When you run Pileup interactively, it prints the pairwise similarity scores to the screen. You see output like this:
Determining pairwise similarity scores... 1 x 2 1.19 1 x 3 1.20 //////////////////////// 26 x 28 0.87 27 x 28 0.86 |
Sample session:
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Mail received when batch job finishes:
Date: Wed, 4 Jun 1997 14:18:23 -0400 (EDT) From: Susan Chacko <susanc@helix.nih.gov> Subject: pileup Welcome to the WISCONSIN PACKAGE Version 8.1-UNIX, August 1995 [....etc....] Running pileup using : .. -monitor -INfile1=@hsp2.list -GAPweight=5.000000 -LENgthweight=0.300000 -OUTfile1=hsp2.msf -DENsity=3.333433 -FIGure -Default 1 BBHSP60 1931 bp 2 BBHSPRO 2116 bp 3 BBOSPAGE 819 bp Determining pairwise similarity scores... 1 x 2 0.36 1 x 3 0.37 2 x 3 0.38 Aligning... 1 ........................................-..... 2 .................................................. ..............................................-... ....... Total sequences: 3 Alignment length: 2,120 CPU time: 09.97 Output file:/u5/susanc/hsp2.msf |