Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: NTFQ01010321.1 Kokia drynarioides strain JFW-HI SEQ_125183, 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: 4721
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.34

Warning! 66 characters in sequence are not A, C, G, or T


Found at i:91 original size:2 final size:2

Alignment explanation


    Indices: 84--108  Score: 50
    Period size: 2  Copynumber: 12.5  Consensus size: 2

         74 AAAAACCAAT

                                                 
         84 TA TA TA TA TA TA TA TA TA TA TA TA T
          1 TA TA TA TA TA TA TA TA TA TA TA TA T

        109 GATTACATGT


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
   2   23  1.00

ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52


Consensus pattern (2 bp):   
TA

Found at i:3119 original size:14 final size:14

Alignment explanation


    Indices: 3100--3126  Score: 54
    Period size: 14  Copynumber: 1.9  Consensus size: 14

       3090 CTAAGAAAAG

                          
       3100 TTATCTTATGTAAT
          1 TTATCTTATGTAAT

                         
       3114 TTATCTTATGTAA
          1 TTATCTTATGTAA

       3127 AGACATTAAT


Statistics
Matches: 13,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  14   13  1.00

ACGTcount: A:0.30, C:0.07, G:0.07, T:0.56


Consensus pattern (14 bp):   
TTATCTTATGTAAT

Found at i:3962 original size:17 final size:17

Alignment explanation


    Indices: 3940--3979  Score: 80
    Period size: 17  Copynumber: 2.4  Consensus size: 17

       3930 CCCTTGCCAA

                             
       3940 GAGAATCTCCAAGATTT
          1 GAGAATCTCCAAGATTT

                             
       3957 GAGAATCTCCAAGATTT
          1 GAGAATCTCCAAGATTT

                  
       3974 GAGAAT
          1 GAGAAT

       3980 AGATTCTCAA


Statistics
Matches: 23,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  17   23  1.00

ACGTcount: A:0.38, C:0.15, G:0.20, T:0.28


Consensus pattern (17 bp):   
GAGAATCTCCAAGATTT

Found at i:4441 original size:15 final size:15

Alignment explanation


    Indices: 4421--4451  Score: 62
    Period size: 15  Copynumber: 2.1  Consensus size: 15

       4411 CTAGTCTAAT

                           
       4421 TATTTTTATTGTTTA
          1 TATTTTTATTGTTTA

                           
       4436 TATTTTTATTGTTTA
          1 TATTTTTATTGTTTA

             
       4451 T
          1 T

       4452 TAGCATTGAA


Statistics
Matches: 16,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  15   16  1.00

ACGTcount: A:0.19, C:0.00, G:0.06, T:0.74


Consensus pattern (15 bp):   
TATTTTTATTGTTTA

Found at i:4580 original size:24 final size:22

Alignment explanation


    Indices: 4537--4596  Score: 61
    Period size: 22  Copynumber: 2.7  Consensus size: 22

       4527 TTGTTATTTT

                                  
       4537 TTTATTTTTTATTTAATTTGAA
          1 TTTATTTTTTATTTAATTTGAA

                            **      
       4559 TTTATTGTTATTATTTTGTTTG--
          1 TTTATT-TT-TTATTTAATTTGAA

                            
       4581 TTTATTTATTTATTTA
          1 TTTATTT-TTTATTTA

       4597 TCATTAAATT


Statistics
Matches: 32,  Mismatches: 3, Indels: 7
        0.76            0.07        0.17

Matches are distributed among these distances:
  21    7  0.22
  22   13  0.41
  23    2  0.06
  24   10  0.31

ACGTcount: A:0.22, C:0.00, G:0.07, T:0.72


Consensus pattern (22 bp):   
TTTATTTTTTATTTAATTTGAA
Done.