Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01000195.1 Kokia drynarioides strain JFW-HI SEQ_110881, 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, 631

Length: 1052
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.38


Found at i:34 original size:23 final size:23

Alignment explanation


    Indices: 1--116  Score: 95
    Period size: 23  Copynumber: 5.3  Consensus size: 23

                                   
          1 AGAGAGCACACAAAGTGCTAAAC
          1 AGAGAGCACACAAAGTGCTAAAC

                  *                
         24 AGAGAGTACACAAA--G-T--AC
          1 AGAGAGCACACAAAGTGCTAAAC

              *                  * 
         42 --TGAGCACACAAAGTGCTAATC
          1 AGAGAGCACACAAAGTGCTAAAC

                                    *
         63 AGAGAGCACACAAAGTGCTAATAAT
          1 AGAGAGCACACAAAGTGCT-A-AAC

                                 ** 
         88 AGAGAGCACACACAA-TGCTATTC
          1 AGAGAGCACACA-AAGTGCTAAAC

                  
        111 AGAGAG
          1 AGAGAG

        117 TGTGCTAGTG


Statistics
Matches: 73,  Mismatches: 10, Indels: 20
        0.71            0.10        0.19

Matches are distributed among these distances:
  16   10  0.14
  18    3  0.04
  19    1  0.01
  20    1  0.01
  21    2  0.03
  23   35  0.48
  24    2  0.03
  25   17  0.23
  26    2  0.03

ACGTcount: A:0.45, C:0.20, G:0.22, T:0.14


Consensus pattern (23 bp):   
AGAGAGCACACAAAGTGCTAAAC

Found at i:58 original size:39 final size:39

Alignment explanation


    Indices: 4--78  Score: 132
    Period size: 39  Copynumber: 1.9  Consensus size: 39

          1 AGA

                                      *            
          4 GAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTACT
          1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT

                              *                 
         43 GAGCACACAAAGTGCTAATCAGAGAGCACACAAAGT
          1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGT

         79 GCTAATAATA


Statistics
Matches: 34,  Mismatches: 2, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  39   34  1.00

ACGTcount: A:0.45, C:0.21, G:0.21, T:0.12


Consensus pattern (39 bp):   
GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT

Found at i:91 original size:25 final size:23

Alignment explanation


    Indices: 43--116  Score: 96
    Period size: 23  Copynumber: 3.1  Consensus size: 23

         33 ACAAAGTACT

                                   
         43 GAGCACACAAAGTGCTAATCAGA
          1 GAGCACACAAAGTGCTAATCAGA

                                 *   
         66 GAGCACACAAAGTGCTAATAATAGA
          1 GAGCACACAAAGTGCTAAT--CAGA

                              *     
         91 GAGCACACACAA-TGCTATTCAGA
          1 GAGCACACA-AAGTGCTAATCAGA

               
        114 GAG
          1 GAG

        117 TGTGCTAGTG


Statistics
Matches: 45,  Mismatches: 3, Indels: 6
        0.83            0.06        0.11

Matches are distributed among these distances:
  23   25  0.56
  25   18  0.40
  26    2  0.04

ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15


Consensus pattern (23 bp):   
GAGCACACAAAGTGCTAATCAGA
Done.