Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005548.1 Kokia drynarioides strain JFW-HI SEQ_119650, 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: 16269
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35


Found at i:1502 original size:15 final size:14

Alignment explanation


    Indices: 1472--1506  Score: 61
    Period size: 14  Copynumber: 2.5  Consensus size: 14

       1462 TGTTTGACTG

                          
       1472 AAAATGATTTTTGA
          1 AAAATGATTTTTGA

                         *
       1486 AAAATGATTTTTGG
          1 AAAATGATTTTTGA

                   
       1500 AAAATGA
          1 AAAATGA

       1507 CTTACTTTTT


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

Matches are distributed among these distances:
  14   20  1.00

ACGTcount: A:0.46, C:0.00, G:0.17, T:0.37


Consensus pattern (14 bp):   
AAAATGATTTTTGA

Found at i:7221 original size:36 final size:36

Alignment explanation


    Indices: 7181--7254  Score: 112
    Period size: 36  Copynumber: 2.1  Consensus size: 36

       7171 TGATGACTGT

                    **                          
       7181 TGTGAAAGTGAATATGTGGGTATGTTATTCATGCCA
          1 TGTGAAAGAAAATATGTGGGTATGTTATTCATGCCA

                 *                           *  
       7217 TGTGACAGAAAATATGTGGGTATGTTATTCATGTCA
          1 TGTGAAAGAAAATATGTGGGTATGTTATTCATGCCA

              
       7253 TG
          1 TG

       7255 AGACTGATTA


Statistics
Matches: 34,  Mismatches: 4, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  36   34  1.00

ACGTcount: A:0.28, C:0.08, G:0.27, T:0.36


Consensus pattern (36 bp):   
TGTGAAAGAAAATATGTGGGTATGTTATTCATGCCA

Found at i:9690 original size:15 final size:15

Alignment explanation


    Indices: 9669--9707  Score: 53
    Period size: 15  Copynumber: 2.6  Consensus size: 15

       9659 AAATAAATGT

                       *   
       9669 AATATAAAAAATTAA
          1 AATATAAAAAAATAA

                            
       9684 CAA-ATAAAAAAATAA
          1 -AATATAAAAAAATAA

                     
       9699 AATATAAAA
          1 AATATAAAA

       9708 TTATTAAAAT


Statistics
Matches: 21,  Mismatches: 1, Indels: 3
        0.84            0.04        0.12

Matches are distributed among these distances:
  14    2  0.10
  15   17  0.81
  16    2  0.10

ACGTcount: A:0.77, C:0.03, G:0.00, T:0.21


Consensus pattern (15 bp):   
AATATAAAAAAATAA

Found at i:12024 original size:15 final size:15

Alignment explanation


    Indices: 12004--12039  Score: 56
    Period size: 15  Copynumber: 2.4  Consensus size: 15

      11994 ATTTTAATAA

                            
      12004 TTTTATCTT-TTAATT
          1 TTTTAT-TTGTTAATT

                           
      12019 TTTTATTTGTTAATT
          1 TTTTATTTGTTAATT

                  
      12034 TTTTAT
          1 TTTTAT

      12040 ATTACATTTA


Statistics
Matches: 20,  Mismatches: 0, Indels: 2
        0.91            0.00        0.09

Matches are distributed among these distances:
  14    2  0.10
  15   18  0.90

ACGTcount: A:0.19, C:0.03, G:0.03, T:0.75


Consensus pattern (15 bp):   
TTTTATTTGTTAATT
Done.