Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01008903.1 Kokia drynarioides strain JFW-HI SEQ_123591, 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: 3191
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35


Found at i:603 original size:16 final size:17

Alignment explanation


    Indices: 583--671  Score: 60
    Period size: 16  Copynumber: 5.1  Consensus size: 17

        573 CTGATATATG

                             
        583 TTTCTAGAAATATGATA
          1 TTTCTAGAAATATGATA

                    *         
        600 -TTCT-GATATGAT-ATA
          1 TTTCTAGAAAT-ATGATA

                           * 
        615 TTTCTAGAAATATGACA
          1 TTTCTAGAAATATGATA

                 *               *
        632 TTTTGATATGATATATAT-ATG
          1 -TTT-CTA-GA-A-ATATGATA

                             
        653 TTTCTAGAAATATGATA
          1 TTTCTAGAAATATGATA

              
        670 TT
          1 TT

        672 CTAATATGAT


Statistics
Matches: 54,  Mismatches: 8, Indels: 20
        0.66            0.10        0.24

Matches are distributed among these distances:
  15    7  0.13
  16   16  0.30
  17   11  0.20
  18    5  0.09
  19    4  0.07
  20    5  0.09
  21    2  0.04
  22    4  0.07

ACGTcount: A:0.37, C:0.06, G:0.12, T:0.45


Consensus pattern (17 bp):   
TTTCTAGAAATATGATA

Found at i:624 original size:32 final size:32

Alignment explanation


    Indices: 578--683  Score: 122
    Period size: 32  Copynumber: 3.1  Consensus size: 32

        568 TTAACCTGAT

                *                           
        578 ATATGTTTCTAGAAATATGATATTCTGATATG
          1 ATATATTTCTAGAAATATGATATTCTGATATG

                                *   *       
        610 ATATATTTCTAGAAATATGACATTTTGATATG
          1 ATATATTTCTAGAAATATGATATTCTGATATG

                                            *     
        642 ATATATATATGTTTCTAGAAATATGATATTCTAATATG
          1 ----ATATA--TTTCTAGAAATATGATATTCTGATATG

                
        680 ATAT
          1 ATAT

        684 TTGAATATGT


Statistics
Matches: 62,  Mismatches: 6, Indels: 10
        0.79            0.08        0.13

Matches are distributed among these distances:
  32   29  0.47
  34    4  0.06
  36    5  0.08
  38   24  0.39

ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44


Consensus pattern (32 bp):   
ATATATTTCTAGAAATATGATATTCTGATATG

Found at i:658 original size:38 final size:39

Alignment explanation


    Indices: 605--691  Score: 115
    Period size: 38  Copynumber: 2.3  Consensus size: 39

        595 TGATATTCTG

                                         * *       
        605 ATATGATATATTTCTAGAAATATGACATTTTGATATGAT
          1 ATATGATATATTTCTAGAAATATGACATTCTAATATGAT

                     *               *             
        644 ATAT-ATATGTTTCTAGAAATATGATATTCTAATATGAT
          1 ATATGATATATTTCTAGAAATATGACATTCTAATATGAT

              *        
        682 ATTTGA-ATAT
          1 ATATGATATAT

        692 GTGTACATTA


Statistics
Matches: 41,  Mismatches: 6, Indels: 3
        0.82            0.12        0.06

Matches are distributed among these distances:
  38   36  0.88
  39    5  0.12

ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45


Consensus pattern (39 bp):   
ATATGATATATTTCTAGAAATATGACATTCTAATATGAT
Done.