Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008650.1 Kokia drynarioides strain JFW-HI SEQ_123331, 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: 2100
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37


Found at i:1429 original size:28 final size:23

Alignment explanation


    Indices: 1372--1419  Score: 87
    Period size: 23  Copynumber: 2.1  Consensus size: 23

       1362 TTTTGTTTAT

                                   
       1372 GTAGTTAAATAATATTGTACTTC
          1 GTAGTTAAATAATATTGTACTTC

                   *               
       1395 GTAGTTAGATAATATTGTACTTC
          1 GTAGTTAAATAATATTGTACTTC

              
       1418 GT
          1 GT

       1420 CTATTAGTTA


Statistics
Matches: 24,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  23   24  1.00

ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44


Consensus pattern (23 bp):   
GTAGTTAAATAATATTGTACTTC

Found at i:1964 original size:19 final size:19

Alignment explanation


    Indices: 1932--1995  Score: 58
    Period size: 19  Copynumber: 3.3  Consensus size: 19

       1922 ATAAAAATAT

                               
       1932 TAAAAATTAGAAAAAATTA
          1 TAAAAATTAGAAAAAATTA

                           **   
       1951 TAAAAATT-GTAAAATTTTA
          1 TAAAAATTAG-AAAAAATTA

                 *     *         
       1970 TAAAAGTCATAAAAAAAATTA
          1 TAAAAAT--TAGAAAAAATTA

                 
       1991 TAAAA
          1 TAAAA

       1996 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:1995 original size:9 final size:9

Alignment explanation


    Indices: 1887--1984  Score: 51
    Period size: 9  Copynumber: 10.8  Consensus size: 9

       1877 AAAAAAATCA

                  *  
       1887 ATAAAAGTT
          1 ATAAAAATT

                     
       1896 AT-AAAATT
          1 ATAAAAATT

              *   *   
       1904 ATTAAATTGT
          1 ATAAAAAT-T

                      
       1914 AATAAAAA--
          1 -ATAAAAATT

                     
       1922 ATAAAAA-T
          1 ATAAAAATT

                      
       1930 ATTAAAAATT
          1 A-TAAAAATT

              *       
       1940 AGAAAAAATT
          1 A-TAAAAATT

                     
       1950 ATAAAAATT
          1 ATAAAAATT

            *      *  
       1959 GTAAAATTTT
          1 ATAAAA-ATT

                  * *
       1969 ATAAAAGTC
          1 ATAAAAATT

                   
       1978 ATAAAAA
          1 ATAAAAA

       1985 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.