Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007264.1 Kokia drynarioides strain JFW-HI SEQ_121880, 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: 27146
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34


Found at i:1794 original size:25 final size:27

Alignment explanation


    Indices: 1766--1824  Score: 81
    Period size: 25  Copynumber: 2.3  Consensus size: 27

       1756 AATAAGTTTA

                                       
       1766 TATATTATATATAAAAAT-AATT-ATG
          1 TATATTATATATAAAAATAAATTAATG

                                        
       1791 TATATTCA-ATATAAAAATAAATTAATG
          1 TATATT-ATATATAAAAATAAATTAATG

                    
       1818 TAT-TTAT
          1 TATATTAT

       1825 TTTTTAAAAC


Statistics
Matches: 30,  Mismatches: 0, Indels: 7
        0.81            0.00        0.19

Matches are distributed among these distances:
  25   17  0.57
  26    7  0.23
  27    6  0.20

ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44


Consensus pattern (27 bp):   
TATATTATATATAAAAATAAATTAATG

Found at i:2807 original size:15 final size:16

Alignment explanation


    Indices: 2776--2813  Score: 51
    Period size: 15  Copynumber: 2.4  Consensus size: 16

       2766 TTAACATCTT

                             
       2776 TTATCAATTATATATAA
          1 TTAT-AATTATATATAA

                            
       2793 TTATAATTA-ATATAA
          1 TTATAATTATATATAA

             *    
       2808 TAATAA
          1 TTATAA

       2814 ATTTAGTCAT


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  15   11  0.55
  16    5  0.25
  17    4  0.20

ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45


Consensus pattern (16 bp):   
TTATAATTATATATAA

Found at i:4527 original size:2 final size:2

Alignment explanation


    Indices: 4520--4546  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

       4510 AGATCTGTGT

                                                    
       4520 TC TC TC TC TC TC TC TC TC TC TC TC TC T
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC T

       4547 GTGTGTGTGT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52


Consensus pattern (2 bp):   
TC

Found at i:10462 original size:2 final size:2

Alignment explanation


    Indices: 10455--10494  Score: 80
    Period size: 2  Copynumber: 20.0  Consensus size: 2

      10445 GGTTTTGTTT

                                                                       
      10455 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
          1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA

      10495 TGTTTGGAAA


Statistics
Matches: 38,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   38  1.00

ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00


Consensus pattern (2 bp):   
GA

Found at i:12659 original size:18 final size:18

Alignment explanation


    Indices: 12638--12676  Score: 53
    Period size: 19  Copynumber: 2.1  Consensus size: 18

      12628 AATCTGAAAT

                               
      12638 TTTTATAAA-TATTTTGAA
          1 TTTTA-AAATTATTTTGAA

                               
      12656 TTTTAAAATTTATTTTGAA
          1 TTTTAAAA-TTATTTTGAA

              
      12675 TT
          1 TT

      12677 ATTTTGTAAT


Statistics
Matches: 19,  Mismatches: 0, Indels: 3
        0.86            0.00        0.14

Matches are distributed among these distances:
  17    3  0.16
  18    5  0.26
  19   11  0.58

ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59


Consensus pattern (18 bp):   
TTTTAAAATTATTTTGAA

Found at i:13619 original size:27 final size:30

Alignment explanation


    Indices: 13589--13644  Score: 73
    Period size: 31  Copynumber: 1.9  Consensus size: 30

      13579 ATGATATGCA

                                          
      13589 TTAT-AAAATT-TAA-ATATGTAATTAATT
          1 TTATGAAAATTATAATATATGTAATTAATT

                  *                      
      13616 TTATGGTAAATTATAATATATGTAATTAA
          1 TTAT-GAAAATTATAATATATGTAATTAA

      13645 AATTATATAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 4
        0.83            0.03        0.14

Matches are distributed among these distances:
  27    4  0.17
  29    5  0.21
  30    3  0.12
  31   12  0.50

ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46


Consensus pattern (30 bp):   
TTATGAAAATTATAATATATGTAATTAATT

Found at i:17862 original size:41 final size:41

Alignment explanation


    Indices: 17827--17929  Score: 172
    Period size: 41  Copynumber: 2.5  Consensus size: 41

      17817 ATGAGCATAG

                                                     
      17827 GATTATGAATAAGGAAGACTCATGTCTCGAGATGAGAATGA
          1 GATTATGAATAAGGAAGACTCATGTCTCGAGATGAGAATGA

                                                     
      17868 GATTATGAATAAGGAAGACTCATGTCTCGAGATGAGAATGA
          1 GATTATGAATAAGGAAGACTCATGTCTCGAGATGAGAATGA

              *                   
      17909 GAATATGGTAA-AAGGAAGACT
          1 GATTAT-G-AATAAGGAAGACT

      17930 TACGACTCAA


Statistics
Matches: 59,  Mismatches: 1, Indels: 3
        0.94            0.02        0.05

Matches are distributed among these distances:
  41   46  0.78
  42   11  0.19
  43    2  0.03

ACGTcount: A:0.41, C:0.09, G:0.27, T:0.23


Consensus pattern (41 bp):   
GATTATGAATAAGGAAGACTCATGTCTCGAGATGAGAATGA

Done.