Difference between X1, X2 & X3 and S1 & S2 in TBLASTN report

Question

[islama]

Hi,

I am having difficulties understanding the replationships of some terms in tblastn report. Any help would be appreciated.

First, X1, X2 and X3. I know they are cutoff thresholds and are used in different steps of the local alignments. What I would like to know is, in which steps of local alignments X2 and X3 are used? Are they fixed values or are changed with database size and query size?

Second, S1 and S2. Why two different S values? Are they for ungapped and gapped steps?

Thanks in advance.

[Pierre Lindenbaum]

First, X1, X2 and X3

what is this ? Where do you see this ? Please provide a minimal input.

[Pierre Lindenbaum]

please validate (green mark on the left) Philipp 's answer C: How to use a different window size for TBLASTN?