Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01013756.1 Kokia drynarioides strain JFW-HI SEQ_128784, 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: 2227
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40


Found at i:537 original size:49 final size:49

Alignment explanation


    Indices: 484--608  Score: 144
    Period size: 51  Copynumber: 2.5  Consensus size: 49

        474 CTTGGTATAA

                       *   *                            *   * 
        484 TAACAAATTTATCCCTCAA-AGTTTACATTCTATCAATTTGGTCTTGATT
          1 TAACAAATTTAACCCACAACA-TTTACATTCTATCAATTTGGTCATGAGT

                                   *      *                    
        533 TAACAAATTTAACCCACAACATTAACATATTTCATCAATTTGGTCATGAGT
          1 TAACAAATTTAACCCACAACATTTACAT-TCT-ATCAATTTGGTCATGAGT

                 *             *     
        584 TAACATATTTAACCCACAATATTTA
          1 TAACAAATTTAACCCACAACATTTA

        609 TATATTCTAT


Statistics
Matches: 64,  Mismatches: 9, Indels: 4
        0.83            0.12        0.05

Matches are distributed among these distances:
  49   23  0.36
  50    3  0.05
  51   38  0.59

ACGTcount: A:0.37, C:0.19, G:0.06, T:0.38


Consensus pattern (49 bp):   
TAACAAATTTAACCCACAACATTTACATTCTATCAATTTGGTCATGAGT

Found at i:621 original size:51 final size:51

Alignment explanation


    Indices: 510--621  Score: 154
    Period size: 51  Copynumber: 2.2  Consensus size: 51

        500 CAAAGTTTAC

                             *   *                             
        510 ATTCTATCAATTTGGTCTTGATTTAACAAATTTAACCCACAACATTAACAT
          1 ATTCTATCAATTTGGTCATGAGTTAACAAATTTAACCCACAACATTAACAT

                                         *             *   * *  
        561 ATT-TCATCAATTTGGTCATGAGTTAACATATTTAACCCACAATATTTATAT
          1 ATTCT-ATCAATTTGGTCATGAGTTAACAAATTTAACCCACAACATTAACAT

                      
        612 ATTCTATCAA
          1 ATTCTATCAA

        622 CATTTATGCA


Statistics
Matches: 53,  Mismatches: 6, Indels: 4
        0.84            0.10        0.06

Matches are distributed among these distances:
  50    1  0.02
  51   51  0.96
  52    1  0.02

ACGTcount: A:0.37, C:0.18, G:0.06, T:0.39


Consensus pattern (51 bp):   
ATTCTATCAATTTGGTCATGAGTTAACAAATTTAACCCACAACATTAACAT

Found at i:1385 original size:18 final size:19

Alignment explanation


    Indices: 1363--1402  Score: 57
    Period size: 18  Copynumber: 2.2  Consensus size: 19

       1353 TTTTTTTTGG

                     *         
       1363 ATTTTT-TATTTTTAAA-T
          1 ATTTTTATAATTTTAAATT

                               
       1380 ATTTTTATAATTTTAAATT
          1 ATTTTTATAATTTTAAATT

                
       1399 ATTT
          1 ATTT

       1403 GTTGACATTA


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

Matches are distributed among these distances:
  17    6  0.30
  18    9  0.45
  19    5  0.25

ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68


Consensus pattern (19 bp):   
ATTTTTATAATTTTAAATT
Done.