Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006700.1 Kokia drynarioides strain JFW-HI SEQ_121295, 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: 5375
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34


Found at i:562 original size:19 final size:19

Alignment explanation


    Indices: 530--593  Score: 58
    Period size: 19  Copynumber: 3.3  Consensus size: 19

        520 ATAAAAATAT

                               
        530 TAAAAATTAGAAAAAATTA
          1 TAAAAATTAGAAAAAATTA

                           **   
        549 TAAAAATT-GTAAAATTTTA
          1 TAAAAATTAG-AAAAAATTA

                 *     *         
        568 TAAAAGTCATAAAAAAAATTA
          1 TAAAAAT--TAGAAAAAATTA

                 
        589 TAAAA
          1 TAAAA

        594 TGCATCTAAA


Statistics
Matches: 35,  Mismatches: 6, Indels: 6
        0.74            0.13        0.13

Matches are distributed among these distances:
  18    1  0.03
  19   21  0.60
  21   13  0.37

ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30


Consensus pattern (19 bp):   
TAAAAATTAGAAAAAATTA

Found at i:593 original size:9 final size:9

Alignment explanation


    Indices: 485--582  Score: 51
    Period size: 9  Copynumber: 10.8  Consensus size: 9

        475 AAAAAAATCA

                  *  
        485 ATAAAAGTT
          1 ATAAAAATT

                     
        494 AT-AAAATT
          1 ATAAAAATT

              *   *   
        502 ATTAAATTGT
          1 ATAAAAAT-T

                      
        512 AATAAAAA--
          1 -ATAAAAATT

                     
        520 ATAAAAA-T
          1 ATAAAAATT

                      
        528 ATTAAAAATT
          1 A-TAAAAATT

              *       
        538 AGAAAAAATT
          1 A-TAAAAATT

                     
        548 ATAAAAATT
          1 ATAAAAATT

            *      *  
        557 GTAAAATTTT
          1 ATAAAA-ATT

                  * *
        567 ATAAAAGTC
          1 ATAAAAATT

                   
        576 ATAAAAA
          1 ATAAAAA

        583 AAATTATAAA


Statistics
Matches: 69,  Mismatches: 13, Indels: 14
        0.72            0.14        0.15

Matches are distributed among these distances:
   7    7  0.10
   8    8  0.12
   9   31  0.45
  10   18  0.26
  11    5  0.07

ACGTcount: A:0.62, C:0.01, G:0.05, T:0.32


Consensus pattern (9 bp):   
ATAAAAATT
Done.