Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01001448.1 Kokia drynarioides strain JFW-HI SEQ_112964, 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: 4201
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35


Found at i:233 original size:29 final size:30

Alignment explanation


    Indices: 167--246  Score: 90
    Period size: 29  Copynumber: 2.6  Consensus size: 30

        157 ATACCAAAAT

                        *  *               
        167 TATACATGAACTATGGTTTAATGTACAATTG
          1 TATACATGAACTTTGATTT-ATGTACAATTG

                                   *      
        198 TATACATGAACTTTGATTT-TGTGCAATTG
          1 TATACATGAACTTTGATTTATGTACAATTG

             *         *        
        227 TGTACATGAGATTTTGATTT
          1 TATACATGA-ACTTTGATTT

        247 GATTTATTTC


Statistics
Matches: 43,  Mismatches: 5, Indels: 3
        0.84            0.10        0.06

Matches are distributed among these distances:
  29   17  0.40
  30    9  0.21
  31   17  0.40

ACGTcount: A:0.30, C:0.09, G:0.17, T:0.44


Consensus pattern (30 bp):   
TATACATGAACTTTGATTTATGTACAATTG

Found at i:502 original size:29 final size:27

Alignment explanation


    Indices: 436--502  Score: 71
    Period size: 31  Copynumber: 2.3  Consensus size: 27

        426 GAGTTTCACG

                                *      
        436 TGTATAATTGCACCAAATTATAATTCA
          1 TGTATAATTGCACCAAATTAAAATTCA

                             *           * 
        463 TGTATACAATTGCACATTAAATTAAAATTTA
          1 TGTAT--AATTGCAC--CAAATTAAAATTCA

                     
        494 TGTATAATT
          1 TGTATAATT

        503 TTGAGATTTA


Statistics
Matches: 33,  Mismatches: 3, Indels: 6
        0.79            0.07        0.14

Matches are distributed among these distances:
  27    5  0.15
  29   12  0.36
  31   16  0.48

ACGTcount: A:0.42, C:0.10, G:0.07, T:0.40


Consensus pattern (27 bp):   
TGTATAATTGCACCAAATTAAAATTCA

Found at i:3030 original size:27 final size:28

Alignment explanation


    Indices: 2996--3049  Score: 83
    Period size: 28  Copynumber: 2.0  Consensus size: 28

       2986 TTCGTTAAGA

                        *    *          
       2996 ATTTAAAATT-TTTGTTTATGTTCGTTT
          1 ATTTAAAATTATGTGTTCATGTTCGTTT

                                       
       3023 ATTTAAAATTATGTGTTCATGTTCGTT
          1 ATTTAAAATTATGTGTTCATGTTCGTT

       3050 AGTTTAATAT


Statistics
Matches: 24,  Mismatches: 2, Indels: 1
        0.89            0.07        0.04

Matches are distributed among these distances:
  27   10  0.42
  28   14  0.58

ACGTcount: A:0.24, C:0.06, G:0.13, T:0.57


Consensus pattern (28 bp):   
ATTTAAAATTATGTGTTCATGTTCGTTT

Found at i:3055 original size:28 final size:27

Alignment explanation


    Indices: 2979--3056  Score: 77
    Period size: 28  Copynumber: 2.7  Consensus size: 27

       2969 TTCATGTTCG

                *                       * 
       2979 GTTCGTGTTCGTTAAGAATTTAAAATTTTT
          1 GTTCATGTTCGTT-AG--TTTAAAATTTGT

               *                         
       3009 GTTTATGTTCGTTTA-TTTAAAATTATGT
          1 GTTCATGTTCG-TTAGTTTAAAATT-TGT

                                
       3037 GTTCATGTTCGTTAGTTTAA
          1 GTTCATGTTCGTTAGTTTAA

       3057 TATTCACAAA


Statistics
Matches: 41,  Mismatches: 4, Indels: 8
        0.77            0.08        0.15

Matches are distributed among these distances:
  27   12  0.29
  28   17  0.41
  30   10  0.24
  31    2  0.05

ACGTcount: A:0.24, C:0.06, G:0.17, T:0.53


Consensus pattern (27 bp):   
GTTCATGTTCGTTAGTTTAAAATTTGT
Done.