Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005478.1 Kokia drynarioides strain JFW-HI SEQ_119529, 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: 13026
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34


Found at i:502 original size:15 final size:15

Alignment explanation


    Indices: 484--540  Score: 69
    Period size: 15  Copynumber: 3.8  Consensus size: 15

        474 TTTTGGGTAG

                           
        484 TTTGTAATTGGATCA
          1 TTTGTAATTGGATCA

                  *    *   
        499 TTTGTATTTGGGTCA
          1 TTTGTAATTGGATCA

             *         **  
        514 TCTGTAATTGGGCCA
          1 TTTGTAATTGGATCA

                        
        529 TTTGTAATTGGA
          1 TTTGTAATTGGA

        541 CTTTGTTTTG


Statistics
Matches: 35,  Mismatches: 7, Indels: 0
        0.83            0.17        0.00

Matches are distributed among these distances:
  15   35  1.00

ACGTcount: A:0.21, C:0.09, G:0.25, T:0.46


Consensus pattern (15 bp):   
TTTGTAATTGGATCA

Found at i:564 original size:13 final size:14

Alignment explanation


    Indices: 529--569  Score: 54
    Period size: 13  Copynumber: 3.2  Consensus size: 14

        519 AATTGGGCCA

                          
        529 TTTG-TAATTGGAC
          1 TTTGTTAATTGGAC

                          
        542 TTTGTT--TTGGAC
          1 TTTGTTAATTGGAC

                          
        554 TTT-TTAATTGGAC
          1 TTTGTTAATTGGAC

               
        567 TTT
          1 TTT

        570 CTAAATTTAA


Statistics
Matches: 25,  Mismatches: 0, Indels: 6
        0.81            0.00        0.19

Matches are distributed among these distances:
  11    2  0.08
  12    9  0.36
  13   13  0.52
  14    1  0.04

ACGTcount: A:0.17, C:0.07, G:0.20, T:0.56


Consensus pattern (14 bp):   
TTTGTTAATTGGAC

Found at i:593 original size:17 final size:16

Alignment explanation


    Indices: 571--631  Score: 68
    Period size: 16  Copynumber: 3.7  Consensus size: 16

        561 TTGGACTTTC

                             
        571 TAAATTTAATTTTATAA
          1 TAAATTTAATTTTA-AA

                         *   
        588 TAAATTTAAATTTCAAA
          1 TAAATTT-AATTTTAAA

                *    *      
        605 TAAACTTAAATTTAAA
          1 TAAATTTAATTTTAAA

                  *    
        621 TAAATTCAATT
          1 TAAATTTAATT

        632 AAAAAATAAC


Statistics
Matches: 36,  Mismatches: 7, Indels: 3
        0.78            0.15        0.07

Matches are distributed among these distances:
  16   15  0.42
  17   15  0.42
  18    6  0.17

ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44


Consensus pattern (16 bp):   
TAAATTTAATTTTAAA

Found at i:6435 original size:19 final size:19

Alignment explanation


    Indices: 6411--6451  Score: 73
    Period size: 19  Copynumber: 2.2  Consensus size: 19

       6401 GCACTAAGAT

                               
       6411 AAATTGGAATTAAGTTAAA
          1 AAATTGGAATTAAGTTAAA

                    *          
       6430 AAATTGGATTTAAGTTAAA
          1 AAATTGGAATTAAGTTAAA

               
       6449 AAA
          1 AAA

       6452 GAGAAACAAT


Statistics
Matches: 21,  Mismatches: 1, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
  19   21  1.00

ACGTcount: A:0.54, C:0.00, G:0.15, T:0.32


Consensus pattern (19 bp):   
AAATTGGAATTAAGTTAAA
Done.