Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01009785.1 Kokia drynarioides strain JFW-HI SEQ_124506, 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: 8839
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36


Found at i:4838 original size:94 final size:92

Alignment explanation


    Indices: 4736--4927  Score: 296
    Period size: 94  Copynumber: 2.1  Consensus size: 92

       4726 AATCATATTT

                                  *                                         *
       4736 AATAAATAATAAATTAATTTAGTCAACTTTATTAAATATGATTGATTGAATTTAATA-TTTTATG
          1 AATAAATAATAAATTAATTTAGGCAACTTTATTAAATATGATTGATTGAATTTAATATTTTTATA

                                          
       4800 GTAAATATTTTTTTCTTAAATAATTGATTG
         66 GTAAATA--TTTTT-TTAAATAATTGATTG

                           *                                *     *          
       4830 AATAAATAATAAATTGATTTAGGCAACTTTATTAAATATGATTGATTGGATTTAGTATTTTTATA
          1 AATAAATAATAAATTAATTTAGGCAACTTTATTAAATATGATTGATTGAATTTAATATTTTTATA

                              *        
       4895 GTAAATATTTTTTTAAATGATTGATTG
         66 GTAAATATTTTTTTAAATAATTGATTG

                  
       4922 AATAAA
          1 AATAAA

       4928 AAAAAACTTA


Statistics
Matches: 91,  Mismatches: 6, Indels: 4
        0.90            0.06        0.04

Matches are distributed among these distances:
  92   20  0.22
  93    5  0.05
  94   53  0.58
  95   13  0.14

ACGTcount: A:0.41, C:0.03, G:0.10, T:0.46


Consensus pattern (92 bp):   
AATAAATAATAAATTAATTTAGGCAACTTTATTAAATATGATTGATTGAATTTAATATTTTTATA
GTAAATATTTTTTTAAATAATTGATTG

Found at i:5462 original size:29 final size:31

Alignment explanation


    Indices: 5429--5494  Score: 82
    Period size: 31  Copynumber: 2.2  Consensus size: 31

       5419 GATAGTTTAG

                                     *     
       5429 GTACCACATT-GA-ATATTTTCAAAGTACAT
          1 GTACCACATTGGATATATTTTCAAAATACAT

                  *         *    *         
       5458 GTACCATATTGGATATTTTTTGAAAATACAT
          1 GTACCACATTGGATATATTTTCAAAATACAT

                  
       5489 GTACCA
          1 GTACCA

       5495 AATATGCATG


Statistics
Matches: 31,  Mismatches: 4, Indels: 2
        0.84            0.11        0.05

Matches are distributed among these distances:
  29    9  0.29
  30    2  0.06
  31   20  0.65

ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36


Consensus pattern (31 bp):   
GTACCACATTGGATATATTTTCAAAATACAT

Found at i:8766 original size:18 final size:18

Alignment explanation


    Indices: 8727--8766  Score: 55
    Period size: 17  Copynumber: 2.3  Consensus size: 18

       8717 TTTAAAATTC

                           ** 
       8727 AAAAATTCAAAAATTTGT
          1 AAAAATTCAAAAATTAAT

                              
       8745 AAAAATT-AAAAATTAAT
          1 AAAAATTCAAAAATTAAT

                 
       8762 AAAAA
          1 AAAAA

       8767 CTATAAATAT


Statistics
Matches: 20,  Mismatches: 2, Indels: 1
        0.87            0.09        0.04

Matches are distributed among these distances:
  17   13  0.65
  18    7  0.35

ACGTcount: A:0.68, C:0.03, G:0.03, T:0.28


Consensus pattern (18 bp):   
AAAAATTCAAAAATTAAT
Done.