Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01015123.1 Kokia drynarioides strain JFW-HI SEQ_130167, 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: 24583
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33

Warning! 200 characters in sequence are not A, C, G, or T


Found at i:11416 original size:20 final size:19

Alignment explanation


    Indices: 11379--11417  Score: 51
    Period size: 20  Copynumber: 2.0  Consensus size: 19

      11369 CTCAAATTGA

                         *     
      11379 TTAAATATTAAAAGTATAT
          1 TTAAATATTAAAAATATAT

                  *             
      11398 TTAAATTTTAAAAAATATAT
          1 TTAAATATT-AAAAATATAT

      11418 ATATAATAAA


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  19    8  0.47
  20    9  0.53

ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44


Consensus pattern (19 bp):   
TTAAATATTAAAAATATAT

Found at i:14463 original size:15 final size:16

Alignment explanation


    Indices: 14440--14475  Score: 56
    Period size: 15  Copynumber: 2.3  Consensus size: 16

      14430 ATATTTTAAC

                            
      14440 AAATAAAATTAA-AAA
          1 AAATAAAATTAACAAA

                *           
      14455 AAATGAAATTAACAAA
          1 AAATAAAATTAACAAA

                 
      14471 AAATA
          1 AAATA

      14476 TAGTGAGAAA


Statistics
Matches: 18,  Mismatches: 2, Indels: 1
        0.86            0.10        0.05

Matches are distributed among these distances:
  15   11  0.61
  16    7  0.39

ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19


Consensus pattern (16 bp):   
AAATAAAATTAACAAA

Found at i:19925 original size:17 final size:18

Alignment explanation


    Indices: 19892--19925  Score: 52
    Period size: 17  Copynumber: 1.9  Consensus size: 18

      19882 ATGAAATATT

                      *       
      19892 TTAAATAATATAAAAATA
          1 TTAAATAATAAAAAAATA

                             
      19910 TTAAAT-ATAAAAAAAT
          1 TTAAATAATAAAAAAAT

      19926 TTCATCCAAA


Statistics
Matches: 15,  Mismatches: 1, Indels: 1
        0.88            0.06        0.06

Matches are distributed among these distances:
  17    9  0.60
  18    6  0.40

ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32


Consensus pattern (18 bp):   
TTAAATAATAAAAAAATA

Found at i:22149 original size:19 final size:20

Alignment explanation


    Indices: 22125--22170  Score: 67
    Period size: 20  Copynumber: 2.4  Consensus size: 20

      22115 TCTGGCTTGG

                                
      22125 CAGACA-ATGGTGGGTGATC
          1 CAGACATATGGTGGGTGATC

                   *            
      22144 CAGACATGTGGTGGGTGATC
          1 CAGACATATGGTGGGTGATC

             *     
      22164 CTGACAT
          1 CAGACAT

      22171 GTGATCCTGT


Statistics
Matches: 24,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  19    6  0.25
  20   18  0.75

ACGTcount: A:0.24, C:0.17, G:0.35, T:0.24


Consensus pattern (20 bp):   
CAGACATATGGTGGGTGATC

Found at i:22157 original size:20 final size:20

Alignment explanation


    Indices: 22132--22173  Score: 75
    Period size: 20  Copynumber: 2.1  Consensus size: 20

      22122 TGGCAGACAA

                                
      22132 TGGTGGGTGATCCAGACATG
          1 TGGTGGGTGATCCAGACATG

                         *      
      22152 TGGTGGGTGATCCTGACATG
          1 TGGTGGGTGATCCAGACATG

              
      22172 TG
          1 TG

      22174 ATCCTGTTTA


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

Matches are distributed among these distances:
  20   21  1.00

ACGTcount: A:0.17, C:0.14, G:0.40, T:0.29


Consensus pattern (20 bp):   
TGGTGGGTGATCCAGACATG
Done.