Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010673.1 Kokia drynarioides strain JFW-HI SEQ_125619, 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: 3060
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.31

Warning! 50 characters in sequence are not A, C, G, or T


Found at i:415 original size:29 final size:30

Alignment explanation


    Indices: 360--557  Score: 150
    Period size: 28  Copynumber: 6.8  Consensus size: 30

        350 ATCCGGGAGT

                                           
        360 AAAAATGGTAATTTTTGGAAGTTTCGGGGTC
          1 AAAAATGGTAATTTTTGGAAG-TTCGGGGTC

                     *                     
        391 AAAAATGG-GATTTTTGGAAGTTCGGGGGT-
          1 AAAAATGGTAATTTTTGGAAGTTC-GGGGTC

                                    **    
        420 -AAAATGGTAATTTTTGGAAGTT-TAGGTC
          1 AAAAATGGTAATTTTTGGAAGTTCGGGGTC

                                            
        448 AAAAAT-G-AGATTTTTGGAAGTTCGGGGGT-
          1 AAAAATGGTA-ATTTTTGGAAGTTC-GGGGTC

                                 *  ***    
        477 --AAATGGTAATTTTTGGAAATTTTAAGGTC
          1 AAAAATGGTAATTTTTGG-AAGTTCGGGGTC

                     *      *    *         
        506 AAAAATGG-GATTTTTAGAAGATCGGGGGT-
          1 AAAAATGGTAATTTTTGGAAGTTC-GGGGTC

                           *        
        535 -AAAATGGTAATTTTCGGACAGTT
          1 AAAAATGGTAATTTTTGGA-AGTT

        558 TAGGGACCTT


Statistics
Matches: 130,  Mismatches: 21, Indels: 33
        0.71            0.11        0.18

Matches are distributed among these distances:
  27    8  0.06
  28   40  0.31
  29   36  0.28
  30   32  0.25
  31   14  0.11

ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34


Consensus pattern (30 bp):   
AAAAATGGTAATTTTTGGAAGTTCGGGGTC

Found at i:425 original size:59 final size:57

Alignment explanation


    Indices: 361--561  Score: 296
    Period size: 59  Copynumber: 3.5  Consensus size: 57

        351 TCCGGGAGTA

                                     *                                 
        361 AAAATGGTAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
          1 AAAATGGTAATTTTTGGAAGTTT--AGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT

                                               *                     
        420 AAAATGGTAATTTTTGGAAGTTTAGGTCAAAAATGAGATTTTTGGAAGTTCGGGGGT
          1 AAAATGGTAATTTTTGGAAGTTTAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT

                                *                        *    *        
        477 -AAATGGTAATTTTTGGAAATTTTAAGGTCAAAAATGGGATTTTTAGAAGATCGGGGGT
          1 AAAATGGTAATTTTTGG-AAGTTT-AGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT

                          *            
        535 AAAATGGTAATTTTCGGACAGTTTAGG
          1 AAAATGGTAATTTTTGGA-AGTTTAGG

        562 GACCTTCGGG


Statistics
Matches: 130,  Mismatches: 8, Indels: 9
        0.88            0.05        0.06

Matches are distributed among these distances:
  56   16  0.12
  57   37  0.28
  58   35  0.27
  59   42  0.32

ACGTcount: A:0.31, C:0.04, G:0.30, T:0.34


Consensus pattern (57 bp):   
AAAATGGTAATTTTTGGAAGTTTAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT

Found at i:1756 original size:3 final size:3

Alignment explanation


    Indices: 1743--1797  Score: 65
    Period size: 3  Copynumber: 18.0  Consensus size: 3

       1733 TTATTAGTGA

                                                      *       **      * 
       1743 TAT TCAT TAT TAT TAT TAT TAT TAT TAT TAT TTT TAT TGC TAT TGT
          1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT

                       
       1789 TAT TAT TAT
          1 TAT TAT TAT

       1798 GACTAAAGAT


Statistics
Matches: 43,  Mismatches: 8, Indels: 2
        0.81            0.15        0.04

Matches are distributed among these distances:
   3   40  0.93
   4    3  0.07

ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65


Consensus pattern (3 bp):   
TAT

Done.