Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014209.1 Kokia drynarioides strain JFW-HI SEQ_129242, 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: 7372
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34


Found at i:3690 original size:26 final size:27

Alignment explanation


    Indices: 3638--3700  Score: 74
    Period size: 26  Copynumber: 2.4  Consensus size: 27

       3628 AAAAGTAATT

                      *       *  **    
       3638 AATAAAAATAGTAAATTATAATTG-AA
          1 AATAAAAATAATAAATTACAAAGGAAA

                                       
       3664 AATAAAAATAATAAATTACAAAGGAAA
          1 AATAAAAATAATAAATTACAAAGGAAA

                *     
       3691 AATATAAATA
          1 AATAAAAATA

       3701 TACCTTTCAA


Statistics
Matches: 31,  Mismatches: 5, Indels: 1
        0.84            0.14        0.03

Matches are distributed among these distances:
  26   20  0.65
  27   11  0.35

ACGTcount: A:0.67, C:0.02, G:0.06, T:0.25


Consensus pattern (27 bp):   
AATAAAAATAATAAATTACAAAGGAAA

Found at i:5183 original size:16 final size:16

Alignment explanation


    Indices: 5159--5191  Score: 50
    Period size: 17  Copynumber: 2.1  Consensus size: 16

       5149 TTCATTCCCC

                            
       5159 TTCCCTTTTC-TTCTT
          1 TTCCCTTTTCTTTCTT

                             
       5174 TTCCCTTTTTCTTTCTT
          1 TTCCC-TTTTCTTTCTT

             
       5191 T
          1 T

       5192 CCTTCTCTTC


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

Matches are distributed among these distances:
  15    5  0.31
  16    5  0.31
  17    6  0.38

ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70


Consensus pattern (16 bp):   
TTCCCTTTTCTTTCTT

Found at i:6424 original size:25 final size:24

Alignment explanation


    Indices: 6396--6449  Score: 65
    Period size: 23  Copynumber: 2.2  Consensus size: 24

       6386 TTATTTTGTA

                                     
       6396 ACTCTTCTGCCATTATGTTTATAAC
          1 ACTCTT-TGCCATTATGTTTATAAC

                    *          *    
       6421 ACTC-TTGTCATTATGTTTGTAAC
          1 ACTCTTTGCCATTATGTTTATAAC

            *     
       6444 TCTCTT
          1 ACTCTT

       6450 GTCATAATGT


Statistics
Matches: 25,  Mismatches: 3, Indels: 3
        0.81            0.10        0.10

Matches are distributed among these distances:
  23   19  0.76
  24    2  0.08
  25    4  0.16

ACGTcount: A:0.20, C:0.22, G:0.09, T:0.48


Consensus pattern (24 bp):   
ACTCTTTGCCATTATGTTTATAAC

Found at i:6432 original size:23 final size:23

Alignment explanation


    Indices: 6406--6461  Score: 85
    Period size: 23  Copynumber: 2.4  Consensus size: 23

       6396 ACTCTTCTGC

                                   
       6406 CATTATGTTTATAACACTCTTGT
          1 CATTATGTTTATAACACTCTTGT

                      *    *       
       6429 CATTATGTTTGTAACTCTCTTGT
          1 CATTATGTTTATAACACTCTTGT

               *      
       6452 CATAATGTTT
          1 CATTATGTTT

       6462 TGTTTTAAAT


Statistics
Matches: 30,  Mismatches: 3, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  23   30  1.00

ACGTcount: A:0.23, C:0.16, G:0.11, T:0.50


Consensus pattern (23 bp):   
CATTATGTTTATAACACTCTTGT
Done.