Hi, I just updated my blast from 2.2.6 to 2.2.9 and am suddenly getting very strange results. Sequences are appearing to have the same expect value although the matches in the hsp are very different. I am wondering if any one has seen a similar issue. I am also finding that if I set the -e option to be higher, I can even get matches with just four bases, although I have a word size of seven. Something is going very wrong! Here are the stats on my machine and blast command + example output: dual xeon 2.8 GHz, 4GB RAM, OS, RH linux: enterprise 3.0, kernel 2.4.21-9 options on the blast command line: -W 7, -e 1, -i input, -o output , -d myinternalblastdb, --p blastn I'm using precompliled 2.2.9 from the NCBI. From blast: > 5846704 Length = 177 Score = 24.3 bits (12), Expect = 0.16 Identities = 18/20 (90%) Strand = Plus / Minus Query: 13 ctccagacattgggcgggtt 32 |||||| ||||| ||||||| Sbjct: 127 ctccaggcattgagcgggtt 108 > 5714596 Length = 9401 Score = 24.3 bits (12), Expect = 0.16 Identities = 8/20 (40%) Strand = Plus / Minus Query: 13 ctccagacattgggcgggtt 32 | ||| | ||| Sbjct: 202 tccaagaaaggacccggtcg 183 -Bonnie