Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01006435.1 Kokia drynarioides strain JFW-HI SEQ_121017, 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: 14703
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35


Found at i:3473 original size:2 final size:2

Alignment explanation


    Indices: 3466--3492  Score: 54
    Period size: 2  Copynumber: 13.5  Consensus size: 2

       3456 CATTTCTATT

                                                    
       3466 TC TC TC TC TC TC TC TC TC TC TC TC TC T
          1 TC TC TC TC TC TC TC TC TC TC TC TC TC T

       3493 TTTATTTATT


Statistics
Matches: 25,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   25  1.00

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


Consensus pattern (2 bp):   
TC

Found at i:5612 original size:22 final size:23

Alignment explanation


    Indices: 5550--5613  Score: 67
    Period size: 22  Copynumber: 2.8  Consensus size: 23

       5540 TAAATTTTTA

                                    
       5550 AAAATTATAAAAATATAAACTATT
          1 AAAATTATAAAAATAT-AACTATT

                 *      *       *  
       5574 AAAATAATAAAATTATAA-TTTT
          1 AAAATTATAAAAATATAACTATT

             **               
       5596 ACTATTATAAAAATATAA
          1 AAAATTATAAAAATATAA

       5614 GATTTAATTC


Statistics
Matches: 33,  Mismatches: 7, Indels: 2
        0.79            0.17        0.05

Matches are distributed among these distances:
  22   17  0.52
  23    2  0.06
  24   14  0.42

ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36


Consensus pattern (23 bp):   
AAAATTATAAAAATATAACTATT

Found at i:8551 original size:23 final size:23

Alignment explanation


    Indices: 8525--8570  Score: 92
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       8515 TTAATCATTA

                                   
       8525 CATTAGGAAACAAATCTAGAAGT
          1 CATTAGGAAACAAATCTAGAAGT

                                   
       8548 CATTAGGAAACAAATCTAGAAGT
          1 CATTAGGAAACAAATCTAGAAGT

       8571 TATATGATTA


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

Matches are distributed among these distances:
  23   23  1.00

ACGTcount: A:0.48, C:0.13, G:0.17, T:0.22


Consensus pattern (23 bp):   
CATTAGGAAACAAATCTAGAAGT

Found at i:11138 original size:6 final size:6

Alignment explanation


    Indices: 11127--11160  Score: 68
    Period size: 6  Copynumber: 5.7  Consensus size: 6

      11117 AACTCGTAGC

                                                   
      11127 TTGAGA TTGAGA TTGAGA TTGAGA TTGAGA TTGA
          1 TTGAGA TTGAGA TTGAGA TTGAGA TTGAGA TTGA

      11161 AAGGAATGAA


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   28  1.00

ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35


Consensus pattern (6 bp):   
TTGAGA

Found at i:14394 original size:30 final size:30

Alignment explanation


    Indices: 14360--14454  Score: 145
    Period size: 30  Copynumber: 3.2  Consensus size: 30

      14350 CAACTTAACA

                   **              *      
      14360 AACAAATATCTCTAAAATAATAATAAAATT
          1 AACAAATGCCTCTAAAATAATAACAAAATT

                                          
      14390 AACAAATGCCTCTAAAATAATAACAAAATT
          1 AACAAATGCCTCTAAAATAATAACAAAATT

                  *    *                  
      14420 AACAAACGCCTTTAAAATAATAACAAAATT
          1 AACAAATGCCTCTAAAATAATAACAAAATT

                 
      14450 AACAA
          1 AACAA

      14455 TAAAATAAGT


Statistics
Matches: 60,  Mismatches: 5, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
  30   60  1.00

ACGTcount: A:0.59, C:0.15, G:0.02, T:0.24


Consensus pattern (30 bp):   
AACAAATGCCTCTAAAATAATAACAAAATT
Done.