Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007337.1 Kokia drynarioides strain JFW-HI SEQ_121953, 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: 9543
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31


Found at i:5659 original size:70 final size:69

Alignment explanation


    Indices: 5576--5765  Score: 299
    Period size: 70  Copynumber: 2.7  Consensus size: 69

       5566 GTAGTAAAAT

                    *                                        *               
       5576 TTAACCAATAATAACAAGCCACCTAAGGCTTGTTCTAGACATTTCTACCTTTATCATCCATCAAG
          1 TTAACC-ACAATAACAAGCCACCTAAGGCTTGTTCTAGACATTTCTACCATTATCATCCATCAAG

                 
       5641 CCAAA
         65 CCAAA

                            *         *                 *                    
       5646 TTAACCACCAATAACATGCCACCTAAAGCTTGTTCTAGACATTTGTACCATTATCATCCATCAAG
          1 TTAACCA-CAATAACAAGCCACCTAAGGCTTGTTCTAGACATTTCTACCATTATCATCCATCAAG

                 
       5711 CCAAA
         65 CCAAA

                                                   *          
       5716 TTAACCACAATTAACAAGCCACCTAAGGCTTGTTCTAGATATTTCTACCA
          1 TTAACCACAA-TAACAAGCCACCTAAGGCTTGTTCTAGACATTTCTACCA

       5766 ATTGAAAAAT


Statistics
Matches: 109,  Mismatches: 9, Indels: 4
        0.89            0.07        0.03

Matches are distributed among these distances:
  69    4  0.04
  70  105  0.96

ACGTcount: A:0.35, C:0.27, G:0.09, T:0.28


Consensus pattern (69 bp):   
TTAACCACAATAACAAGCCACCTAAGGCTTGTTCTAGACATTTCTACCATTATCATCCATCAAGC
CAAA

Found at i:8212 original size:20 final size:20

Alignment explanation


    Indices: 8178--8216  Score: 53
    Period size: 20  Copynumber: 1.9  Consensus size: 20

       8168 AATTTTATAA

                      *          
       8178 AATATAAATATTTTAATTTTG
          1 AATATAAATAATTT-ATTTTG

                               
       8199 AATAT-AATAATTTATTTT
          1 AATATAAATAATTTATTTT

       8217 ACTTTTATAT


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

Matches are distributed among these distances:
  19    5  0.29
  20    7  0.41
  21    5  0.29

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


Consensus pattern (20 bp):   
AATATAAATAATTTATTTTG
Done.