Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004326.1 Kokia drynarioides strain JFW-HI SEQ_117650, 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: 7892
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.32

Warning! 48 characters in sequence are not A, C, G, or T


Found at i:73 original size:29 final size:30

Alignment explanation


    Indices: 23--84  Score: 72
    Period size: 30  Copynumber: 2.1  Consensus size: 30

         13 GCAATAATTC

                 *      * *        *      
         23 TTAAATATATTTTTTTGTAAATTTAATTAT
          1 TTAAAAATATTTATATGTAAATTCAATTAT

                                        * 
         53 TTAAAAATATTTATATG-AAATTCAATTTT
          1 TTAAAAATATTTATATGTAAATTCAATTAT

               
         82 TTA
          1 TTA

         85 TTGGTAATTT


Statistics
Matches: 27,  Mismatches: 5, Indels: 1
        0.82            0.15        0.03

Matches are distributed among these distances:
  29   13  0.48
  30   14  0.52

ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55


Consensus pattern (30 bp):   
TTAAAAATATTTATATGTAAATTCAATTAT

Found at i:6782 original size:119 final size:119

Alignment explanation


    Indices: 6570--6842  Score: 411
    Period size: 119  Copynumber: 2.3  Consensus size: 119

       6560 GATTTAAGTG

                    *        *  *                        *        **         
       6570 AAAACTCTTAAATAATTTGACGATTTAAATGAAAACTCTCAAATCTGAAATAATTTCAACTTCAA
          1 AAAACTCTCAAATAATTCGATGATTTAAATG-AAACTCTCAAATCCGAAATAATCCCAACTTCAA

               *        *                              *   *   *   
       6635 AAAGTTACAAAATGATTACTGAATTATTCAAAGTTTTCATTTAGTCAGTTATATA
         65 AAAATTACAAAAAGATTACTGAATTATTCAAAGTTTTCATTTAATCACTTAAATA

                               *                              *              
       6690 AAAACTCTCAAATAATTCGGTGATTTAAATGAAACTCTCAAATCCGAAATGATCCCAACTTCAAA
          1 AAAACTCTCAAATAATTCGATGATTTAAATGAAACTCTCAAATCCGAAATAATCCCAACTTCAAA

                                                                  
       6755 AAATTACAAAAAGATTACTGAATTATTCAAAGTTTTCATTTAATCACTTAAATA
         66 AAATTACAAAAAGATTACTGAATTATTCAAAGTTTTCATTTAATCACTTAAATA

                              *               
       6809 AAAACTCTCAAATAATTCAATGATTTAAATGAAA
          1 AAAACTCTCAAATAATTCGATGATTTAAATGAAA

       6843 ACTTTCGAAT


Statistics
Matches: 138,  Mismatches: 15, Indels: 1
        0.90            0.10        0.01

Matches are distributed among these distances:
 119  111  0.80
 120   27  0.20

ACGTcount: A:0.45, C:0.14, G:0.08, T:0.33


Consensus pattern (119 bp):   
AAAACTCTCAAATAATTCGATGATTTAAATGAAACTCTCAAATCCGAAATAATCCCAACTTCAAA
AAATTACAAAAAGATTACTGAATTATTCAAAGTTTTCATTTAATCACTTAAATA
Done.