AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_operons059_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944256966
 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
CCGTTCCAACATTTCAATGAGAACTTAAAAACCAAGCTATTCGA	0	12	1
AAACCAAGCTATTCGATGCTAAAACTAAGTATTTTGCATAGAAT	0	40	1
TGCATAGAATATGGTAAAATAAATCTTAAAAATTGCCAATTTTT	0	74	1
AAATTGCCAATTTTTAACATGAACATGGTGATATCAGA      	0	103	1
TCCCTTTCATTTTTAAACTATAATATATAAATCTTGTCAGGTGA	1	17	0
AATGAAAGGGATTACATTTATAATGGTGGTATATA         	1	50	1
 ATCAACTAGATATGATGTAGAAACTGGACACTTTAAGATGATC	3	9	1
TACTTAATTAATGCGAAGAGAAACCTAAAAATATCGATCATCTT	3	44	0
          ***  **    **  *    *  *
MAP Score: 4.71912

Motif 2
CGTTCCAACATTTCAATGAGAACTTAAAAACCAAGCTA	0	13	1
AAACCAAGCTATTCGATGCTAAAACTAAGTATTTTGCA	0	40	1
TATTTTGCATAGAATATGGTAAAATAAATCTTAAAAAT	0	69	1
TGTTCATGTTAAAAATTGGCAATTTTTAAGATTTATTT	0	90	0
    GTTACCATCACCTGACAAGATTTATATATTATAG	1	6	1
GGGATTGATAAAATTTTGGACAGGCTAAC         	2	1	0
GATATGATGTAGAAACTGGACACTTTAAGATGATCGAT	3	18	1
TACTTAATTAATGCGAAGAGAAACCTAAAAATATCGAT	3	50	0
          *     *** **  ****
MAP Score: 2.42033

Motif 3
ATACTTAGTTTTAGCATCGAATAGCTTGGTTTTTA	0	37	0
AACTAAGTATTTTGCATAGAATATGGTAAAATAAA	0	62	1
ATGTTAAAAATTGGCAATTTTTAAGATTTATTTTA	0	88	0
TTGCCAATTTTTAACATGAACATGGTGATATCAGA	0	106	1
AATGAAAGGGATTACATTTATAATGGTGGTATATA	1	50	1
TAGGTTTCTCTTCGCATTAATTAAGTATTGAGGTG	3	61	1
          ** ****  * ** *
MAP Score: 1.47027