AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_sum_all076_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944236719
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PH1156	127	161aa long hypothetical thiamine biosynthetic bifunctional protein
#1	PH1161	150	218aa long hypothetical transcriptional regulator

Motif 1
GAGCAACATCAATTCAACTAAGGATAAAGA	0	90	1
AATTAATCAATCTTTGACAAAACAAAGGCA	1	25	0
TGTAAAATAAATTTTAAAAATTAATCAATC	1	43	0
TTTTAAAATTTATTTTACAAAAATTTGTCA	1	54	1
ATTTTACAAAAATTTGTCAACTAAACACAT	1	65	1
TAAACACATAATTATAACAAGGTTATGGAA	1	86	1
AAGGTTATGGAATTTAACAAAAAAGTTATA	1	104	1
          **********
MAP Score: 3.22147

Motif 2
GGAGAAATTGAAGTTGTACATAATTACGGA	0	10	1
AATTGCCTTTGTTTTGTCAAAGATTGATTA	1	22	1
AAGATTGATTAATTTTTAAAATTTATTTTA	1	41	1
TTTAAAATTTATTTTACAAAAATTTGTCAA	1	55	1
ATTTTACAAAAATTTGTCAACTAAACACAT	1	65	1
AAGGTTATGGAATTTAACAAAAAAGTTATA	1	104	1
TTTAACAAAAAAGTTATAAAAGAACGCTGA	1	116	1
          **********
MAP Score: 3.09223