 TTATTCAATTACATGTTTGTGAAT

                                   
        899 TTATTCAATTACATGTTTGTGAA
          1 TTATTCAATTACATGTTTGTGAA

        922 CAAGTTCATT


Statistics
Matches: 22,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  24   22  1.00

ACGTcount: A:0.28, C:0.09, G:0.13, T:0.51


Consensus pattern (24 bp):   
TTATTCAATTACATGTTTGTGAAT

Found at i:929 original size:24 final size:24

Alignment explanation


    Indices: 877--938  Score: 65
    Period size: 24  Copynumber: 2.6  Consensus size: 24

        867 TTCATTTATT

                      *           **
        877 ATTCAATTACTTGTTTGTGAATTT
          1 ATTCAATTACATGTTTGTGAATCA

                                    
        901 ATTCAATTACATGTTTGTGAA-CA
          1 ATTCAATTACATGTTTGTGAATCA

                  *         
        924 AGTTCATTTA-ATGTT
          1 A-TTCAATTACATGTT

        939 CATGAACATT


Statistics
Matches: 33,  Mismatches: 4, Indels: 3
        0.82            0.10        0.08

Matches are distributed among these distances:
  23    6  0.18
  24   27  0.82

ACGTcount: A:0.29, C:0.10, G:0.13, T:0.48


Consensus pattern (24 bp):   
ATTCAATTACATGTTTGTGAATCA

Found at i:1040 original size:15 final size:15

Alignment explanation


    Indices: 1020--1062  Score: 61
    Period size: 16  Copynumber: 2.9  Consensus size: 15

       1010 CTTAACGAAT

                           
       1020 ACAAACTAAACATAA
          1 ACAAACTAAACATAA

                       *    
       1035 ACAAACTTAAAAATAA
          1 ACAAAC-TAAACATAA

                         
       1051 ACAAAC-AAACAT
          1 ACAAACTAAACAT

       1063 GAATTGAAAT


Statistics
Matches: 25,  Mismatches: 2, Indels: 3
        0.83            0.07        0.10

Matches are distributed among these distances:
  14    5  0.20
  15    6  0.24
  16   14  0.56

ACGTcount: A:0.67, C:0.19, G:0.00, T:0.14


Consensus pattern (15 bp):   
ACAAACTAAACATAA

Done.