Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01012127.1 Kokia drynarioides strain JFW-HI SEQ_127126, 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: 8943
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36

Warning! 5 characters in sequence are not A, C, G, or T


Found at i:9 original size:4 final size:4

Alignment explanation


    Indices: 1--38  Score: 51
    Period size: 4  Copynumber: 9.5  Consensus size: 4

                                       *                    
          1 TCTT TCTT TCTT TCTT TCTCT TTTT TCTT TCTT T-TT TC
          1 TCTT TCTT TCTT TCTT TCT-T TCTT TCTT TCTT TCTT TC

         39 CTTCATTTTT


Statistics
Matches: 30,  Mismatches: 2, Indels: 4
        0.83            0.06        0.11

Matches are distributed among these distances:
   3    3  0.10
   4   24  0.80
   5    3  0.10

ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76


Consensus pattern (4 bp):   
TCTT

Found at i:4574 original size:20 final size:20

Alignment explanation


    Indices: 4545--4582  Score: 58
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       4535 AAAAGCTCTT

                        *       
       4545 CGATTAGTCTCGTCGGATCC
          1 CGATTAGTCTCGACGGATCC

                 *            
       4565 CGATTTGTCTCGACGGAT
          1 CGATTAGTCTCGACGGAT

       4583 GTTCTTCCAT


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  20   16  1.00

ACGTcount: A:0.16, C:0.26, G:0.26, T:0.32


Consensus pattern (20 bp):   
CGATTAGTCTCGACGGATCC

Found at i:7966 original size:22 final size:21

Alignment explanation


    Indices: 7916--7969  Score: 72
    Period size: 22  Copynumber: 2.5  Consensus size: 21

       7906 TTTTAAATTT

                            *    
       7916 GATTTAAATTTAAATTTAATC
          1 GATTTAAATTTAAATTGAATC

                                 *
       7937 GATATTAAATTTAAATTGAATT
          1 GAT-TTAAATTTAAATTGAATC

                       
       7959 GAATTTAAATT
          1 G-ATTTAAATT

       7970 AAAAAAAAAT


Statistics
Matches: 29,  Mismatches: 2, Indels: 3
        0.85            0.06        0.09

Matches are distributed among these distances:
  21    3  0.10
  22   24  0.83
  23    2  0.07

ACGTcount: A:0.44, C:0.02, G:0.07, T:0.46


Consensus pattern (21 bp):   
GATTTAAATTTAAATTGAATC

Found at i:8731 original size:12 final size:13

Alignment explanation


    Indices: 8703--8736  Score: 61
    Period size: 12  Copynumber: 2.7  Consensus size: 13

       8693 GAGATTTTAT

                         
       8703 TATTATTAAAGAA
          1 TATTATTAAAGAA

                         
       8716 TATTATTAAA-AA
          1 TATTATTAAAGAA

                     
       8728 TATTATTAA
          1 TATTATTAA

       8737 TGGTTAATAA


Statistics
Matches: 21,  Mismatches: 0, Indels: 1
        0.95            0.00        0.05

Matches are distributed among these distances:
  12   11  0.52
  13   10  0.48

ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44


Consensus pattern (13 bp):   
TATTATTAAAGAA
Done.