AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_operons013_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944255871
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PH0822	159	121aa long hypothetical protein
#1	PH0880	112	116aa long hypothetical protein
#2	PH0896	300	295aa long hypothetical cation efflux system protein czcD
#3	PH0981	62	309aa long hypothetical protein
#4	PH0982	61	286aa long hypothetical protein
#5	PH1078	293	450aa long hypothetical fmu protein
#6	PH1079	24	221aa long hypothetical protein
#7	PH1227	117	189aa long hypothetical protein

Motif 1
TACTGGGCAAAAATGTGTAACTAAAGACAAGTTT	0	72	1
ATCTATGAAAAAATGCTCATATAAATAAACCTTT	0	124	0
TTTGCCTTTGAAAGGAGCTCCTTAACCTCTTCTT	2	117	1
TTAAATTTATTTAGGCTTACCTAATCGTGGTGAT	3	35	1
TTTAAAAACGTTAGGCTAACCTAATTCTAGGAGG	4	30	1
CTCAGGGTGAAGAAGGGGAGCTAATGAAAGGGAC	5	13	0
TTCTTCACCCTGAGGAGGAGATAATTAGGATCGT	5	33	1
CCGTCTTCAAACAGGCTCTTCTTAACGATCCTAA	5	57	0
TGTTAGGATTTTATGATTTGCTAAAAGCTATGAA	5	126	1
         GTTAGGGTATCCTAACTTTAATTC 	6	1	1
TCACCCGGAATTAGGTGGCCCTAACAAGTTATAT	7	16	1
CAAAATTTTGAGAGGTGGTGATAA          	7	103	1
          * *** * * ****
MAP Score: 12.0167

Motif 2
GGCAAATAAGCTTTTTCCATTTATCATTCCGA	1	38	0
ATGGAAAAAGCTTATTTGCCATCTAAAATTCT	1	50	1
ATAGGATAATCTTCTCTCCCTTCTTTACCTTC	2	85	1
CCTTCTTTACCTTCTTTGCCTTTGAAAGGAGC	2	103	1
TCCTTAACCTCTTCTTCAACTTCCTCTTTCTT	2	135	1
TGTTTGAAAACTTTTTTTATATTACTTCACTT	2	258	1
TTTTATATTACTTCACTTCCATAAAGTGGGGG	2	272	1
        CCCTTCACCTCCTAGAATTAGGTT	4	47	0
ATTAGCTCCCCTTCTTCACCCTGAGGAGGAGA	5	22	1
ATTTCGGGCCCTTTTCCTCTGTTCATAGCTTT	5	149	0
ACATCATTATCTTATCCCCTATCTCGACTATT	5	178	0
GAAGTTGGGTCTTGACTACTATCCCTCAACCC	5	217	1
          ******* ** *
MAP Score: 11.4645

Motif 3
GGTAAAGAAGGGAGAGAAGATTATCCTATT	2	84	0
AAAGGCAAAGAAGGTAAAGAAGGGAGAGAA	2	96	0
AGTTGAAGAAGAGGTTAAGGAGCTCCTTTC	2	126	0
AAGAAAGAGGAAGTTGAAGAAGAGGTTAAG	2	137	0
CCACTTTATGGAAGTGAAGTAATATAAAAA	2	271	0
TCACTTCCATAAAGTGGGGGATCAAA    	2	284	1
CTAATTCTAGGAGGTGAAGGG         	4	50	1
TCTCCTCCTCAGGGTGAAGAAGGGGAGCTA	5	24	0
TCTTCACCCTGAGGAGGAGATAATTAGGAT	5	34	1
GCTATGAACAGAGGAAAAGGGCCCGAAATA	5	152	1
AGTCGAGATAGGGGATAAGATAATGATGTA	5	181	1
ATTATATCCTGGGTTGAGGGATAGTAGTCA	5	229	0
     GAATTAAAGTTAGGATACCCTAAC 	6	9	0
CACCTAATTCCGGGTGAGGAGTT       	7	3	0
AAAATTTTGAGAGGTGGTGATAA       	7	104	1
          **********
MAP Score: 10.8191

Motif 4
TGACATATAAAGGAAATGTAAAATGAAAATTA	0	16	0
AGATATATCGAACACATTTAAACTTTACTGGG	0	47	1
TTCATAACTTAGGTCATTTAAACTTGTCTTTA	0	93	0
TAAATGACCTAAGTTATGAAAAGGTTTATTTA	0	105	1
GTAATCGCCCAATCTATGAAAAAATGCTCATA	0	137	0
AGTTCCAGAAAATGCATAAAAAAGGAAATCGG	1	10	1
GATGGCAAATAAGCTTTTTCCATTTATCATTC	1	41	0
TTACAACCGAAAGGCATTTCAATCGCCAGCCC	2	186	1
CTGACTACTTAATGTTTGAAAACTTTTTTTAT	2	246	1
TATGGAAGTGAAGTAATATAAAAAAAGTTTTC	2	263	0
GGTAAGCCTAAATAAATTTAAAGCTTGACCAA	3	24	0
AGGTTAGCCTAACGTTTTTAAACGTTGTGCAT	4	20	0
AAAATTTCCCCAGGTTTTTCAAGAAGGCCGTC	5	86	0
GATTTGCTAAAAGCTATGAACAGAGGAAAAGG	5	140	1
GTAGGCTAGAAAGCATTATAAAACCAATGTCA	5	260	1
TGGCCCTAACAAGTTATATAAGGTTTATTAGA	7	31	1
TGCATATGCACAGATATATAAAGTTTTCGACT	7	71	0
          *** *** ****
MAP Score: 7.43752

Motif 5
CAAAGAAGGTAAAGAAGGGAGAGAAGATTA	2	91	0
AGAGGAAGTTGAAGAAGAGGTTAAGGAGCT	2	132	0
AAAGATGATAAAGAAAGAGGAAGTTGAAGA	2	147	0
TCACTTCCATAAAGTGGGGGATCAAA    	2	284	1
CTAATTCTAGGAGGTGAAGGG         	4	50	1
CCTCAGGGTGAAGAAGGGGAGCTAATGAAA	5	18	0
TCTTCACCCTGAGGAGGAGATAATTAGGAT	5	34	1
GCTATGAACAGAGGAAAAGGGCCCGAAATA	5	152	1
CGAAATAGTCGAGATAGGGGATAAGATAAT	5	175	1
AAAATTTTGAGAGGTGGTGATAA       	7	104	1
          **********
MAP Score: 6.54255

Motif 6
ATTTTTGCCCAGTAAAGTTTAAATGTGTTCGATATATCT	0	47	0
GTTTAAATGACCTAAGTTATGAAAAGGTTTATTTATATG	0	102	1
   GTAATCGCCCAATCTATGAAAAAATGCTCATATAAA	0	133	0
GCTCTGACTACTTAATGTTTGAAAACTTTTTTTATATTA	2	243	1
TTTTGGTTTGGTCAAGCTTTAAATTTATTTAGGCTTACC	3	17	1
TGTGCATATGCACAACGTTTAAAAACGTTAGGCTAACCT	4	13	1
AAAAACCTGGGGAAATTTTTCAAGCTGTGTTAGGATTTT	5	99	1
AGGTGGCCCTAACAAGTTATATAAGGTTTATTAGAATTA	7	28	1
TTAGGCCAGTCGAAAACTTTATATATCTGTGCATATGCA	7	64	1
TGTGCATATGCACAAAATTTTGAGAGGTGGTGATAA   	7	91	1
          *  **  *** **    **
MAP Score: 5.47187

Motif 7
AAGTTATGAAAAGGTTTATTTATATGAGCATTTTT	0	115	1
GATGGCAAATAAGCTTTTTCCATTTATCATTCCGA	1	38	0
GGAGGATGTTCCACTTGATGAAGTTGATATCGATA	2	19	0
GTAGTCAGAGCAAATTGGTAAAAGTCAAAATAATG	2	219	0
TAATGTTTGAAAACTTTTTTTATATTACTTCACTT	2	255	1
 TTTGATCCCCCACTTTATGGAAGTGAAGTAATAT	2	276	0
TAACGTTTTTAAACGTTGTGCATATGCACAATA  	4	8	0
AAAACCTGGGGAAATTTTTCAAGCTGTGTTAGGAT	5	100	1
TAATTCTAATAAACCTTATATAACTTGTTAGGGCC	7	32	0
GGCCAGTCGAAAACTTTATATATCTGTGCATATGC	7	67	1
CCACCTCTCAAAATTTTGTGCATATGCACAGATAT	7	86	0
          ******* *  *  *
MAP Score: 2.06311