SET #1

DIALIGN helped identify at least one region of > 6bp that is perfectly conserved across 3 or 
more genes and well conserved across 2 others.  I highlighted this area by placing brackets [] 
around it, with the motif being "ATTTAA".  There were 2 other regions with strong conservation 
across at least 3 genes, which I highlighted with parens ().

Pyrococcus Abyssi PAB1159         1    ---------- 
Pyrococcus Horikoshii PH1987      1   (ATTAGCAACT)
Methanobacterium Ther. MTH1425    1    ---------- 
Methanococcus Jannaschii MJ1130   1    ---------- 
Thermoplasma Volcanium TVN1276    1   (AATATCAATA)
Thermoplasma Acidophilum TA0324   1   (AATATCAATG)
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Pyrococcus Abyssi PAB1159        17   (AA ATCGTTGA)
Pyrococcus Horikoshii PH1987     64   (AA AACGTTAG)
Methanobacterium Ther. MTH1425   19   (AT AACCGGAG)
Methanococcus Jannaschii MJ1130   3   (AA AACTTTTT)
Thermoplasma Volcanium TVN1276   64   (AA AATTTACC)
Thermoplasma Acidophilum TA0324  82       TCGTTcc 
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Pyrococcus Abyssi PAB1159        47   [AATTTAAT]
Pyrococcus Horikoshii PH1987     93   [AATTTAAC]
Methanobacterium Ther. MTH1425   48    AGTTACAC 
Methanococcus Jannaschii MJ1130  42   [ATTTAAAT]
Thermoplasma Volcanium TVN1276   99   [ATTTAAAT]
Thermoplasma Acidophilum TA0324 113   [ATTTAAAT]
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CLUSTALW didn't align things nearly as well.  Out of its alignment I only really see 1 region 
where there appears to be good conservation across at least 3 genes.  I marked the area with 
brackets [].

CLUSTAL W (1.81) multiple sequence alignment
                                                                        
Pyrococcus Horikoshii PH1987     [TT----AATTTA]
Methanococcus Jannaschii MJ1130  [AT----AATTGA]
Pyrococcus Abyssi PAB1159        [TTT---AATTTA]
Methanobacterium Ther. MTH1425   [TT----AGTTAC]
Thermoplasma Acidophilum TA0324   TTCCTGCGCTGA 
Thermoplasma Volcanium TVN1276    TATGGATAATTA 
                                           *   

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SET #2

For this set here are the organisms & gene IDs:
Pyrococcus Abyssi PAB0931
Pyrococcus Horikoshii PH0636
Haemophilus influenzae HI0078
Pasteurella multocida PM0945
Thermoplasma Volcanium TVN1244
Thermoplasma Acidophilum TA1147

On this set DIALIGN found a couple regions where things were well conserved across 4 or 5 genes 
and perfectly conserved across 2.  I've marked these regions in parens ().

Pyrococcus Abyssi PAB0931         1  (ATCACCAAAAA-ATTTTACC)
Pyrococcus Horikoshii PH0636      1  (ATCACCAAAAAgAATTTACC)
Haemophilus influenzae HI0078     1  (TCCCTCTAAAA-AATTAAgg)
Pasteurella multocida PM0945      1  (TTCCTCTAATA-GTTTTATA)
Thermoplasma Volcanium TVN1244    1  (TTAAACTAAAT-TAATAATA)
Thermoplasma Acidophilum TA1147   1  (ATCAGCAAAGC-AATCCGTC)
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Pyrococcus Abyssi PAB0931        38  (TTTAAA---- ---CGTTGC-)
Pyrococcus Horikoshii PH0636     38  (TTTAAA---- ---GCTTGC-)
Haemophilus influenzae HI0078    37  (TTCCACAATC GAGGTAAAA-)
Pasteurella multocida PM0945     39  (TTTCATAAAA GCGCATTAA-)
Thermoplasma Volcanium TVN1244   61  (TATCACATAT TCGCATTAT-)
Thermoplasma Acidophilum TA1147 100  (TCAAACGGTA TCGGATTATc)
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                                      *****                                                 

The CLUSTALW alignment found several places where 2 or 3 genes were reasonably conserved.  
It even found a couple regions where things seemed well conserved over 4 or 5 genes, 
which I marked with parens ().

CLUSTAL W (1.81) multiple sequence alignment

Pyrococcus Abyssi PAB0931       (TGCCAAAAC)-CGA(CAGTCTAAT)-------AAGAGAA-TACCCCGAT(TTTAGC)
Pyrococcus Horikoshii PH0636    (TGCCAAAAC)-CGA(CATCCTAAT)-------AAAATTCCTGGATGGAG(ATTAAG)
Thermoplasma Acidophilum TA1147  TATCGGATT -ATC(CATGCCAAT)GG-----AGGATCAATGCATATAT(ATTAAC)
Haemophilus influenzae HI0078   (AGGTAAAAG)-TGC(TATAAAAGT)GC-----GGTTTGTTTTTATTTCA(TTTTAC)
Pasteurella multocida PM0945    (TGGCAAATT)ACGC(TATGCTAAA)TT-----TATAACACTCCTATACA(CTTAAG)
Thermoplasma Volcanium TVN1244   TATAGGAGA TTTA(GAAACCAAA)TCTCCGAAACCGTAGCAGATGGTA(ATTGAT)
                                       *         *    *                             **