Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009149.1 Kokia drynarioides strain JFW-HI SEQ_123853, 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: 21190
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34


Found at i:4747 original size:19 final size:19

Alignment explanation


    Indices: 4723--4765  Score: 77
    Period size: 19  Copynumber: 2.3  Consensus size: 19

       4713 GATACATATA

                       *       
       4723 TATATGGATTATAATAATC
          1 TATATGGATTACAATAATC

                               
       4742 TATATGGATTACAATAATC
          1 TATATGGATTACAATAATC

                 
       4761 TATAT
          1 TATAT

       4766 ATTAAATATT


Statistics
Matches: 23,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  19   23  1.00

ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42


Consensus pattern (19 bp):   
TATATGGATTACAATAATC

Found at i:5879 original size:24 final size:24

Alignment explanation


    Indices: 5851--5897  Score: 76
    Period size: 24  Copynumber: 2.0  Consensus size: 24

       5841 AATACTCAAT

                    *               
       5851 TAGTATCCGTGTAACAAAATGCCG
          1 TAGTATCCATGTAACAAAATGCCG

                          *        
       5875 TAGTATCCATGTAATAAAATGCC
          1 TAGTATCCATGTAACAAAATGCC

       5898 ATTGTAATTA


Statistics
Matches: 21,  Mismatches: 2, Indels: 0
        0.91            0.09        0.00

Matches are distributed among these distances:
  24   21  1.00

ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28


Consensus pattern (24 bp):   
TAGTATCCATGTAACAAAATGCCG

Found at i:8428 original size:16 final size:17

Alignment explanation


    Indices: 8407--8439  Score: 59
    Period size: 16  Copynumber: 2.0  Consensus size: 17

       8397 ACTTTAAAAA

                             
       8407 TAATTTTTA-ATTATTT
          1 TAATTTTTACATTATTT

                             
       8423 TAATTTTTACATTATTT
          1 TAATTTTTACATTATTT

       8440 CCCTCTCTTT


Statistics
Matches: 16,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  16    9  0.56
  17    7  0.44

ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67


Consensus pattern (17 bp):   
TAATTTTTACATTATTT

Found at i:8896 original size:19 final size:20

Alignment explanation


    Indices: 8859--8897  Score: 53
    Period size: 20  Copynumber: 2.0  Consensus size: 20

       8849 ATCTTCATAT

                       *        
       8859 TTTTATTTTTAGGAATTTAA
          1 TTTTATTTTTACGAATTTAA

                          *     
       8879 TTTTATTTTT-CGAGTTTAA
          1 TTTTATTTTTACGAATTTAA

       8898 AAATGTAGCT


Statistics
Matches: 17,  Mismatches: 2, Indels: 1
        0.85            0.10        0.05

Matches are distributed among these distances:
  19    7  0.41
  20   10  0.59

ACGTcount: A:0.26, C:0.03, G:0.10, T:0.62


Consensus pattern (20 bp):   
TTTTATTTTTACGAATTTAA

Found at i:9460 original size:30 final size:30

Alignment explanation


    Indices: 9424--9485  Score: 124
    Period size: 30  Copynumber: 2.1  Consensus size: 30

       9414 CTATTAAGAG

                                          
       9424 TTACATGAACATTTTAACCAAATTGAAGTA
          1 TTACATGAACATTTTAACCAAATTGAAGTA

                                          
       9454 TTACATGAACATTTTAACCAAATTGAAGTA
          1 TTACATGAACATTTTAACCAAATTGAAGTA

              
       9484 TT
          1 TT

       9486 TGAGTTGATC


Statistics
Matches: 32,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  30   32  1.00

ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35


Consensus pattern (30 bp):   
TTACATGAACATTTTAACCAAATTGAAGTA
Done.