AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_operons026_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944256391
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PH1107	299	299aa long hypothetical protein
#1	PH1516	149	303aa long hypothetical dihydroorotate dehydrogenase
#2	PH1517	93	460aa long hypothetical protein
#3	PH1739	113	212aa long hypothetical protein

Motif 1
CTACCGGAATTACCTCCACTAGATCTCCAT	0	62	1
ACCTCCACTAGATCTCCATCCCTGACCTCC	0	73	1
CTCCATCCCTGACCTCCTTTTCTTCTAACG	0	86	1
TATTAAAGCCGACCTCCCTCAGAATATCCT	0	152	1
GAATATCCTTTACCTTCATTCCTTCTCTCC	0	173	1
CTTCATTCCTTCTCTCCATTTGATCTCTTT	0	186	1
CTCTCCATTTGATCTCTTTCTCTATTCCCC	0	197	1
     TATTTTATCTCCCTCTATCAGGATA	1	5	1
TATAAGATAAGGCCTCCCTTTAATAGAATT	1	65	1
CCTCCCAGGATCTTTCCATTTTTGATTTTT	2	66	0
TAGTTAAAAGGATTTCCATCCACCCGGAAC	3	49	0
          **********
MAP Score: 13.9812

Motif 2
TTAGAAGAAAAGGAGGTCAGGGATGGAGATCTAGTGG	0	77	0
GTGCGATAGCAAAAGTAAATGGAAAAGTAGCGTTAGA	0	109	0
AGAGATCAAATGGAGAGAAGGAATGAAGGTAAAGGAT	0	177	0
GATAAGGGTGAAAGTGATTGGAAGGGGAATAGAGAAA	0	213	0
CACCTCCTTAAAAATGAGGGGGTTGAGATGATAAGGG	0	242	0
CTCATTTTTAAGGAGGTGAGGATAAAAATATTCTCTG	0	261	1
ATTATCGACATAATGAGACGGGAAAAGTTATAACATT	2	24	1
TCAAAAATGGAAAGATCCTGGGAGGGATAAAA     	2	71	1
ATAGGGTAGAAAAGGACTAGGGAAGAAA         	3	1	0
GGAACCTTTATGAAGGATAGGGTAGAAAAGGACTAGG	3	17	0
TATCCTTCATAAAGGTTCCGGGTGGATGGAAATCCTT	3	35	1
GGTAAATGTCAAGCTAATTGGGGGGAGTGAA      	3	92	1
          *** *    ***  ***
MAP Score: 9.59182

Motif 3
ACTACCGGAATTACCTCCACTAGATCTCCAT	0	61	1
TCCACTAGATCTCCATCCCTGACCTCCTTTT	0	76	1
GTATTAAAGCCGACCTCCCTCAGAATATCCT	0	151	1
AGAATATCCTTTACCTTCATTCCTTCTCTCC	0	172	1
CCTTCATTCCTTCTCTCCATTTGATCTCTTT	0	185	1
TGATCTCTTTCTCTATTCCCCTTCCAATCAC	0	206	1
CCCTTATCATCTCAACCCCCTCATTTTTAAG	0	242	1
TATTTTTATCCTCACCTCCTTAAAAATGAGG	0	260	0
      TATTTTATCTCCCTCTATCAGGATA	1	4	1
TTAAAAGGATTTCCATCCACCCGGAACCTTT	3	45	0
          TTCACTCCCCCCAATTAGCTT	3	102	0
          *** *******
MAP Score: 9.54041

Motif 4
TCCACTAGATCTCCATCCCTGACCTCCTTTTCTTCTA	0	76	1
CCCTAGTCCTTTTCTACCCTATCCTTCATAAAGGTTC	3	16	1
TCCATTTGATCTCTTTCTCTATTCCCCTTCCAATCAC	0	200	1
CTTCCAATCACTTTCACCCTTATCATCTCAACCCCCT	0	226	1
CCAGAGAATATTTTTATCCTCACCTCCTTAAAAATGA	0	262	0
TCGACAAATGTTATAACTTTTCCCGTCTCATTATGTC	2	30	0
TATCCTTTACCTTCATTCCTTCTCTCCATTTGATCTC	0	176	1
CCTCCAGAAACTACCGGAATTACCTCCACTAGATCTC	0	52	1
CCTCCTTTTCTTCTAACGCTACTTTTCCATTTACTTT	0	98	1
GATAAAAATATTCTCTGGTTGATCCTCT         	0	281	1
        TATTTTATCTCCCTCTATCAGGATATCAG	1	2	1
TTTTAACTAGTTAAAAGGATTTCCATCCACCCGGAAC	3	49	0
TTTCCATTTACTTTTGCTATCGCACTCTCAGTATTAA	0	121	1
          ** *  * **  ** **
MAP Score: 9.10135

Motif 5
CCACTAGATCTCCATCCCTGACCTCCTTTTC	0	77	1
ATCCCTGACCTCCTTTTCTTCTAACGCTACT	0	90	1
TCTAACGCTACTTTTCCATTTACTTTTGCTA	0	109	1
CTCAGAATATCCTTTACCTTCATTCCTTCTC	0	169	1
TTACCTTCATTCCTTCTCTCCATTTGATCTC	0	182	1
CCATTTGATCTCTTTCTCTATTCCCCTTCCA	0	201	1
TTCTCTATTCCCCTTCCAATCACTTTCACCC	0	214	1
ATCACTTTCACCCTTATCATCTCAACCCCCT	0	232	1
AATATTTTTATCCTCACCTCCTTAAAAATGA	0	262	0
AATGTTATAACTTTTCCCGTCTCATTATGTC	2	30	0
CCTCCCAGGATCTTTCCATTTTTGATTTTTC	2	65	0
         TTTTATCCCTCCCAGGATCTTT	2	81	0
         TTTCTTCCCTAGTCCTTTTCTA	3	1	1
TCTTCCCTAGTCCTTTTCTACCCTATCCTTC	3	12	1
          ********* *
MAP Score: 6.69423

Motif 6
AACTACCGGAATTACCTCCACTAGATCTCC	0	60	1
TCCACTAGATCTCCATCCCTGACCTCCTTT	0	76	1
CATCCCTGACCTCCTTTTCTTCTAACGCTA	0	89	1
CAGAATATCCTTTACCTTCATTCCTTCTCT	0	171	1
ACCTTCATTCCTTCTCTCCATTTGATCTCT	0	184	1
TCTCCATTTGATCTCTTTCTCTATTCCCCT	0	198	1
TCTTTCTCTATTCCCCTTCCAATCACTTTC	0	211	1
TCCCCTTCCAATCACTTTCACCCTTATCAT	0	222	1
TTTCACCCTTATCATCTCAACCCCCTCATT	0	237	1
TATTTTTATCCTCACCTCCTTAAAAATGAG	0	261	0
    TATTTTATCTCCCTCTATCAGGATAT	1	6	1
AAGATAAGGCCTCCCTTTAATAGAATTGAC	1	68	1
      TTTTATCCCTCCCAGGATCTTTCC	2	79	0
GTGGATGGAAATCCTTTTAACTAGTTAAAA	3	56	1
      TTCACTCCCCCCAATTAGCTTGAC	3	99	0
          **********
MAP Score: 5.91743

Motif 7
AAGGAGGTCAGGGATGGAGATCTAGTGGAGGTAATTCCGGTAGT	0	61	0
CTGAGAGTGCGATAGCAAAAGTAAATGGAAAAGTAGCGTTAGAA	0	108	0
ATCAAATGGAGAGAAGGAATGAAGGTAAAGGATATTCTGAGGGA	0	166	0
TGATAAGGGTGAAAGTGATTGGAAGGGGAATAGAGAAAGAGATC	0	207	0
TCTCAACCCCCTCATTTTTAAGGAGGTGAGGATAAAAATATTCT	0	251	1
CCTCTATCAGGATATCAGCCCTAGTTGGATGATAGCTGGTATCA	1	21	1
GATCTGACTTGTCAATTCTATTAAAGGGAGGCCTTATCTTATAT	1	64	0
AGTTATTATCGACATAATGAGACGGGAAAAGTTATAACATTTGT	2	20	1
AATCAAAAATGGAAAGATCCTGGGAGGGATAAAA          	2	69	1
TGAAGGATAGGGTAGAAAAGGACTAGGGAAGAAA          	3	0	0
CCCTATCCTTCATAAAGGTTCCGGGTGGATGGAAATCCTTTTAA	3	32	1
TTTGGTAAATGTCAAGCTAATTGGGGGGAGTGAA          	3	89	1
          *  *         ****** *  *
MAP Score: 5.55699