Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01014531.1 Kokia drynarioides strain JFW-HI SEQ_129570, 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: 9127
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35

Warning! 80 characters in sequence are not A, C, G, or T


Found at i:3488 original size:52 final size:52

Alignment explanation


    Indices: 3432--3532  Score: 175
    Period size: 52  Copynumber: 1.9  Consensus size: 52

       3422 ATGATTTTAG

                                    *                           
       3432 GGTTTAAGGACTAAATTATTAAAATAATAAAAGTACATGTATTTTTTGTAAA
          1 GGTTTAAGGACTAAATTATTAAAACAATAAAAGTACATGTATTTTTTGTAAA

                             *              *                
       3484 GGTTTAAGGACTAAATTGTTAAAACAATAAAATTACATGTATTTTTTGT
          1 GGTTTAAGGACTAAATTATTAAAACAATAAAAGTACATGTATTTTTTGT

       3533 GAAATAATGC


Statistics
Matches: 46,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  52   46  1.00

ACGTcount: A:0.42, C:0.05, G:0.14, T:0.40


Consensus pattern (52 bp):   
GGTTTAAGGACTAAATTATTAAAACAATAAAAGTACATGTATTTTTTGTAAA

Found at i:3975 original size:26 final size:26

Alignment explanation


    Indices: 3932--4064  Score: 102
    Period size: 26  Copynumber: 5.4  Consensus size: 26

       3922 TTGAAGGAAT

                *                     
       3932 TACTAAACTGGCTTGTAAGAGCGATA
          1 TACTGAACTGGCTTGTAAGAGCGATA

                      *  *            
       3958 TACTGAACTGACTCGTAAGA--G-T-
          1 TACTGAACTGGCTTGTAAGAGCGATA

            *                     *   
       3980 GA-T--ACTGGCTTGTAAGAGCAATA
          1 TACTGAACTGGCTTGTAAGAGCGATA

                 *           *        
       4003 TACTGCACTGGCTTGTAGGAGCGATA
          1 TACTGAACTGGCTTGTAAGAGCGATA

              *  *       *       *   *
       4029 TAGTGTACTGGCTCGTAAGAGTGATT
          1 TACTGAACTGGCTTGTAAGAGCGATA

                       
       4055 TACT-AACTGG
          1 TACTGAACTGG

       4065 GCTCGTATGA


Statistics
Matches: 82,  Mismatches: 18, Indels: 15
        0.71            0.16        0.13

Matches are distributed among these distances:
  19   12  0.15
  21    1  0.01
  22    2  0.02
  23    2  0.02
  24    2  0.02
  25    5  0.06
  26   58  0.71

ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29


Consensus pattern (26 bp):   
TACTGAACTGGCTTGTAAGAGCGATA

Found at i:8620 original size:10 final size:10

Alignment explanation


    Indices: 8607--8639  Score: 50
    Period size: 10  Copynumber: 3.4  Consensus size: 10

       8597 TTTAACTTTC

                      
       8607 TTTATATATT
          1 TTTATATATT

                *     
       8617 TTTAGA-ATT
          1 TTTATATATT

                      
       8626 TTTATATATT
          1 TTTATATATT

                
       8636 TTTA
          1 TTTA

       8640 AAACATATAT


Statistics
Matches: 20,  Mismatches: 2, Indels: 2
        0.83            0.08        0.08

Matches are distributed among these distances:
   9    8  0.40
  10   12  0.60

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


Consensus pattern (10 bp):   
TTTATATATT

Found at i:8650 original size:19 final size:19

Alignment explanation


    Indices: 8609--8653  Score: 54
    Period size: 19  Copynumber: 2.4  Consensus size: 19

       8599 TAACTTTCTT

                        *  ** *
       8609 TATATATTTTTAGAATTTT
          1 TATATATTTTTAAAACATA

                               
       8628 TATATATTTTTAAAACATA
          1 TATATATTTTTAAAACATA

                   
       8647 TATATAT
          1 TATATAT

       8654 ATATATTTGA


Statistics
Matches: 22,  Mismatches: 4, Indels: 0
        0.85            0.15        0.00

Matches are distributed among these distances:
  19   22  1.00

ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56


Consensus pattern (19 bp):   
TATATATTTTTAAAACATA

Found at i:8684 original size:20 final size:20

Alignment explanation


    Indices: 8649--8703  Score: 67
    Period size: 20  Copynumber: 2.7  Consensus size: 20

       8639 AAAACATATA

                *                
       8649 TATATATATATTTGAAATTTT
          1 TATAAATAT-TTTGAAATTTT

                           *    
       8670 TATAAATATTTTGAATTTTT
          1 TATAAATATTTTGAAATTTT

                           
       8690 TA-AAATTATTTTGA
          1 TATAAA-TATTTTGA

       8704 TTATTCTGTA


Statistics
Matches: 31,  Mismatches: 2, Indels: 3
        0.86            0.06        0.08

Matches are distributed among these distances:
  19    3  0.10
  20   20  0.65
  21    8  0.26

ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56


Consensus pattern (20 bp):   
TATAAATATTTTGAAATTTT
Done.