Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006653.1 Kokia drynarioides strain JFW-HI SEQ_121244, 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: 9801
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32


Found at i:3381 original size:17 final size:16

Alignment explanation


    Indices: 3361--3414  Score: 65
    Period size: 17  Copynumber: 3.3  Consensus size: 16

       3351 TCCTTTGCTT

                             
       3361 TTTTTATATTTTATTTA
          1 TTTTTAT-TTTTATTTA

                **           
       3378 TTTTGGTGTTTTATTTA
          1 TTTTTAT-TTTTATTTA

                            
       3395 -TTTTATTTTTATTTA
          1 TTTTTATTTTTATTTA

                 
       3410 TTTTT
          1 TTTTT

       3415 CGTTATTCAC


Statistics
Matches: 31,  Mismatches: 5, Indels: 3
        0.79            0.13        0.08

Matches are distributed among these distances:
  15    9  0.29
  16    8  0.26
  17   14  0.45

ACGTcount: A:0.17, C:0.00, G:0.06, T:0.78


Consensus pattern (16 bp):   
TTTTTATTTTTATTTA

Found at i:5012 original size:18 final size:18

Alignment explanation


    Indices: 4985--5021  Score: 56
    Period size: 18  Copynumber: 2.1  Consensus size: 18

       4975 TGGTTAACAA

                 *            
       4985 TCAACGAGTCGGTCAAAG
          1 TCAACAAGTCGGTCAAAG

                         *    
       5003 TCAACAAGTCGGTTAAAG
          1 TCAACAAGTCGGTCAAAG

             
       5021 T
          1 T

       5022 TAACGGGTTA


Statistics
Matches: 17,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  18   17  1.00

ACGTcount: A:0.35, C:0.19, G:0.24, T:0.22


Consensus pattern (18 bp):   
TCAACAAGTCGGTCAAAG

Found at i:7552 original size:18 final size:18

Alignment explanation


    Indices: 7508--7562  Score: 67
    Period size: 18  Copynumber: 3.1  Consensus size: 18

       7498 ACTACAATGC

                    * *       
       7508 AAAATGCACTAACAAAT-
          1 AAAATGCAATGACAAATA

                 *            
       7525 AAAATTCAATGACAAATA
          1 AAAATGCAATGACAAATA

                           *  
       7543 AAAATGCAATGACAACTA
          1 AAAATGCAATGACAAATA

              
       7561 AA
          1 AA

       7563 TAGAATGCAT


Statistics
Matches: 32,  Mismatches: 5, Indels: 1
        0.84            0.13        0.03

Matches are distributed among these distances:
  17   14  0.44
  18   18  0.56

ACGTcount: A:0.60, C:0.15, G:0.07, T:0.18


Consensus pattern (18 bp):   
AAAATGCAATGACAAATA
Done.