Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000705.1 Kokia drynarioides strain JFW-HI SEQ_111708, 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: 5982
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29


Found at i:1612 original size:5 final size:5

Alignment explanation


    Indices: 1602--1632  Score: 55
    Period size: 5  Copynumber: 6.4  Consensus size: 5

       1592 TATACGGAGT

                                                  
       1602 AATAA AATAA AATAA AAT-A AATAA AATAA AA
          1 AATAA AATAA AATAA AATAA AATAA AATAA AA

       1633 ATAGTAGCAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 2
        0.93            0.00        0.07

Matches are distributed among these distances:
   4    4  0.16
   5   21  0.84

ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19


Consensus pattern (5 bp):   
AATAA

Found at i:1625 original size:9 final size:9

Alignment explanation


    Indices: 1602--1631  Score: 51
    Period size: 9  Copynumber: 3.2  Consensus size: 9

       1592 TATACGGAGT

                      
       1602 AATAAAATAA
          1 AATAAAAT-A

                     
       1612 AATAAAATA
          1 AATAAAATA

                     
       1621 AATAAAATA
          1 AATAAAATA

              
       1630 AA
          1 AA

       1632 AATAGTAGCA


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

Matches are distributed among these distances:
   9   12  0.60
  10    8  0.40

ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20


Consensus pattern (9 bp):   
AATAAAATA

Found at i:1625 original size:14 final size:14

Alignment explanation


    Indices: 1606--1632  Score: 54
    Period size: 14  Copynumber: 1.9  Consensus size: 14

       1596 CGGAGTAATA

                          
       1606 AAATAAAATAAAAT
          1 AAATAAAATAAAAT

                         
       1620 AAATAAAATAAAA
          1 AAATAAAATAAAA

       1633 ATAGTAGCAA


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   13  1.00

ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19


Consensus pattern (14 bp):   
AAATAAAATAAAAT

Found at i:5926 original size:35 final size:34

Alignment explanation


    Indices: 5876--5943  Score: 102
    Period size: 35  Copynumber: 2.0  Consensus size: 34

       5866 AAAAATATTC

                                    *          
       5876 ATTTACTAAAATAATA-TAAAAAGTTATTTATTTT
          1 ATTTACTAAAATAATATTAAAAA-ATATTTATTTT

                                              
       5910 ATTTGACTAAAATAATATTAAAAAATATTTATTT
          1 ATTT-ACTAAAATAATATTAAAAAATATTTATTT

       5944 AATAAAAAAT


Statistics
Matches: 31,  Mismatches: 1, Indels: 3
        0.89            0.03        0.09

Matches are distributed among these distances:
  34    4  0.13
  35   21  0.68
  36    6  0.19

ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46


Consensus pattern (34 bp):   
ATTTACTAAAATAATATTAAAAAATATTTATTTT
Done.