Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008047.1 Kokia drynarioides strain JFW-HI SEQ_122703, 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: 4743
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38


Found at i:755 original size:57 final size:57

Alignment explanation


    Indices: 667--781  Score: 221
    Period size: 57  Copynumber: 2.0  Consensus size: 57

        657 TTTATTAAGA

                       *                                             
        667 TATTGTTAATGTTGATTTTATTGTTACTTTAATGGGAATTAATATTATAATTATACC
          1 TATTGTTAATGCTGATTTTATTGTTACTTTAATGGGAATTAATATTATAATTATACC

                                                                     
        724 TATTGTTAATGCTGATTTTATTGTTACTTTAATGGGAATTAATATTATAATTATACC
          1 TATTGTTAATGCTGATTTTATTGTTACTTTAATGGGAATTAATATTATAATTATACC

             
        781 T
          1 T

        782 GTTTATGGGT


Statistics
Matches: 57,  Mismatches: 1, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  57   57  1.00

ACGTcount: A:0.31, C:0.06, G:0.12, T:0.50


Consensus pattern (57 bp):   
TATTGTTAATGCTGATTTTATTGTTACTTTAATGGGAATTAATATTATAATTATACC

Found at i:928 original size:16 final size:18

Alignment explanation


    Indices: 907--942  Score: 58
    Period size: 16  Copynumber: 2.1  Consensus size: 18

        897 GTTTGTAATG

                              
        907 TTTTATAT-TT-TGTTAT
          1 TTTTATATATTATGTTAT

                              
        923 TTTTATATATTATGTTAT
          1 TTTTATATATTATGTTAT

              
        941 TT
          1 TT

        943 ATAACACATA


Statistics
Matches: 18,  Mismatches: 0, Indels: 2
        0.90            0.00        0.10

Matches are distributed among these distances:
  16    8  0.44
  17    2  0.11
  18    8  0.44

ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72


Consensus pattern (18 bp):   
TTTTATATATTATGTTAT

Found at i:1087 original size:33 final size:34

Alignment explanation


    Indices: 1016--1088  Score: 89
    Period size: 32  Copynumber: 2.2  Consensus size: 34

       1006 TCTTCAGTTG

                                              
       1016 AATATATATAAAATATTAATAAATAAAAAAATAT
          1 AATATATATAAAATATTAATAAATAAAAAAATAT

                     *           **     *     
       1050 AATAT-TATTAAATATTAA-ATTTAAAATAATAT
          1 AATATATATAAAATATTAATAAATAAAAAAATAT

                    
       1082 AA-ATATA
          1 AATATATA

       1089 CATTTTTTCA


Statistics
Matches: 34,  Mismatches: 4, Indels: 4
        0.81            0.10        0.10

Matches are distributed among these distances:
  31    2  0.06
  32   15  0.44
  33   12  0.35
  34    5  0.15

ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37


Consensus pattern (34 bp):   
AATATATATAAAATATTAATAAATAAAAAAATAT

Found at i:4641 original size:63 final size:62

Alignment explanation


    Indices: 4574--4743  Score: 220
    Period size: 63  Copynumber: 2.7  Consensus size: 62

       4564 AATTCTCTTA

                                                                             
       4574 TTATTATTATTTTTATTCATTTATTTATTATTTTTATGAATATAAATAAAT-A-TAAAATAATAT
          1 TTATT-TTA-TTTTATT-ATTTATTTATTATTTTTATGAATATAAATAAATAAGTAAAATAATAT

                                  *                                          
       4637 TTATTTTATTTTATTATTTATTCATTTATTATTGTATGAATATAAATAAATAAATGTAAAATAAT
          1 TTATTTTATTTTATTATTTATTTA-TTATT-TT-TATGAATATAAATAAAT-AA-GTAAAATAAT

              
       4702 AT
         61 AT

             *     *                                 
       4704 TAATTTTGTTTTATTATTTATTTATTA-TTTTATGAATATA
          1 TTATTTTATTTTATTATTTATTTATTATTTTTATGAATATA


Statistics
Matches: 96,  Mismatches: 4, Indels: 14
        0.84            0.04        0.12

Matches are distributed among these distances:
  60    8  0.08
  61   12  0.12
  62    5  0.05
  63   32  0.33
  64    2  0.02
  65    2  0.02
  66    3  0.03
  67   32  0.33

ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56


Consensus pattern (62 bp):   
TTATTTTATTTTATTATTTATTTATTATTTTTATGAATATAAATAAATAAGTAAAATAATAT

Done.