Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01007257.1 Kokia drynarioides strain JFW-HI SEQ_121873, 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: 22479
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35


Found at i:3574 original size:16 final size:16

Alignment explanation


    Indices: 3548--3601  Score: 65
    Period size: 16  Copynumber: 3.4  Consensus size: 16

       3538 CAAACATAAC

                             
       3548 TATTCTCAAACAAAAAT
          1 TATTCT-AAACAAAAAT

             *          *  *
       3565 TGTTCTAAACAACAAC
          1 TATTCTAAACAAAAAT

                            
       3581 TATTCTAAA-AAAAAT
          1 TATTCTAAACAAAAAT

                  
       3596 TATTCT
          1 TATTCT

       3602 TCCAGGAGAG


Statistics
Matches: 31,  Mismatches: 6, Indels: 2
        0.79            0.15        0.05

Matches are distributed among these distances:
  15   10  0.32
  16   16  0.52
  17    5  0.16

ACGTcount: A:0.48, C:0.17, G:0.02, T:0.33


Consensus pattern (16 bp):   
TATTCTAAACAAAAAT

Found at i:4523 original size:2 final size:2

Alignment explanation


    Indices: 4516--4557  Score: 75
    Period size: 2  Copynumber: 21.0  Consensus size: 2

       4506 TTGTTTTATA

                                                                *         
       4516 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CG CT CT CT
          1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT

       4558 TCTATTACAT


Statistics
Matches: 38,  Mismatches: 2, Indels: 0
        0.95            0.05        0.00

Matches are distributed among these distances:
   2   38  1.00

ACGTcount: A:0.00, C:0.50, G:0.02, T:0.48


Consensus pattern (2 bp):   
CT

Found at i:6958 original size:27 final size:27

Alignment explanation


    Indices: 6918--6972  Score: 67
    Period size: 28  Copynumber: 2.0  Consensus size: 27

       6908 TATTAAAAGG

                                       
       6918 TTTAAAAAACATA-TAAATAAATTTAT
          1 TTTAAAAAACATATTAAATAAATTTAT

                      *       *  *      
       6944 TTTAAAAATAGATATTAATTATATTTAT
          1 TTTAAAAA-ACATATTAAATAAATTTAT

             
       6972 T
          1 T

       6973 AAACATAAAA


Statistics
Matches: 24,  Mismatches: 3, Indels: 2
        0.83            0.10        0.07

Matches are distributed among these distances:
  26    8  0.33
  27    4  0.17
  28   12  0.50

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


Consensus pattern (27 bp):   
TTTAAAAAACATATTAAATAAATTTAT

Found at i:18555 original size:22 final size:20

Alignment explanation


    Indices: 18518--18565  Score: 62
    Period size: 22  Copynumber: 2.4  Consensus size: 20

      18508 TATTTGAAAA

                                
      18518 TTCAATTTCATCGATCTAAT
          1 TTCAATTTCATCGATCTAAT

                     *            
      18538 TTCAGATTTTATCTGATCTAAT
          1 TTCA-ATTTCATC-GATCTAAT

                   
      18560 TT-AATT
          1 TTCAATT

      18566 ATAAAAATCA


Statistics
Matches: 25,  Mismatches: 1, Indels: 4
        0.83            0.03        0.13

Matches are distributed among these distances:
  20    7  0.28
  21    8  0.32
  22   10  0.40

ACGTcount: A:0.29, C:0.15, G:0.06, T:0.50


Consensus pattern (20 bp):   
TTCAATTTCATCGATCTAAT

Found at i:22462 original size:2 final size:2

Alignment explanation


    Indices: 22455--22479  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

      22445 TTTCTAGAGC

                                                 
      22455 TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA T


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Done.