Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01002913.1 Kokia drynarioides strain JFW-HI SEQ_115344, 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: 4430
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42


Found at i:2178 original size:13 final size:13

Alignment explanation


    Indices: 2157--2222  Score: 57
    Period size: 13  Copynumber: 5.2  Consensus size: 13

       2147 CTAATCTCAA

                *      * 
       2157 TTATTTTTATTGT
          1 TTATATTTATTAT

                          
       2170 TTATATTTATTAGT
          1 TTATATTTATTA-T

                     *   
       2184 TTAT-TTTAGTAT
          1 TTATATTTATTAT

                         
       2196 TTA-ATTT-TTAT
          1 TTATATTTATTAT

              *           
       2207 TTTTATTTATTTAT
          1 TTATATTTA-TTAT

              
       2221 TT
          1 TT

       2223 TGTTTATTTA


Statistics
Matches: 43,  Mismatches: 5, Indels: 9
        0.75            0.09        0.16

Matches are distributed among these distances:
  11    5  0.12
  12   11  0.26
  13   16  0.37
  14   11  0.26

ACGTcount: A:0.23, C:0.00, G:0.05, T:0.73


Consensus pattern (13 bp):   
TTATATTTATTAT

Found at i:2596 original size:87 final size:87

Alignment explanation


    Indices: 2494--2667  Score: 330
    Period size: 87  Copynumber: 2.0  Consensus size: 87

       2484 ATTACATGTC

                                       *                                     
       2494 CTATTGTATATTTGACTTAATTATTTTCGAGTTTTTTTTCATATTTGTGTTTTATATATATTTAT
          1 CTATTGTATATTTGACTTAATTATTTTAGAGTTTTTTTTCATATTTGTGTTTTATATATATTTAT

                                  
       2559 TGTTGCCTATATTATTAATTAA
         66 TGTTGCCTATATTATTAATTAA

                                                                             
       2581 CTATTGTATATTTGACTTAATTATTTTAGAGTTTTTTTTCATATTTGTGTTTTATATATATTTAT
          1 CTATTGTATATTTGACTTAATTATTTTAGAGTTTTTTTTCATATTTGTGTTTTATATATATTTAT

                    *             
       2646 TGTTGCCTTTATTATTAATTAA
         66 TGTTGCCTATATTATTAATTAA

       2668 TTAATATTTA


Statistics
Matches: 85,  Mismatches: 2, Indels: 0
        0.98            0.02        0.00

Matches are distributed among these distances:
  87   85  1.00

ACGTcount: A:0.25, C:0.06, G:0.09, T:0.59


Consensus pattern (87 bp):   
CTATTGTATATTTGACTTAATTATTTTAGAGTTTTTTTTCATATTTGTGTTTTATATATATTTAT
TGTTGCCTATATTATTAATTAA

Found at i:3578 original size:13 final size:14

Alignment explanation


    Indices: 3559--3600  Score: 68
    Period size: 13  Copynumber: 3.0  Consensus size: 14

       3549 ATTTGTGATC

                          
       3559 CTTTGCATTTTATT
          1 CTTTGCATTTTATT

                          
       3573 -TTTGCATTTTATT
          1 CTTTGCATTTTATT

                           
       3586 GCTTTGCATTTTATT
          1 -CTTTGCATTTTATT

       3601 GAATATATGT


Statistics
Matches: 26,  Mismatches: 0, Indels: 3
        0.90            0.00        0.10

Matches are distributed among these distances:
  13   13  0.50
  15   13  0.50

ACGTcount: A:0.14, C:0.12, G:0.10, T:0.64


Consensus pattern (14 bp):   
CTTTGCATTTTATT

Found at i:3593 original size:15 final size:15

Alignment explanation


    Indices: 3559--3601  Score: 72
    Period size: 15  Copynumber: 3.0  Consensus size: 15

       3549 ATTTGTGATC

                           
       3559 CTTTGCATTTTATT-
          1 CTTTGCATTTTATTG

                           
       3573 -TTTGCATTTTATTG
          1 CTTTGCATTTTATTG

                           
       3587 CTTTGCATTTTATTG
          1 CTTTGCATTTTATTG

       3602 AATATATGTT


Statistics
Matches: 27,  Mismatches: 0, Indels: 3
        0.90            0.00        0.10

Matches are distributed among these distances:
  13   13  0.48
  15   14  0.52

ACGTcount: A:0.14, C:0.12, G:0.12, T:0.63


Consensus pattern (15 bp):   
CTTTGCATTTTATTG
Done.