Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01003694.1 Kokia drynarioides strain JFW-HI SEQ_116627, 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: 17356
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.35


Found at i:1449 original size:15 final size:16

Alignment explanation


    Indices: 1431--1463  Score: 50
    Period size: 15  Copynumber: 2.1  Consensus size: 16

       1421 AACTAAATAA

                    *       
       1431 AATAAAAATAA-AAAT
          1 AATAAAAAGAACAAAT

                            
       1446 AATAAAAAGAACAAAT
          1 AATAAAAAGAACAAAT

              
       1462 AA
          1 AA

       1464 AAATAACACC


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  15   10  0.62
  16    6  0.38

ACGTcount: A:0.79, C:0.03, G:0.03, T:0.15


Consensus pattern (16 bp):   
AATAAAAAGAACAAAT

Found at i:8510 original size:13 final size:13

Alignment explanation


    Indices: 8492--8518  Score: 54
    Period size: 13  Copynumber: 2.1  Consensus size: 13

       8482 TTCGAATTAT

                         
       8492 AAAAAAAAAGAAA
          1 AAAAAAAAAGAAA

                         
       8505 AAAAAAAAAGAAA
          1 AAAAAAAAAGAAA

             
       8518 A
          1 A

       8519 CCATCAATTA


Statistics
Matches: 14,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  13   14  1.00

ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00


Consensus pattern (13 bp):   
AAAAAAAAAGAAA

Found at i:14257 original size:31 final size:31

Alignment explanation


    Indices: 14211--14286  Score: 125
    Period size: 31  Copynumber: 2.5  Consensus size: 31

      14201 AATAGTAGGT

                *   *                      
      14211 GAAAATGGAGAAAATGAGAAGAAAAAGGAAG
          1 GAAAGTGGTGAAAATGAGAAGAAAAAGGAAG

                                     *     
      14242 GAAAGTGGTGAAAATGAGAAGAAAAGGGAAG
          1 GAAAGTGGTGAAAATGAGAAGAAAAAGGAAG

                          
      14273 GAAAGTGGTGAAAA
          1 GAAAGTGGTGAAAA

      14287 AGAGGAATGC


Statistics
Matches: 42,  Mismatches: 3, Indels: 0
        0.93            0.07        0.00

Matches are distributed among these distances:
  31   42  1.00

ACGTcount: A:0.55, C:0.00, G:0.36, T:0.09


Consensus pattern (31 bp):   
GAAAGTGGTGAAAATGAGAAGAAAAAGGAAG
Done.