Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008609.1 Kokia drynarioides strain JFW-HI SEQ_123287, 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: 5256
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40


Found at i:716 original size:26 final size:26

Alignment explanation


    Indices: 669--718  Score: 66
    Period size: 26  Copynumber: 1.9  Consensus size: 26

        659 ATAGACTCAC

                         *            
        669 TTTTCTATAATTAGTCCTTGCTTTGT
          1 TTTTCTATAATTACTCCTTGCTTTGT

                *                    
        695 TTTTTTATAATTACT-CTATGCTTT
          1 TTTTCTATAATTACTCCT-TGCTTT

        719 CACATAAACG


Statistics
Matches: 21,  Mismatches: 2, Indels: 2
        0.84            0.08        0.08

Matches are distributed among these distances:
  25    2  0.10
  26   19  0.90

ACGTcount: A:0.18, C:0.14, G:0.08, T:0.60


Consensus pattern (26 bp):   
TTTTCTATAATTACTCCTTGCTTTGT

Found at i:2068 original size:31 final size:30

Alignment explanation


    Indices: 2023--2090  Score: 73
    Period size: 31  Copynumber: 2.2  Consensus size: 30

       2013 AAAAATAATT

                 *   *       *             
       2023 TTTTTGAAATTTAAAGTGATCTAAAAACATA
          1 TTTTTAAAAATTAAA-TAATCTAAAAACATA

                               *      *   
       2054 TTTTTAAAAATTAAATAATTTAAAAATATA
          1 TTTTTAAAAATTAAATAATCTAAAAACATA

                   
       2084 TATTTTA
          1 T-TTTTA

       2091 TGAATCTGGA


Statistics
Matches: 31,  Mismatches: 5, Indels: 2
        0.82            0.13        0.05

Matches are distributed among these distances:
  30   13  0.42
  31   18  0.58

ACGTcount: A:0.49, C:0.03, G:0.04, T:0.44


Consensus pattern (30 bp):   
TTTTTAAAAATTAAATAATCTAAAAACATA

Found at i:2090 original size:15 final size:15

Alignment explanation


    Indices: 2044--2090  Score: 51
    Period size: 15  Copynumber: 3.1  Consensus size: 15

       2034 TAAAGTGATC

                  *        
       2044 TAAAAACATAT-TTT
          1 TAAAAATATATATTT

                     *   *  
       2058 TAAAAATTAAATAATT
          1 TAAAAA-TATATATTT

                           
       2074 TAAAAATATATATTT
          1 TAAAAATATATATTT

              
       2089 TA
          1 TA

       2091 TGAATCTGGA


Statistics
Matches: 26,  Mismatches: 5, Indels: 3
        0.76            0.15        0.09

Matches are distributed among these distances:
  14    6  0.23
  15   12  0.46
  16    8  0.31

ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43


Consensus pattern (15 bp):   
TAAAAATATATATTT
Done.