AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_fusions010_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944255000
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PH0502	151	641aa long hypothetical protein
#1	PH0503	35	330aa long hypothetical oligopeptide transport system permease protein AppB
#2	PH1410	117	332aa long hypothetical dipeptide transport system permease protein dppB

Motif 1
GAGGATTAAAAGGGGGGATTAATTCAGATT	0	66	0
ATTATTTTGTTGGGGGGAATATT       	1	22	1
TAACATGATGAGGGGGAGATTGA       	0	3	0
ATGTACAAGGAGGGGCAAAT          	2	107	1
ATTCAGATTTAAGGGAAGTTATAAAAACAT	0	45	0
GTGTTTAAATAAGGGCAATAAAGAAAAGAG	2	23	0
          **********
MAP Score: 7.77497

Motif 2
GTAACATGATGAGGGGGAGATTGA      	0	4	0
AGGATTAAAAGGGGGGATTAATTCAGATTT	0	65	0
TTATTTTGTTGGGGGGAATATT        	1	23	1
GTGTTTAAATAAGGGCAATAAAGAAAAGAG	2	23	0
AATGTACAAGGAGGGGCAAAT         	2	106	1
          **********
MAP Score: 6.05159