Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008417.1 Kokia drynarioides strain JFW-HI SEQ_123088, 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: 2522
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34


Found at i:1850 original size:17 final size:17

Alignment explanation


    Indices: 1830--1870  Score: 57
    Period size: 17  Copynumber: 2.4  Consensus size: 17

       1820 ACTACAATGC

                              
       1830 AAATGTGAG-AACAATTA
          1 AAATGT-AGTAACAATTA

                     *       
       1847 AAATGTAGTGACAATTA
          1 AAATGTAGTAACAATTA

                   
       1864 AAATGTA
          1 AAATGTA

       1871 ATGACAACTA


Statistics
Matches: 22,  Mismatches: 1, Indels: 2
        0.88            0.04        0.08

Matches are distributed among these distances:
  16    2  0.09
  17   20  0.91

ACGTcount: A:0.51, C:0.05, G:0.17, T:0.27


Consensus pattern (17 bp):   
AAATGTAGTAACAATTA

Found at i:1875 original size:17 final size:17

Alignment explanation


    Indices: 1840--1877  Score: 67
    Period size: 17  Copynumber: 2.2  Consensus size: 17

       1830 AAATGTGAGA

                          *  
       1840 ACAATTAAAATGTAGTG
          1 ACAATTAAAATGTAATG

                             
       1857 ACAATTAAAATGTAATG
          1 ACAATTAAAATGTAATG

                
       1874 ACAA
          1 ACAA

       1878 CTAGAGAAAA


Statistics
Matches: 20,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  17   20  1.00

ACGTcount: A:0.53, C:0.08, G:0.13, T:0.26


Consensus pattern (17 bp):   
ACAATTAAAATGTAATG

Found at i:2323 original size:15 final size:15

Alignment explanation


    Indices: 2285--2327  Score: 52
    Period size: 15  Copynumber: 2.9  Consensus size: 15

       2275 GGGAAACATC

                          * 
       2285 TTCTTT-TTCTTCCTT
          1 TTCTTTCTTCTT-CAT

              *            
       2300 TTTTTTCTTCTTCAT
          1 TTCTTTCTTCTTCAT

                         
       2315 TTCTTTCTTCTTC
          1 TTCTTTCTTCTTC

       2328 TTATGCTTTA


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  15   19  0.79
  16    5  0.21

ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72


Consensus pattern (15 bp):   
TTCTTTCTTCTTCAT
Done.