Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008248.1 Kokia drynarioides strain JFW-HI SEQ_122913, 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: 319511
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33

Warning! 30 characters in sequence are not A, C, G, or T


File 2 of 2

Found at i:304788 original size:25 final size:26

Alignment explanation


    Indices: 304760--304813  Score: 85
    Period size: 25  Copynumber: 2.1  Consensus size: 26

     304750 TAACATTTTT

                                       
     304760 AAAACCCAAACCCA-AT-AACCCTTTA
          1 AAAACCCAAA-CCATATAAACCCTTTA

                                      
     304785 AAAACCCAAACCATATAAACCCTTTA
          1 AAAACCCAAACCATATAAACCCTTTA

               
     304811 AAA
          1 AAA

     304814 TCCATTAAGC


Statistics
Matches: 27,  Mismatches: 0, Indels: 3
        0.90            0.00        0.10

Matches are distributed among these distances:
  24    3  0.11
  25   12  0.44
  26   12  0.44

ACGTcount: A:0.52, C:0.31, G:0.00, T:0.17


Consensus pattern (26 bp):   
AAAACCCAAACCATATAAACCCTTTA

Found at i:306013 original size:3 final size:3

Alignment explanation


    Indices: 305999--306033  Score: 63
    Period size: 3  Copynumber: 12.0  Consensus size: 3

     305989 CAAAATTTAC

                                                           
     305999 ATT ATT -TT ATT ATT ATT ATT ATT ATT ATT ATT ATT
          1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT

     306034 TTGGGTTGTA


Statistics
Matches: 31,  Mismatches: 0, Indels: 2
        0.94            0.00        0.06

Matches are distributed among these distances:
   2    2  0.06
   3   29  0.94

ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69


Consensus pattern (3 bp):   
ATT

Found at i:311311 original size:20 final size:20

Alignment explanation


    Indices: 311286--311332  Score: 58
    Period size: 20  Copynumber: 2.4  Consensus size: 20

     311276 GTCAATTTAA

                         *      
     311286 GAACCCTAGTATACTCTAGG
          1 GAACCCTAGTATAATCTAGG

                    *      *    
     311306 GAACCCTATTATAATTTAGG
          1 GAACCCTAGTATAATCTAGG

              *    
     311326 GACCCCT
          1 GAACCCT

     311333 GAGGAAAAAA


Statistics
Matches: 23,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  20   23  1.00

ACGTcount: A:0.30, C:0.26, G:0.17, T:0.28


Consensus pattern (20 bp):   
GAACCCTAGTATAATCTAGG

Found at i:311915 original size:26 final size:25

Alignment explanation


    Indices: 311860--311923  Score: 83
    Period size: 25  Copynumber: 2.5  Consensus size: 25

     311850 TTAAATCCAT

                 *   *               
     311860 TAACCTTTTTAAAACCCAAACCCAA
          1 TAACCCTTTAAAAACCCAAACCCAA

                                  ** 
     311885 TAACCCTTTAAAAACCCAAACCTTA
          1 TAACCCTTTAAAAACCCAAACCCAA

                          
     311910 TAAACCCTTTAAAA
          1 T-AACCCTTTAAAA

     311924 TCCATTAAGT


Statistics
Matches: 34,  Mismatches: 4, Indels: 1
        0.87            0.10        0.03

Matches are distributed among these distances:
  25   22  0.65
  26   12  0.35

ACGTcount: A:0.45, C:0.30, G:0.00, T:0.25


Consensus pattern (25 bp):   
TAACCCTTTAAAAACCCAAACCCAA

Found at i:319105 original size:18 final size:19

Alignment explanation


    Indices: 319070--319115  Score: 51
    Period size: 18  Copynumber: 2.5  Consensus size: 19

     319060 TTCTGTTATA

                          *    
     319070 GTTGCATTT-GCTCTTGTG
          1 GTTGCATTTGGCTCATGTG

                               
     319088 GTTGCATTTGGCT-ATGTG
          1 GTTGCATTTGGCTCATGTG

            **        
     319106 CCTGCATTTG
          1 GTTGCATTTG

     319116 ATCAGGAATT


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  18   21  0.88
  19    3  0.12

ACGTcount: A:0.09, C:0.17, G:0.28, T:0.46


Consensus pattern (19 bp):   
GTTGCATTTGGCTCATGTG

Done.