Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01004984.1 Kokia drynarioides strain JFW-HI SEQ_118731, 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: 36145
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.36


Found at i:8187 original size:19 final size:19

Alignment explanation


    Indices: 8163--8202  Score: 55
    Period size: 19  Copynumber: 2.1  Consensus size: 19

       8153 TGTGAAAATA

                                
       8163 TTAAAAA-ATCCATTATTTT
          1 TTAAAAAGAT-CATTATTTT

                      *        
       8182 TTAAAAAGATTATTATTTT
          1 TTAAAAAGATCATTATTTT

              
       8201 TT
          1 TT

       8203 TCTATATTTT


Statistics
Matches: 19,  Mismatches: 1, Indels: 2
        0.86            0.05        0.09

Matches are distributed among these distances:
  19   17  0.89
  20    2  0.11

ACGTcount: A:0.40, C:0.05, G:0.03, T:0.53


Consensus pattern (19 bp):   
TTAAAAAGATCATTATTTT

Found at i:9776 original size:3 final size:3

Alignment explanation


    Indices: 9768--9798  Score: 62
    Period size: 3  Copynumber: 10.3  Consensus size: 3

       9758 CAATTGAATT

                                                     
       9768 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
          1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T

       9799 ATCTCTCTTT


Statistics
Matches: 28,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   3   28  1.00

ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68


Consensus pattern (3 bp):   
TTC

Found at i:17510 original size:6 final size:6

Alignment explanation


    Indices: 17372--17507  Score: 200
    Period size: 6  Copynumber: 22.7  Consensus size: 6

      17362 TTATTGTTAC

                                                                   
      17372 TATTGT TATTGT TATTGT TATTGT TATTGT TATTGT TATTGT TATTGT
          1 TATTGT TATTGT TATTGT TATTGT TATTGT TATTGT TATTGT TATTGT

                                                          *      * 
      17420 TATTGT TATTGT TATTGT TATTGT TATTGT TATTGT TATTAT TATTAT
          1 TATTGT TATTGT TATTGT TATTGT TATTGT TATTGT TATTGT TATTGT

                *      *      *      *      *      *      
      17468 TATTAT TATTAT TATTAT TATTAT TATTAT TATTAT TATT
          1 TATTGT TATTGT TATTGT TATTGT TATTGT TATTGT TATT

      17508 ATTTGCAATT


Statistics
Matches: 129,  Mismatches: 1, Indels: 0
        0.99            0.01        0.00

Matches are distributed among these distances:
   6  129  1.00

ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67


Consensus pattern (6 bp):   
TATTGT

Found at i:26569 original size:6 final size:6

Alignment explanation


    Indices: 26560--26604  Score: 90
    Period size: 6  Copynumber: 7.5  Consensus size: 6

      26550 TACTAACACC

                                                                
      26560 CCTATT CCTATT CCTATT CCTATT CCTATT CCTATT CCTATT CCT
          1 CCTATT CCTATT CCTATT CCTATT CCTATT CCTATT CCTATT CCT

      26605 TCGTTAAAGC


Statistics
Matches: 39,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   6   39  1.00

ACGTcount: A:0.16, C:0.36, G:0.00, T:0.49


Consensus pattern (6 bp):   
CCTATT

Found at i:28984 original size:5 final size:5

Alignment explanation


    Indices: 28970--29020  Score: 50
    Period size: 5  Copynumber: 10.0  Consensus size: 5

      28960 GAAAGAAATG

                  *                            *                    *    
      28970 GAAAA AAAAA GAAAA GAAAA GTTAAAA GAACA GAAAA GAAAA -AAAA TAAAA
          1 GAAAA GAAAA GAAAA GAAAA G--AAAA GAAAA GAAAA GAAAA GAAAA GAAAA

      29021 TTGCTCAAAA


Statistics
Matches: 39,  Mismatches: 4, Indels: 6
        0.80            0.08        0.12

Matches are distributed among these distances:
   4    4  0.10
   5   30  0.77
   7    5  0.13

ACGTcount: A:0.78, C:0.02, G:0.14, T:0.06


Consensus pattern (5 bp):   
GAAAA

Found at i:29013 original size:17 final size:17

Alignment explanation


    Indices: 28961--29013  Score: 54
    Period size: 17  Copynumber: 3.2  Consensus size: 17

      28951 GGAGAAGTAG

                   * *       
      28961 AAAGAAATGGAAA-AAA
          1 AAAGAAAAGAAAAGAAA

                          ** 
      28977 AAAGAAAAGAAAAGTTA
          1 AAAGAAAAGAAAAGAAA

                  *          
      28994 AAAGAACAGAAAAGAAA
          1 AAAGAAAAGAAAAGAAA

               
      29011 AAA
          1 AAA

      29014 AATAAAATTG


Statistics
Matches: 29,  Mismatches: 7, Indels: 1
        0.78            0.19        0.03

Matches are distributed among these distances:
  16   11  0.38
  17   18  0.62

ACGTcount: A:0.75, C:0.02, G:0.17, T:0.06


Consensus pattern (17 bp):   
AAAGAAAAGAAAAGAAA
Done.