AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_operons023_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944256268
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PH0241	284	434aa long hypothetical asparaginyl-tRNA synthetase
#1	PH0243	69	601aa long hypothetical glutamine--fructose-6-phosphate aminotransferase
#2	PH0686	30	263aa long hypothetical ORFZ protein
#3	PH0783	30	200aa long hypothetical protein
#4	PH1280	300	715aa long hypothetical protein

Motif 1
TGAACCGGGGGTTCCGACCGGGCCGACAGGGGAT	0	110	1
GTCATCATCTGCTCAGCAAAGCAAAAGCTCTTCA	0	143	0
TCAAATAGCAGGTCAGCGAAGGGCGTGGTCATCA	0	170	0
          GATCAGCTCGGATCCAGTTCTTCA	1	0	1
         CGCTCAGCAAGGCCCTGTCATCACT	3	1	1
ACGATTTCAAGATCTGAGAGGCTCGCAGAAGACA	4	121	1
          * ** ** **** *
MAP Score: 8.41328

Motif 2
GGAATCGTGAACCGGGGGTTCCGACCGGGCCGACAGGGGAT	0	103	1
ATGCATATGGAAATTTGGCTCAGTGATGGATT         	0	262	1
AAAATTGTCAAATAGCAGGTCAGCGAAGGGCGTGGTCATCA	0	170	0
TGGGCGATGAAGAACTGGATCCGAGCTGATC          	1	0	0
TTCCCCGGAGAGGGCGGGAACCGGGCCGGTTAAAAATTATA	0	66	0
TCAGTATACGATTTCAAGATCTGAGAGGCTCGCAGAAGACA	4	114	1
CTAGATTTTTAATGTTGGATCTTTTAAGGATTTTTAAGTTA	4	59	0
TAAACACTATAAACCTAGATAAGGACTGCGTACATA     	4	274	1
GGGCGTGGTCATCATCTGCTCAGCAAAGCAAAAGCTCTTCA	0	143	0
          *     ** ** *  * ** *
MAP Score: 7.47455

Motif 3
CAAAGCAAAAGCTCTTCATCCCCTGTCGGCCC	0	129	0
GTCATCATCTGCTCAGCAAAGCAAAAGCTCTT	0	145	0
TCAAATAGCAGGTCAGCGAAGGGCGTGGTCAT	0	172	0
TGGAAATTTGGCTCAGTGATGGATT       	0	269	1
CTCGGATCCAGTTCTTCATCGCCCAGGAAATT	1	16	1
         CGCTCAGCAAGGCCCTGTCATCA	3	1	1
TTTAATGTTGGATCTTTTAAGGATTTTTAAGT	4	61	0
TATGCCAATCGATCAGTATACGATTTCAAGAT	4	102	1
ACGATTTCAAGATCTGAGAGGCTCGCAGAAGA	4	121	1
          * ******* **
MAP Score: 7.41367

Motif 4
TAAAAAGAGGGATGATGAGTTTTTCCC    	0	6	0
GCCGACAGGGGATGAAGAGCTTTTGCTTTGC	0	131	1
CTTTTGCTTTGCTGAGCAGATGATGACCACG	0	150	1
CACGCCCTTCGCTGACCTGCTATTTGACAAT	0	177	1
ATCACAAATAACCGAAGAACTTATATAGAAT	0	233	1
TTTCCTGGGCGATGAAGAACTGGATCCGAGC	1	15	0
GTTCTTCATCGCCCAGGAAATTTTTTTAATA	1	26	1
TCAGAAGGAAGCTCACGAGCTTAGAAAATAT	4	168	1
          ***** *****
MAP Score: 6.12122

Motif 5
TTATTAATCTTAGCGAAAAATAAAAAGAGGGATGAT	0	21	0
TCAAAATTTCTTGGAAAAATTGTCAAATAGCAGGTC	0	190	0
GACTTAATATTGGGGCATATTAAAAAAATTTCCTGG	1	38	0
TGAATTAAAGTTGAATATATTACAAGATC       	4	3	0
TCGATTGGCATAGACTAGATTTTTAATGTTGGATCT	4	78	0
CTCACGAGCTTAGAAAATATTCAAAACTTGAAACTC	4	179	1
TGTTATAATCTTGATTATAATCCTAATCCTAGTTGC	4	222	1
CTAATCCTAGTTGCTTATATTCTCAAGTCATAAACA	4	244	1
          * **  *****   **
MAP Score: 6.04197

Motif 6
         GGGAAAAACTCATCATCCCTCTT	0	1	1
AACCGGGCCGGTTAAAAATTATAGAGAATTAT	0	57	0
GACAATTTTTCCAAGAAATTTTGAACAAAGTA	0	202	1
CACAAATAACCGAAGAACTTATATAGAATGCA	0	235	1
TCTTCATCGCCCAGGAAATTTTTTTAATATGC	1	28	1
TAAGTAATAACTTAAAAATCCTTAAAAGATCC	4	52	1
GATTTTTAATGTTGGATCTTTTAAGGATTTTT	4	65	0
AGAAGACAAGGTTAGAACTTATCAGAAGGAAG	4	147	1
AGCTCACGAGCTTAGAAAATATTCAAAACTTG	4	177	1
ATATTCAAAACTTGAAACTCTTTTTGTTGTTA	4	195	1
          * ******** *
MAP Score: 4.89101

Motif 7
AATCTTAGCGAAAAATAAAAAGAGGGATGAT	0	21	0
AATTTCTTGGAAAAATTGTCAAATAGCAGGT	0	191	0
AAATAACCGAAGAACTTATATAGAATGCATA	0	238	1
AAAGAAGGAGAAAGATTAAAAACC       	2	3	0
TAATTAAGTAATAACTTAAAAATCCTTAAAA	4	48	1
TTAAAAGATCCAACATTAAAAATCTAGTCTA	4	73	1
AGACAAGGTTAGAACTTATCAGAAGGAAGCT	4	150	1
AGGAAGCTCACGAGCTTAGAAAATATTCAAA	4	173	1
GAAAATATTCAAAACTTGAAACTCTTTTTGT	4	191	1
GGATTATAATCAAGATTATAACAACAAAAAG	4	214	0
CTCAAGTCATAAACACTATAAACCTAGATAA	4	265	1
          ******** **
MAP Score: 0.128031