Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003001.1 Kokia drynarioides strain JFW-HI SEQ_115496, 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: 1733
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37


Found at i:602 original size:17 final size:16

Alignment explanation


    Indices: 582--669  Score: 68
    Period size: 17  Copynumber: 5.2  Consensus size: 16

        572 ACTGGACATT

                             
        582 ATTTAAATGAATTTTAA
          1 ATTTAAAT-AATTTTAA

                     *  **   
        599 ATTTAAATTTATAATAA
          1 ATTTAAA-TAATTTTAA

                      *     
        616 ATTTAAATAAATTTAA
          1 ATTTAAATAATTTTAA

                       **    
        632 ATTTAGAATAAACTTAA
          1 ATTTA-AATAATTTTAA

            *          *     
        649 TTTTAAAATAAATTTAA
          1 ATTT-AAATAATTTTAA

                
        666 ATTT
          1 ATTT

        670 GTTGTGCCCG


Statistics
Matches: 57,  Mismatches: 11, Indels: 6
        0.77            0.15        0.08

Matches are distributed among these distances:
  16   10  0.18
  17   45  0.79
  18    2  0.04

ACGTcount: A:0.51, C:0.01, G:0.02, T:0.45


Consensus pattern (16 bp):   
ATTTAAATAATTTTAA

Found at i:605 original size:6 final size:6

Alignment explanation


    Indices: 594--669  Score: 58
    Period size: 6  Copynumber: 13.5  Consensus size: 6

        584 TTAAATGAAT

                                                                     
        594 TTTAAA TTTAAA TTTATAA --TAAA TTTAAA --TAAA TTTAAA TTTAGAA
          1 TTTAAA TTTAAA TTTA-AA TTTAAA TTTAAA TTTAAA TTTAAA TTTA-AA

                   *    *         *               
        640 --TAAA CTTAAT TTTAAA -ATAAA TTTAAA TTT
          1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT

        670 GTTGTGCCCG


Statistics
Matches: 56,  Mismatches: 5, Indels: 18
        0.71            0.06        0.23

Matches are distributed among these distances:
   4    8  0.14
   5    8  0.14
   6   36  0.64
   7    4  0.07

ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46


Consensus pattern (6 bp):   
TTTAAA

Found at i:626 original size:10 final size:10

Alignment explanation


    Indices: 582--633  Score: 59
    Period size: 11  Copynumber: 4.8  Consensus size: 10

        572 ACTGGACATT

                       
        582 ATTTAAATGAA
          1 ATTTAAAT-AA

            *           
        593 TTTTAAATTTAA
          1 ATTTAAA--TAA

                       
        605 ATTTATAATAA
          1 ATTTA-AATAA

                      
        616 ATTTAAATAA
          1 ATTTAAATAA

                    
        626 ATTTAAAT
          1 ATTTAAAT

        634 TTAGAATAAA


Statistics
Matches: 36,  Mismatches: 2, Indels: 7
        0.80            0.04        0.16

Matches are distributed among these distances:
  10   13  0.36
  11   14  0.39
  12    6  0.17
  13    3  0.08

ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46


Consensus pattern (10 bp):   
ATTTAAATAA

Found at i:626 original size:27 final size:27

Alignment explanation


    Indices: 596--648  Score: 88
    Period size: 27  Copynumber: 2.0  Consensus size: 27

        586 AAATGAATTT

                          *      *     
        596 TAAATTTAAATTTATAATAAATTTAAA
          1 TAAATTTAAATTTAGAATAAACTTAAA

                                      
        623 TAAATTTAAATTTAGAATAAACTTAA
          1 TAAATTTAAATTTAGAATAAACTTAA

        649 TTTTAAAATA


Statistics
Matches: 24,  Mismatches: 2, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  27   24  1.00

ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42


Consensus pattern (27 bp):   
TAAATTTAAATTTAGAATAAACTTAAA
Done.