Hi!

First's run results occurred by this command:

    tblastn -query query.fasta -db plant_DB -out output-evalue -html

and in some reads I got two targets. e.g :

    Score =   160 bits (404),  Expect = 1e-44, Method: Composition-based stats.
     Identities = 76/77 (99%), Positives = 77/77 (100%), Gaps = 0/77 (0%)
     Frame = +3
    
    Query  1016  GLPGVNGLSTEQRKRLTIAVELVANPSIIFMDEPTSGLDARAAAIVMRTVRNTVDTGRTV  1075
                 GLPGV+GLSTEQRKRLTIAVELVANPSIIFMDEPTSGLDARAAAIVMRTVRNTVDTGRTV
    Sbjct  3     GLPGVDGLSTEQRKRLTIAVELVANPSIIFMDEPTSGLDARAAAIVMRTVRNTVDTGRTV  182
    
    Query  1076  VCTIHQPSIDIFEAFDE  1092
                 VCTIHQPSIDIFEAFDE
    Sbjct  183   VCTIHQPSIDIFEAFDE  233
    
    
     Score = 50.4 bits (119),  Expect = 2e-06, Method: Composition-based stats.
     Identities = 25/74 (34%), Positives = 45/74 (61%), Gaps = 1/74 (1%)
     Frame = +3
    
    Query  346  VRGISGGQRKRVTTGEMLVGPANALFMDEISTGLDSSTTFQIVKSLRQAIHILGGTAVIS  405
                V G+S  QRKR+T    LV   + +FMDE ++GLD+     +++++R  +   G T V +
    Sbjct  15   VDGLSTEQRKRLTIAVELVANPSIIFMDEPTSGLDARAAAIVMRTVRNTVDT-GRTVVCT  191
    
    Query  406  LLQPAPETYDLFDD  419
                + QP+ + ++ FD+
    Sbjct  192  IHQPSIDIFEAFDE  233

I want to get back only the first target and that's why i changed the `-evalue` parameter into this:

    tblastn -query query.fasta -db plant_DB -out output-evalue -html -evalue 3.1

but the results are still the same.

Any idea to filter them better?

Thank you.
The [E-value threshold in BLAST][1] is an upper limit, so a threshold of '3.1' is greater than the E-value reported for the hits (`1e-44` and `2e-06`), and thus they are reported. The use of [scientific notation][2] for the E-value, can be a bit confusing since the exponent has a large magnitude for very small numbers. In this case we have:

 - `1e-44` = `1 * 10^-44` which is less than `3.1 * 10^0`
 - `2e-06` = `2 * 10^-6` which is less than `3.1 * 10^0`, or in normal decimal notation: `0.000002 < 3.1`

As noted by [Devon][3], in order to exclude the second hit by E-value, you would need to use a value between `1e-44` and `2e-06`, say `1e-07`.

 [1]: http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=FAQ#expect
 [2]: http://en.wikipedia.org/wiki/Scientific_notation
 [3]: /u/7403/