Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01011937.1 Kokia drynarioides strain JFW-HI SEQ_126935, 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: 2745
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.35


Found at i:142 original size:22 final size:21

Alignment explanation


    Indices: 94--148  Score: 65
    Period size: 22  Copynumber: 2.6  Consensus size: 21

         84 TATTAATAAA

                             *  *
         94 ATTATTTATTAATATTTTTTT
          1 ATTATTTATTAATATTTATTG

             *                    
        115 AATATTTATTATATATTTATTG
          1 ATTATTTATTA-ATATTTATTG

            *           
        137 CTTATTTATTAA
          1 ATTATTTATTAA

        149 ATACCACAGA


Statistics
Matches: 28,  Mismatches: 5, Indels: 2
        0.80            0.14        0.06

Matches are distributed among these distances:
  21   11  0.39
  22   17  0.61

ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64


Consensus pattern (21 bp):   
ATTATTTATTAATATTTATTG

Found at i:511 original size:22 final size:22

Alignment explanation


    Indices: 467--522  Score: 58
    Period size: 22  Copynumber: 2.5  Consensus size: 22

        457 AAAATGAAAC

                             **    
        467 GAAAAATGAAAGAGATGTTGAGG
          1 GAAAAA-GAAAGAGATGCAGAGG

                      *           
        490 GAAAAAGAAATAGATGCAGAGG
          1 GAAAAAGAAAGAGATGCAGAGG

            *    *     
        512 CAAAACGAAAG
          1 GAAAAAGAAAG

        523 GAAATGATAA


Statistics
Matches: 27,  Mismatches: 6, Indels: 1
        0.79            0.18        0.03

Matches are distributed among these distances:
  22   21  0.78
  23    6  0.22

ACGTcount: A:0.54, C:0.05, G:0.30, T:0.11


Consensus pattern (22 bp):   
GAAAAAGAAAGAGATGCAGAGG

Found at i:1221 original size:19 final size:19

Alignment explanation


    Indices: 1199--1259  Score: 51
    Period size: 18  Copynumber: 3.3  Consensus size: 19

       1189 AAATTTTCAT

                               
       1199 ATTTTATATATATTTTAAA
          1 ATTTTATATATATTTTAAA

                    *            
       1218 ATTTT-TAAAGT-TTTTAATA
          1 ATTTTATATA-TATTTTAA-A

                                
       1237 ATTATTAT-TA-A-TTTAAA
          1 ATT-TTATATATATTTTAAA

                  
       1254 ATTTTA
          1 ATTTTA

       1260 ACTTAATAAA


Statistics
Matches: 35,  Mismatches: 2, Indels: 13
        0.70            0.04        0.26

Matches are distributed among these distances:
  16    3  0.09
  17    4  0.11
  18   14  0.40
  19   10  0.29
  20    3  0.09
  21    1  0.03

ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57


Consensus pattern (19 bp):   
ATTTTATATATATTTTAAA
Done.