Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007941.1 Kokia drynarioides strain JFW-HI SEQ_122589, 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: 4868
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.33


Found at i:391 original size:34 final size:35

Alignment explanation


    Indices: 349--443  Score: 102
    Period size: 38  Copynumber: 2.7  Consensus size: 35

        339 GTACATGTTC

                                               
        349 ATGCAGCGACATTCCTGGGTGCAGTTG-AATACTT
          1 ATGCAGCGACATTCCTGGGTGCAGTTGAAATACTT

                         *    *     *          *  
        383 ATGCAGCGACATTTCTGGTTGCAATTTGAAAAATATTT
          1 ATGCAGCGACATTCCTGGGTGC-AGTTG--AAATACTT

                       *  *        
        421 ATGCAGCGACAGTCTTGGGTGCA
          1 ATGCAGCGACATTCCTGGGTGCA

        444 TTCCGAAAAT


Statistics
Matches: 49,  Mismatches: 8, Indels: 5
        0.79            0.13        0.08

Matches are distributed among these distances:
  34   20  0.41
  35    4  0.08
  37    1  0.02
  38   24  0.49

ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31


Consensus pattern (35 bp):   
ATGCAGCGACATTCCTGGGTGCAGTTGAAATACTT

Found at i:452 original size:38 final size:37

Alignment explanation


    Indices: 349--456  Score: 93
    Period size: 38  Copynumber: 3.0  Consensus size: 37

        339 GTACATGTTC

                                    *          *  
        349 ATGCAGCGACAT-TCCTGGGTGCAGTT-G--AATACTT
          1 ATGCAGCGACATCT-CTGGGTGCAATTCGAAAATATTT

                        *     *       *           
        383 ATGCAGCGACATTTCTGGTTGCAATTTGAAAAATATTT
          1 ATGCAGCGACATCTCTGGGTGCAATTCG-AAAATATTT

                                                  
        421 ATGCAGCGACAGTCT-TGGGTGC-ATTCCGAAAATATT
          1 ATGCAGCGACA-TCTCTGGGTGCAATT-CGAAAATATT

        457 ATTGCGGTGA


Statistics
Matches: 61,  Mismatches: 6, Indels: 11
        0.78            0.08        0.14

Matches are distributed among these distances:
  34   22  0.36
  35    2  0.03
  37   11  0.18
  38   24  0.39
  39    2  0.03

ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31


Consensus pattern (37 bp):   
ATGCAGCGACATCTCTGGGTGCAATTCGAAAATATTT

Found at i:3951 original size:16 final size:16

Alignment explanation


    Indices: 3930--3960  Score: 53
    Period size: 16  Copynumber: 1.9  Consensus size: 16

       3920 ATAATGTGAG

                            
       3930 AATAAAGATAAAATGT
          1 AATAAAGATAAAATGT

                   *       
       3946 AATAAAGGTAAAATG
          1 AATAAAGATAAAATG

       3961 GGAACCACAA


Statistics
Matches: 14,  Mismatches: 1, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  16   14  1.00

ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23


Consensus pattern (16 bp):   
AATAAAGATAAAATGT
Done.