AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_operons049_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944256852
 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
TTGTTTTGTCAAAGATTGATTAATTTTTAAAAT	1	30	1
AATAAATTTTAAAAATTAATCAATCTTTGACAA	1	35	0
TTTATTTTACAAAAATTTGTCAACTAAACACAT	1	62	1
GAATTTAACAAAAAAGTTATAAAAGAACGCTGA	1	113	1
          *******  * **
MAP Score: 3.02168

Motif 2
TAATTATGTACAACTTCAATTTCTCC    	0	6	0
GAGGGAGGAGCAACATCAATTCAACTAAGG	0	83	1
TTTGACAAAACAAAGGCAATTGGAGGGGAA	1	13	0
AATAAATTTTAAAAATTAATCAATCTTTGA	1	38	0
GATTAATTTTTAAAATTTATTTTACAAAAA	1	47	1
ACTTTTTTGTTAAATTCCATAACCTTGTTA	1	100	0
GAATTTAACAAAAAAGTTATAAAAGAACGC	1	113	1
          **********
MAP Score: 1.16183