Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006637.1 Kokia drynarioides strain JFW-HI SEQ_121227, 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: 10709
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34


Found at i:3594 original size:9 final size:10

Alignment explanation


    Indices: 3552--3598  Score: 53
    Period size: 9  Copynumber: 4.8  Consensus size: 10

       3542 TAATGATTCA

                  *   
       3552 ATATAAATAT
          1 ATATAATTAT

                       
       3562 ATATAATTATT
          1 ATATAATTA-T

              *       
       3573 ATTTAA-TAT
          1 ATATAATTAT

                      
       3582 ATATAATTA-
          1 ATATAATTAT

                    
       3591 ATATAATT
          1 ATATAATT

       3599 GATTTTTATA


Statistics
Matches: 32,  Mismatches: 3, Indels: 5
        0.80            0.08        0.12

Matches are distributed among these distances:
   9   14  0.44
  10   12  0.38
  11    6  0.19

ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49


Consensus pattern (10 bp):   
ATATAATTAT

Found at i:3596 original size:29 final size:33

Alignment explanation


    Indices: 3551--3618  Score: 90
    Period size: 30  Copynumber: 2.2  Consensus size: 33

       3541 TTAATGATTC

                                             
       3551 AATATAAATATATATAATT-ATTATT-TAATAT
          1 AATATAAATATATATAATTGATTATTATAATAT

                   *               *         
       3582 -ATATAATTA-ATATAATTGATTTTTATAATAT
          1 AATATAAATATATATAATTGATTATTATAATAT

                  
       3613 AATATA
          1 AATATA

       3619 TTCAGCCCGG


Statistics
Matches: 32,  Mismatches: 2, Indels: 5
        0.82            0.05        0.13

Matches are distributed among these distances:
  29    8  0.25
  30   13  0.41
  31    6  0.19
  32    5  0.16

ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49


Consensus pattern (33 bp):   
AATATAAATATATATAATTGATTATTATAATAT

Found at i:5014 original size:17 final size:18

Alignment explanation


    Indices: 4980--5017  Score: 51
    Period size: 17  Copynumber: 2.2  Consensus size: 18

       4970 TATTGGGACG

                    *         
       4980 TAATTTTTTTAATATATA
          1 TAATTTTTGTAATATATA

                         *    
       4998 TAATTTTTGT-ATTTATA
          1 TAATTTTTGTAATATATA

               
       5015 TAA
          1 TAA

       5018 ATACATAATT


Statistics
Matches: 18,  Mismatches: 2, Indels: 1
        0.86            0.10        0.05

Matches are distributed among these distances:
  17    9  0.50
  18    9  0.50

ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61


Consensus pattern (18 bp):   
TAATTTTTGTAATATATA
Done.