AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_operons027_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944256402
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PH0114	40	316aa long hypothetical molybdenum cofactor biosynthesis protein
#1	PH0115	298	296aa long hypothetical protein
#2	PH0184	54	149aa long hypothetical molybdopterinconverting factor, subunit
#3	PH0827	135	552aa long hypothetical nitrite reductase
#4	PH1615	61	420aa long hypothetical protein
#5	PH1811	84	159aa long hypothetical molybdenum cofactor biosynthesis protein

Motif 1
TTAGCGCATGACTTATATTTTTAACAATATCT	0	15	1
AAATAGCATCCCTTGACCCCTTTGCAATTTCT	1	21	1
CCCACCGAGACTTTGAAAATTTGATTCCAGAA	1	49	0
AATCTCTGATCCTTCTCAACTTCTCCTTCAAC	1	81	1
CTCAACTTCTCCTTCAACTCTGCAACCCCAAA	1	95	1
GGCAATATTAATTTAACTTCTTTTGCTTAAAT	1	132	0
CGGAGAAAATCCTTCAACTTTTAAAATCTCAA	1	228	1
TATTTAAGTTCCTTGAAATTTAAGATTAGCGG	2	18	0
ATTTCAAGGAACTTAAATATGTTGGGATGAGG	2	31	1
CCCCAATACTATTTAAATTTTTCGGATATATT	3	36	1
AAGGTTAAGACCTAAAAAGCTTTGTCTCTACA	4	29	1
AAAGTTTAGAACTTAAAAACTTTCAAGTAAAT	5	20	1
TCAAGTAAATACTAAAAGTCTTTAATCCTTTA	5	42	1
          *******  ***
MAP Score: 8.00581

Motif 2
TTAGCGCATGACTTATATTTTTAACAATATCTTC	0	15	1
AGAGATTCCCACCGAGACTTTGAAAATTTGATTC	1	54	0
CTCAACTTCTCCTTCAACTCTGCAACCCCAAAAT	1	95	1
AACTCTGCAACCCCAAAATGTTATTTAAGCAAAA	1	110	1
CGGAGAAAATCCTTCAACTTTTAAAATCTCAAAA	1	228	1
   TCTCCTTCCCGCTAATCTTAAATTTCAAGGA	2	7	1
   CCCTCATCCCAACATATTTAAGTTCCTTGAA	2	33	0
ATACCTCCTCCCCAATACTATTTAAATTTTTCGG	3	27	1
TTAGTATTTACTTGAAAGTTTTTAAGTTCTAAAC	5	23	0
TCAAGTAAATACTAAAAGTCTTTAATCCTTTACT	5	42	1
          *** * * * ****
MAP Score: 6.77536

Motif 3
AGAAGTTGAGAAGGATCAGAGATTCCCACCGAGACT	1	69	0
AGTTTATCACAAGGAACAGAACAAGCTAAACAGGGG	3	105	1
  CTCGCCCAGATGTAGAGACAAAGCTTTTTAGGTC	4	37	0
AAACCTGTTAGATGGAAAGAGAAGGCCTATAAGAGA	1	259	1
CAAGAAAAGTGAAGCGGAGAAAATCCTTCAACTTTT	1	214	1
GATAAACTTTATGGTTGAGATATGTCAGATATTTTT	3	77	0
CTTACTGAAGAAGGTTAAGACCTAAAAAGCTTTGTC	4	19	1
GGTTAAAAGAAAAGTTTAGAACTTAAAAACTTTCAA	5	10	1
AATTTTTCGGATATATTAGATATGTCAAAAATATCT	3	51	1
          ****   *** **  *
MAP Score: 4.44907

Motif 4
CCTTTTGAAGAGGCGATATGGGGAGGCCTCGGGGT	1	163	1
AAAACCTGTTAGATGGAAAGAGAAGGCCTATAAGA	1	258	1
GAAATTGCAAAGGGGTCAAGGGATGCTATTTCAAA	1	17	0
AAATTTAAATAGTATTGGGGAGGAGGTATTATCGA	3	21	0
CTTGAAATTTAAGATTAGCGGGAAGGAGA      	2	4	0
AAAAGCCAAGAAAAGTGAAGCGGAGAAAATCCTTC	1	208	1
AAATTTTCAAAGTCTCGGTGGGAATCTCTGATCCT	1	59	1
GAGAAGGCCTATAAGAGATGGGGATTACGTT    	1	277	1
AGGAACTTAAATATGTTGGGATGAGGG        	2	37	1
          **  *  * ******
MAP Score: 4.00113

Motif 5
GGGTTGCAGAGTTGAAGGAGAAGTTGAGAAGGATCAGAGA	1	83	0
CCAAAATGTTATTTAAGCAAAAGAAGTTAAATTAATATTG	1	122	1
CTCGGGGTTGGTTGGGGTAAAAGCCAAGAAAAGTGAAGCG	1	190	1
CTCAAAACCTGTTAGATGGAAAGAGAAGGCCTATAAGAGA	1	255	1
CAACCATAAAGTTTATCACAAGGAACAGAACAAGCTAAAC	3	96	1
         GGTTAAAAGAAAAGTTTAGAACTTAAAAACT	5	1	1
GACTTTTAGTATTTACTTGAAAGTTTTTAAGTTCTAAACT	5	22	0
          ***      ****    ***
MAP Score: 3.28615

Motif 6
GCAACCCCAAAATGTTATTTAAGCAAAAGAAGTTAAATTA	1	116	1
AAAGCCAAGAAAAGTGAAGCGGAGAAAATCCTTCAACTTT	1	209	1
AAAATCCTTCAACTTTTAAAATCTCAAAACCTGTTAGATG	1	233	1
GCTAATCTTAAATTTCAAGGAACTTAAATATGTTGGGATG	2	20	1
TCTCAACCATAAAGTTTATCACAAGGAACAGAACAAGCTA	3	93	1
CTTACTGAAGAAGGTTAAGACCTAAAAAGCTTTGTCTCTA	4	19	1
GGTTAAAAGAAAAGTTTAGAACTTAAAAACTTTCAAGTAA	5	10	1
          ** ** **       *** *
MAP Score: 0.510569

Motif 7
TTAAAAATATAAGTCATGCGCTAACAAAA  	0	8	0
ATTCCAGAAATTGCAAAGGGGTCAAGGGATG	1	27	0
CAAATTTTCAAAGTCTCGGTGGGAATCTCTG	1	58	1
CGATATGGGGAGGCCTCGGGGTTGGTTGGGG	1	176	1
AAGCCAAGAAAAGTGAAGCGGAGAAAATCCT	1	210	1
GAAGGCCTATAAGAGATGGGGATTACGTT  	1	279	1
CTTGAAATTTAAGATTAGCGGGAAGGAGA  	2	8	0
AAAATTTAAATAGTATTGGGGAGGAGGTATT	3	26	0
CAGAACAAGCTAAACAGGGGGGTA       	3	121	1
TAACCTTCTTCAGTAAGGGGTTTGAC     	4	5	0
TCCTTTACTGTACTCTTGGGGATTCTT    	5	67	1
          ****** ****
MAP Score: 0.323331