AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_operons059_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944256972
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PH1348	131	333aa long hypothetical protein
#1	PH1582	75	278aa long hypothetical dipeptide transport protein dppA
#2	PH1583	68	459aa long hypothetical tryptophan synthase beta chain
#3	PH1598	94	503aa long hypothetical pyrimidine-nucleoside phosphorylase

Motif 1
AAAATAAATCTTAAAAATTGCCAATTTTTA	0	89	1
CATGTTCATGTTAAAAATTGGCAATTTTTA	0	100	0
TATATTATAGTTTAAAAATGAAAGGGATTA	1	34	1
AGGGATTACATTTATAATGGTGGTATATA 	1	56	1
TTCGCATTAATTAAGTATTGAGGTGTTGAA	3	71	1
          **********
MAP Score: 3.65583

Motif 2
TAAGTTCTCATTGAAATGTTGGAACGGGG  	0	8	0
    ATCAACTAGATATGATGTAGAAACTGG	3	6	1
ACTGGACACTTTAAGATGATCGATATTTTTA	3	32	1
TAATTAAGTATTGAGGTGTTGAAAGA     	3	78	1
TTGCCAATTTTTAACATGAACATGGTGATAT	0	106	1
CAATACTTAATTAATGCGAAGAGAAACCTAA	3	60	0
CCTATTTCTTTTTACTTGATGCCCCATGAAC	2	40	1
TATTATAGTTTAAAAATGAAAGGGATTACAT	1	36	1
ATACCACCATTATAAATGTAATCCCTTTCAT	1	51	0
          **** ******
MAP Score: 2.68856

Motif 3
TCGATGCTAAAACTAAGTATTTTGCATAGAA	0	52	1
GAATATGGTAAAATAAATCTTAAAAATTGCC	0	80	1
AAACTATAATATATAAATCTTGTCAGGTGAT	1	16	0
TCTTCGCATTAATTAAGTATTGAGGTGTTGA	3	69	1
          ** ********
MAP Score: 2.14461