Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000365.1 Kokia drynarioides strain JFW-HI SEQ_111152, 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: 1816
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37


Found at i:978 original size:17 final size:16

Alignment explanation


    Indices: 953--1028  Score: 57
    Period size: 17  Copynumber: 4.7  Consensus size: 16

        943 TAATTTTATA

                *           
        953 TTAAGTTTAAAATCAT
          1 TTAAATTTAAAATCAT

                        *     
        969 TTCAAATTT-AATTCAAT
          1 TT-AAATTTAAAATC-AT

                       *  *  
        986 TTAAATTTAAAGTAAAT
          1 TTAAATTTAAAAT-CAT

                           *
       1003 TTAAATTTAAAAT-AG
          1 TTAAATTTAAAATCAT

            *          
       1018 ATAAATTTAAA
          1 TTAAATTTAAA

       1029 TTTAAAAATA


Statistics
Matches: 49,  Mismatches: 7, Indels: 9
        0.75            0.11        0.14

Matches are distributed among these distances:
  15   11  0.22
  16   12  0.24
  17   26  0.53

ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42


Consensus pattern (16 bp):   
TTAAATTTAAAATCAT

Found at i:994 original size:6 final size:6

Alignment explanation


    Indices: 983--1034  Score: 52
    Period size: 6  Copynumber: 8.3  Consensus size: 6

        973 AATTTAATTC

                             *                       *                
        983 AATTTA AATTTA AA-GTA AATTTA AATTTAA AATAGATA AATTTA AATTTA
          1 AATTTA AATTTA AATTTA AATTTA AATTT-A AAT--TTA AATTTA AATTTA

              
       1033 AA
          1 AA

       1035 AATAATTTTA


Statistics
Matches: 38,  Mismatches: 4, Indels: 8
        0.76            0.08        0.16

Matches are distributed among these distances:
   5    4  0.11
   6   25  0.66
   7    4  0.11
   8    4  0.11
   9    1  0.03

ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40


Consensus pattern (6 bp):   
AATTTA

Found at i:1024 original size:21 final size:19

Alignment explanation


    Indices: 983--1046  Score: 80
    Period size: 21  Copynumber: 3.4  Consensus size: 19

        973 AATTTAATTC

                               
        983 AATTTAAATTT--AAAGTA
          1 AATTTAAATTTAAAAAGTA

                                 
       1000 AATTTAAATTTAAAATAGATA
          1 AATTTAAATTTAAAA-AG-TA

                               
       1021 AATTTAAATTTAAAAA-TA
          1 AATTTAAATTTAAAAAGTA

             *      
       1039 ATTTTAAA
          1 AATTTAAA

       1047 ACCAATTTAA


Statistics
Matches: 42,  Mismatches: 1, Indels: 7
        0.84            0.02        0.14

Matches are distributed among these distances:
  17   11  0.26
  18    9  0.21
  19    2  0.05
  20    3  0.07
  21   17  0.40

ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41


Consensus pattern (19 bp):   
AATTTAAATTTAAAAAGTA
Done.