Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01005510.1 Kokia drynarioides strain JFW-HI SEQ_119584, 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: 4713
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35


Found at i:1590 original size:96 final size:96

Alignment explanation


    Indices: 1416--1607  Score: 246
    Period size: 96  Copynumber: 2.0  Consensus size: 96

       1406 ATTTTGGGAA

                                           **  *                  *          
       1416 AAGGATATTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCTCAATATTTCA
          1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCACAATATTTCA

                                  *        
       1481 GAATCGAAGATAAAAAAACATTGCCTCGATT
         66 GAATCGAAGATAAAAAAACATTACCTCGATT

                *           *                    *                           
       1512 AAGGGTATTCGATTATTTCGATTTGAAGAAAAATTACGCCTAGTAAGTTAAGGCACAA-ATTTTC
          1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCACAATA-TTTC

                              *  *            
       1576 -GAAACTCGAA-ATAAAAGAATATTACCTCGATT
         65 AG-AA-TCGAAGATAAAAAAACATTACCTCGATT

       1608 TTAAAGTCTT


Statistics
Matches: 83,  Mismatches: 10, Indels: 6
        0.84            0.10        0.06

Matches are distributed among these distances:
  95    2  0.02
  96   76  0.92
  97    5  0.06

ACGTcount: A:0.39, C:0.14, G:0.18, T:0.30


Consensus pattern (96 bp):   
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTACACCTAGTAAGTTAAGGCACAATATTTCA
GAATCGAAGATAAAAAAACATTACCTCGATT

Found at i:4611 original size:63 final size:62

Alignment explanation


    Indices: 4544--4713  Score: 220
    Period size: 63  Copynumber: 2.7  Consensus size: 62

       4534 AATTCTCTTA

                                                                             
       4544 TTATTATTATTTTTATTCATTTATTTATTATTTTTATGAATATAAATAAAT-A-TAAAATAATAT
          1 TTATT-TTA-TTTTATT-ATTTATTTATTATTTTTATGAATATAAATAAATAAGTAAAATAATAT

                                  *                                          
       4607 TTATTTTATTTTATTATTTATTCATTTATTATTGTATGAATATAAATAAATAAATGTAAAATAAT
          1 TTATTTTATTTTATTATTTATTTA-TTATT-TT-TATGAATATAAATAAAT-AA-GTAAAATAAT

              
       4672 AT
         61 AT

             *     *                                 
       4674 TAATTTTGTTTTATTATTTATTTATTA-TTTTATGAATATA
          1 TTATTTTATTTTATTATTTATTTATTATTTTTATGAATATA


Statistics
Matches: 96,  Mismatches: 4, Indels: 14
        0.84            0.04        0.12

Matches are distributed among these distances:
  60    8  0.08
  61   12  0.12
  62    5  0.05
  63   32  0.33
  64    2  0.02
  65    2  0.02
  66    3  0.03
  67   32  0.33

ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56


Consensus pattern (62 bp):   
TTATTTTATTTTATTATTTATTTATTATTTTTATGAATATAAATAAATAAGTAAAATAATAT

Done.