Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006605.1 Kokia drynarioides strain JFW-HI SEQ_121194, 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: 6175
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34


Found at i:506 original size:22 final size:22

Alignment explanation


    Indices: 471--512  Score: 57
    Period size: 22  Copynumber: 1.9  Consensus size: 22

        461 TTTATTTTTA

                  *  *     *      
        471 TTTTTATTTTTAATACTAATAT
          1 TTTTTACTTGTAATAATAATAT

                                
        493 TTTTTACTTGTAATAATAAT
          1 TTTTTACTTGTAATAATAAT

        513 TTATTAATGA


Statistics
Matches: 17,  Mismatches: 3, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  22   17  1.00

ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60


Consensus pattern (22 bp):   
TTTTTACTTGTAATAATAATAT

Found at i:557 original size:13 final size:14

Alignment explanation


    Indices: 530--573  Score: 72
    Period size: 14  Copynumber: 3.2  Consensus size: 14

        520 TGAAAATTGA

                    *     
        530 AAAACAAAACAAAT
          1 AAAACAAAGCAAAT

                          
        544 AAAACAAAGC-AAT
          1 AAAACAAAGCAAAT

                          
        557 AAAACAAAGCAAAT
          1 AAAACAAAGCAAAT

               
        571 AAA
          1 AAA

        574 TTACAACTAA


Statistics
Matches: 28,  Mismatches: 1, Indels: 2
        0.90            0.03        0.06

Matches are distributed among these distances:
  13   13  0.46
  14   15  0.54

ACGTcount: A:0.75, C:0.14, G:0.05, T:0.07


Consensus pattern (14 bp):   
AAAACAAAGCAAAT

Found at i:992 original size:41 final size:41

Alignment explanation


    Indices: 929--1008  Score: 117
    Period size: 41  Copynumber: 2.0  Consensus size: 41

        919 TCTTATTGTA

                                                      
        929 TTTTCAATTTGTTTGTTATTTTACA-AATTATTTTAATATCG
          1 TTTTCAATTTGTTTGTTATTTTA-ATAATTATTTTAATATCG

                *            *           *         
        970 TTTTTAATTTGTTTGTTGTTTTAATAATTGTTTTAATAT
          1 TTTTCAATTTGTTTGTTATTTTAATAATTATTTTAATAT

       1009 TTTTAACTGT


Statistics
Matches: 35,  Mismatches: 3, Indels: 2
        0.88            0.08        0.05

Matches are distributed among these distances:
  40    1  0.03
  41   34  0.97

ACGTcount: A:0.25, C:0.04, G:0.09, T:0.62


Consensus pattern (41 bp):   
TTTTCAATTTGTTTGTTATTTTAATAATTATTTTAATATCG

Found at i:5177 original size:16 final size:16

Alignment explanation


    Indices: 5146--5177  Score: 55
    Period size: 16  Copynumber: 2.0  Consensus size: 16

       5136 GATTATAGTG

                    *       
       5146 TAAATTTACAAAAAAA
          1 TAAATTTAAAAAAAAA

                            
       5162 TAAATTTAAAAAAAAA
          1 TAAATTTAAAAAAAAA

       5178 CCTTTAGAGG


Statistics
Matches: 15,  Mismatches: 1, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  16   15  1.00

ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25


Consensus pattern (16 bp):   
TAAATTTAAAAAAAAA
Done.