Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002706.1 Kokia drynarioides strain JFW-HI SEQ_114992, 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: 3015
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37


Found at i:1504 original size:21 final size:21

Alignment explanation


    Indices: 1451--1512  Score: 60
    Period size: 21  Copynumber: 3.0  Consensus size: 21

       1441 TTGTTTAGAT

                                  
       1451 AATT-ATGT-TTATTTTCTTTA
          1 AATTAATGTATTATTTT-TTTA

                                  
       1471 AATTAA-G-AGTTATTTTTTTA
          1 AATTAATGTA-TTATTTTTTTA

             *                    
       1491 ATTTAATGTATTATTTATTTTA
          1 AATTAATGTATTATTT-TTTTA

       1513 TCATTTTTCA


Statistics
Matches: 35,  Mismatches: 1, Indels: 10
        0.76            0.02        0.22

Matches are distributed among these distances:
  20   14  0.40
  21   15  0.43
  22    6  0.17

ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61


Consensus pattern (21 bp):   
AATTAATGTATTATTTTTTTA

Found at i:1899 original size:8 final size:8

Alignment explanation


    Indices: 1886--1917  Score: 57
    Period size: 8  Copynumber: 4.1  Consensus size: 8

       1876 TTATTAATTC

                    
       1886 TAAAAAAA
          1 TAAAAAAA

                    
       1894 T-AAAAAA
          1 TAAAAAAA

                    
       1901 TAAAAAAA
          1 TAAAAAAA

                    
       1909 TAAAAAAA
          1 TAAAAAAA

             
       1917 T
          1 T

       1918 TTTATTTTGT


Statistics
Matches: 23,  Mismatches: 0, Indels: 2
        0.92            0.00        0.08

Matches are distributed among these distances:
   7    7  0.30
   8   16  0.70

ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16


Consensus pattern (8 bp):   
TAAAAAAA

Found at i:1906 original size:15 final size:15

Alignment explanation


    Indices: 1886--1915  Score: 60
    Period size: 15  Copynumber: 2.0  Consensus size: 15

       1876 TTATTAATTC

                           
       1886 TAAAAAAATAAAAAA
          1 TAAAAAAATAAAAAA

                           
       1901 TAAAAAAATAAAAAA
          1 TAAAAAAATAAAAAA

       1916 ATTTTATTTT


Statistics
Matches: 15,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   15  1.00

ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13


Consensus pattern (15 bp):   
TAAAAAAATAAAAAA

Found at i:1995 original size:17 final size:17

Alignment explanation


    Indices: 1973--2009  Score: 56
    Period size: 17  Copynumber: 2.2  Consensus size: 17

       1963 CTCCTTTGAC

                          *  
       1973 CTTTAACCTTTCATCTT
          1 CTTTAACCTTTCATATT

                   *         
       1990 CTTTAACGTTTCATATT
          1 CTTTAACCTTTCATATT

               
       2007 CTT
          1 CTT

       2010 GTAATTACTT


Statistics
Matches: 18,  Mismatches: 2, Indels: 0
        0.90            0.10        0.00

Matches are distributed among these distances:
  17   18  1.00

ACGTcount: A:0.19, C:0.24, G:0.03, T:0.54


Consensus pattern (17 bp):   
CTTTAACCTTTCATATT
Done.