Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004989.1 Kokia drynarioides strain JFW-HI SEQ_118740, 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: 5952
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35


Found at i:954 original size:7 final size:6

Alignment explanation


    Indices: 919--954  Score: 54
    Period size: 6  Copynumber: 5.8  Consensus size: 6

        909 ACAAAACACA

                     *                               
        919 AAAGAC AAGGAC AAAGAC AAAGAC AAAGACC AAAGA
          1 AAAGAC AAAGAC AAAGAC AAAGAC AAAGA-C AAAGA

        955 GATGAGATGA


Statistics
Matches: 27,  Mismatches: 2, Indels: 1
        0.90            0.07        0.03

Matches are distributed among these distances:
   6   21  0.78
   7    6  0.22

ACGTcount: A:0.64, C:0.17, G:0.19, T:0.00


Consensus pattern (6 bp):   
AAAGAC

Found at i:1907 original size:4 final size:4

Alignment explanation


    Indices: 1898--1927  Score: 60
    Period size: 4  Copynumber: 7.5  Consensus size: 4

       1888 AAATTTACCC

                                                 
       1898 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
          1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT

       1928 TAAAACTGAA


Statistics
Matches: 26,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   4   26  1.00

ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77


Consensus pattern (4 bp):   
TTAT

Found at i:5915 original size:18 final size:18

Alignment explanation


    Indices: 5878--5928  Score: 61
    Period size: 18  Copynumber: 2.9  Consensus size: 18

       5868 AAAAAAGAAA

                               
       5878 AAAAAGAAAAT-ATA-AGT
          1 AAAAAGAAAATAATATA-T

                * *           
       5895 AAAAGGGAAATAATATAT
          1 AAAAAGAAAATAATATAT

                            
       5913 AAAAAGAAAATAATAT
          1 AAAAAGAAAATAATAT

       5929 TTTTTTTTGT


Statistics
Matches: 28,  Mismatches: 4, Indels: 3
        0.80            0.11        0.09

Matches are distributed among these distances:
  17    9  0.32
  18   18  0.64
  19    1  0.04

ACGTcount: A:0.69, C:0.00, G:0.12, T:0.20


Consensus pattern (18 bp):   
AAAAAGAAAATAATATAT
Done.