Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005043.1 Kokia drynarioides strain JFW-HI SEQ_118819, 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: 10297
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.36

Warning! 1 characters in sequence are not A, C, G, or T


Found at i:2213 original size:24 final size:24

Alignment explanation


    Indices: 2185--2247  Score: 81
    Period size: 24  Copynumber: 2.6  Consensus size: 24

       2175 AGAAATAATC

                                    
       2185 TTTCAGTTAAACTCTATTTATTTG
          1 TTTCAGTTAAACTCTATTTATTTG

                 *       * *        
       2209 TTTCAATTAAACTTTGTTTATTTG
          1 TTTCAGTTAAACTCTATTTATTTG

               *   *       
       2233 TTTAAGTCAAACTCT
          1 TTTCAGTTAAACTCT

       2248 TATTAGTCTA


Statistics
Matches: 32,  Mismatches: 7, Indels: 0
        0.82            0.18        0.00

Matches are distributed among these distances:
  24   32  1.00

ACGTcount: A:0.27, C:0.13, G:0.08, T:0.52


Consensus pattern (24 bp):   
TTTCAGTTAAACTCTATTTATTTG

Found at i:5440 original size:20 final size:22

Alignment explanation


    Indices: 5415--5454  Score: 57
    Period size: 20  Copynumber: 1.9  Consensus size: 22

       5405 GATCCCCAAC

                  *               
       5415 AATAATTAAA-AAAT-ATAACT
          1 AATAATCAAATAAATCATAACT

                                
       5435 AATAATCAAATAAATCATAA
          1 AATAATCAAATAAATCATAA

       5455 AAATATTAAA


Statistics
Matches: 17,  Mismatches: 1, Indels: 2
        0.85            0.05        0.10

Matches are distributed among these distances:
  20    9  0.53
  21    4  0.24
  22    4  0.24

ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28


Consensus pattern (22 bp):   
AATAATCAAATAAATCATAACT

Found at i:9068 original size:19 final size:20

Alignment explanation


    Indices: 9043--9092  Score: 75
    Period size: 19  Copynumber: 2.5  Consensus size: 20

       9033 TATGTAAAAC

                                
       9043 GAAATGATAAAATCAATATA
          1 GAAATGATAAAATCAATATA

                             *  
       9063 -AAATGATAAAATCAATGTA
          1 GAAATGATAAAATCAATATA

                  *    
       9082 GAAATGCTAAA
          1 GAAATGATAAA

       9093 GTTCTATTCT


Statistics
Matches: 27,  Mismatches: 2, Indels: 2
        0.87            0.06        0.06

Matches are distributed among these distances:
  19   18  0.67
  20    9  0.33

ACGTcount: A:0.58, C:0.06, G:0.12, T:0.24


Consensus pattern (20 bp):   
GAAATGATAAAATCAATATA
Done.