AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_operons032_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944238471
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	ygbB	300	YgbB family hypothetical protein
#1	CPn0577	300	SWIB (YM74) complex protein
#2	yaeI	247	phosphohydrolase
#3	pgsA_1	300	Glycerol-3-P Phosphatidyltransferase
#4	pgsA_2	300	Glycerol-3-P Phosphatydyltransferase

Motif 1
ACTCAGTTATCATAGGAAAACATTCAGTTT	0	101	1
AATACTCCTTAATAGCAAAAAGAGAGGCGA	0	155	0
AAGATTCTAGAAAACAAAAGCCAATAAAGT	1	41	1
TTCTATGACTTAAACAAAAACCAAGACTTT	1	97	1
CTCTCCAAAAAGAAGAAAAAGTCTTGGTTT	1	114	0
AAGGGGAGTCTTTAGAAAAGATATAACAAA	1	151	0
ACGCTTTCTAAATAGAAAAGGTAAAGAGAA	1	182	1
GTTTCTCGTCAAAACAAAAAAGTGGAATTC	1	209	0
CTCTTTTCTTAATAGAAAAAACTCCATTTT	2	115	0
TATCACCTATAATAGGAAAATTCTTGGGCC	2	164	1
CTTTAAAAAGAATACGAAAAAGGGTGCGAA	3	131	0
TTTTCAATAATTTAGAAAAATTAGAAAATT	4	36	1
CTCTAAGCTAAATAGAAAATTTTCTAATTT	4	53	0
GGGTTCTCGATATACAAAAATGGATCATGC	4	88	1
GCAATTGATTTTAAGGAAAACACGACTTCC	4	120	1
TAAGTAAGCTAGAACAAAAAATACGCAGAC	4	205	1
          **********
MAP Score: 12.1773

Motif 2
CGAAGCACTCTCTTGAGAAATACTCCTTAA	0	173	0
TAATGCGTGAATTTTAGAAATTTTGTAGTA	0	235	1
TGAAAGAAATTCTTAAAAAAAACATATACC	0	272	1
AGCTTCTATGACTTAAACAAAAACCAAGAC	1	94	1
TCAAGGGGAGTCTTTAGAAAAGATATAACA	1	153	0
TTACCTTTTCTATTTAGAAAGCGTCAAGGG	1	176	0
GTTGACTTAGGCTTAAGAAAGCATGAGCTC	2	24	1
GAGTTTTTTCTATTAAGAAAAGAGGAATAC	2	121	1
TAATTTCCGGTCTTTAAAAACGAGAAACTT	2	208	0
TATTAGGCTTTCTTTAAAAAGAATACGAAA	3	142	0
TATTTTCAATAATTTAGAAAAATTAGAAAA	4	34	1
GAGCAATTGATTTTAAGGAAAACACGACTT	4	118	1
GTTCTAGCTTACTTAAGGAAACCCTATAGT	4	190	0
          **********
MAP Score: 11.431

Motif 3
TCTAGCCATTTGTACTCAGTTATCATAGGAAAACATTCAGTT	0	88	1
TTCTCAAGAGAGTGCTTCGATGTAGCGAGAAAGTTTGACAAA	0	184	1
ATTTTAGAAATTTTGTAGTATCTTCTGTGAAAGAAATTCTTA	0	245	1
TTGGCTTTTGTTTTCTAGAATCTTGATTGGAATCGTAGGTTG	1	23	0
AACCAAGACTTTTTCTTCTTTTTGGAGAGAAAGTTCTTTGTT	1	115	1
AGAGAATTCCACTTTTTTGTTTTGACGAGAAACCTCTCTGAG	1	206	1
CTTTTGAAGTATTCCTCTTTTCTTAATAGAAAAAACTCCATT	2	117	0
TTCAAAAGCTTAGTATCACCTATAATAGGAAAATTCTTGGGC	2	151	1
TCGCACCCTTTTTCGTATTCTTTTTAAAGAAAGCCTAATATA	3	132	1
ATTTTGGCTAACTAGTACGATCCTTTTAGGAACCTTATAATT	3	267	0
GCGTATTTTTTGTTCTAGCTTACTTAAGGAAACCCTATAGTT	4	189	0
TGTCCATGAGATGAGTGCCTTACTAAGAGGAAAGCACTGAAA	4	240	0
          * * **    * *     ****
MAP Score: 9.26317

Motif 4
TTCGCCTCTCTTTTTGCTATTAAGGAGTATT	0	154	1
AGCGAGAAAGTTTGACAAATTACTGGAATAA	0	207	1
TACTACAAAATTTCTAAAATTCACGCATTAT	0	234	0
TTTTAGAAATTTTGTAGTATCTTCTGTGAAA	0	246	1
TATATGTTTTTTTTAAGAATTTCTTTCACAG	0	269	0
TGGCTTTTGTTTTCTAGAATCTTGATTGGAA	1	33	0
ACCAAGACTTTTTCTTCTTTTTGGAGAGAAA	1	116	1
GAGAAAGTTCTTTGTTATATCTTTTCTAAAG	1	141	1
AGAATTCCACTTTTTTGTTTTGACGAGAAAC	1	208	1
TCATCCCAACTTTTTTATCTCTCAGAGAGGT	1	237	0
TAAAATGGAGTTTTTTCTATTAAGAAAAGAG	2	114	1
ATACTAAGCTTTTGAAGTATTCCTCTTTTCT	2	136	0
TAGTCTCAAGTTTCTCGTTTTTAAAGACCGG	2	201	1
GTTCGCACCCTTTTTCGTATTCTTTTTAAAG	3	130	1
GCTCAAACGGTTTCTCATCTTGCAACTGTTC	3	189	0
TCTATGCTTGTTTGTAGATTTAGCATGCTCT	3	224	1
AATAGAAAATTTTCTAATTTTTCTAAATTAT	4	42	0
          ***** *****
MAP Score: 9.19229

Motif 5
TTAGAAAATTTTCTATTTAGCTTAGAGCAAGAGGGT	4	56	1
TATTCCTCTTTTCTTAATAGAAAAAACTCCATTTTA	2	114	0
AGCAAGAGGGTTCTCGATATACAAAAATGGATCATG	4	81	1
CTTTTTCGTATTCTTTTTAAAGAAAGCCTAATATAT	3	139	1
CCTTGACGCTTTCTAAATAGAAAAGGTAAAGAGAAT	1	177	1
TGAGAAATACTCCTTAATAGCAAAAAGAGAGGCGAA	0	154	0
AGTCTCAAGTTTCTCGTTTTTAAAGACCGGAAATTA	2	202	1
CCAAGACTTTTTCTTCTTTTTGGAGAGAAAGTTCTT	1	117	1
ATAGAAAATTTTCTAATTTTTCTAAATTATTGAAAA	4	36	0
TCAGAGAGGTTTCTCGTCAAAACAAAAAAGTGGAAT	1	211	0
AAAAGGATCGTACTAGTTAGCCAAAATT        	3	282	1
CCAATCAAGATTCTAGAAAACAAAAGCCAATAAAGT	1	35	1
AAACACGACTTCCTTTTAAATTCAAAGTTATCCTCG	4	137	1
AAGGGCAGGGTACTTAACATATCAGAATGAGAGCTC	2	48	0
          ****  ***    ***
MAP Score: 8.63421

Motif 6
TTCGCCTCTCTTTTTGCTATTAAGGAGTATTTCTC	0	154	1
AATTTTGTAGTATCTTCTGTGAAAGAAATTCTTAA	0	253	1
ACCTGGTATATGTTTTTTTTAAGAATTTCTTTCAC	0	271	0
CAAGACTTTTTCTTCTTTTTGGAGAGAAAGTTCTT	1	118	1
TTCTTTGTTATATCTTTTCTAAAGACTCCCCTTGA	1	148	1
TCTCTTTACCTTTTCTATTTAGAAAGCGTCAAGGG	1	176	0
AGAATTCCACTTTTTTGTTTTGACGAGAAACCTCT	1	208	1
ATCCCAACTTTTTTATCTCTCAGAGAGGTTTCTCG	1	231	0
TAAAATGGAGTTTTTTCTATTAAGAAAAGAGGAAT	2	114	1
GTCTCAAGTTTCTCGTTTTTAAAGACCGGAAATTA	2	203	1
CCCTTTTTCGTATTCTTTTTAAAGAAAGCCTAATA	3	137	1
CATGATCCATTTTTGTATATCGAGAACCCTCTTGC	4	82	0
          * ** * * * ****
MAP Score: 8.42109

Motif 7
GTATTTCTCAAGAGAGTGCTTCGATGTAGC	0	180	1
CGATGTAGCGAGAAAGTTTGACAAATTACT	0	201	1
CTTTTTGGAGAGAAAGTTCTTTGTTATATC	1	132	1
GAAAAGGTAAAGAGAATTCCACTTTTTTGT	1	196	1
TATCTCTCAGAGAGGTTTCTCGTCAAAACA	1	223	0
TAAAGGGTACCGAGGGTTCGAATCCCTCTC	3	58	1
AGAATACGAAAAAGGGTGCGAACTACAACT	3	123	0
ACAAACAAGCATAGAGTTCGCTCAAACGGT	3	209	0
GGGCCGAATTATAAGGTTCCTAAAAGGATC	3	261	1
GCTTAGAGCAAGAGGGTTCTCGATATACAA	4	75	1
TAAAATAACTATAGGGTTTCCTTAAGTAAG	4	183	1
CTCCCCTAATATATGGTTCTTGTCTGTCCA	4	276	0
          **********
MAP Score: 5.98327

Motif 8
GGTTATGGCCAGAGCCGGGATCGAACCGACGAC	0	17	1
CTCAGATGGTAGAGCAGAGGATTGAAGATCCTT	0	52	0
TAGCAAAAAGAGAGGCGAAGAATTCGAAATCTC	0	140	0
AAAGTCAATTAGAGCAAGGACTTCCTAGAGCTT	1	66	1
TGGTAAGAAGAGACCTGAGCTCTTCATCCCAAC	1	258	0
CCCGCCCTAAAGGGCAGGGTACTTAACATATCA	2	60	0
CCTGCCCTTTAGGGCGGGGATATAAAGTGATCT	2	75	1
ACTATTTATGGGGCCCAAGAATTTTCCTATTAT	2	172	0
ATGTCAATGTAGAGCCGAACAGTTGCAAGATGA	3	173	1
GCTCTATAATGGGGCCGAATTATAAGGTTCCTA	3	250	1
TATTTAGCTTAGAGCAAGAGGGTTCTCGATATA	4	69	1
TGCCTTACTAAGAGGAAAGCACTGAAATCACAG	4	234	0
          *********   *
MAP Score: 5.48399

Motif 9
ATATTAAACTGAATGTTTTCCTATGATAACT	0	105	0
GTAATTTGTCAAACTTTCTCGCTACATCGAA	0	199	0
ATATAACAAAGAACTTTCTCTCCAAAAAGAA	1	130	0
ATCTCTCAGAGAGGTTTCTCGTCAAAACAAA	1	221	0
         GGAATTTGTTCGCTGTTGACTT	2	1	1
ATTTAAAATGGAGTTTTTTCTATTAAGAAAA	2	111	1
TAAATAGTCTCAAGTTTCTCGTTTTTAAAGA	2	197	1
AGCCAAGGTAGAGGTTATTCGGAAAGAGAGG	3	82	0
AAGCTAAATAGAAAATTTTCTAATTTTTCTA	4	48	0
CTTAGAGCAAGAGGGTTCTCGATATACAAAA	4	76	1
          *** *******
MAP Score: 5.17519

Motif 10
TAATAGCAAAAAGAGAGGCGAAGAATTCGAAATC	0	142	0
TCTTCTGTGAAAGAAATTCTTAAAAAAAACATAT	0	265	1
GATTCTAGAAAACAAAAGCCAATAAAGTCAATTA	1	43	1
CAATTAGAGCAAGGACTTCCTAGAGCTTCTATGA	1	71	1
CTATGACTTAAACAAAAACCAAGACTTTTTCTTC	1	99	1
CTTTCTTTAAAAAGAATACGAAAAAGGGTGCGAA	3	131	0
ATTCTTTTTAAAGAAAGCCTAATATATGTCAATG	3	148	1
TAGCTTACTTAAGGAAACCCTATAGTTATTTTAT	4	182	0
AAGCTAGAACAAAAAATACGCAGACTGTGATTTC	4	210	1
          ******  ** * *
MAP Score: 4.49433

Motif 11
TTTTTGTTTTGACGAGAAACCTCTCTGAGA	1	219	1
GGTCTTTAAAAACGAGAAACTTGAGACTAT	2	200	0
CCCTGCTAAGGACGCGTACCCCTAAAGGGT	3	36	1
GAAAGAGAGGGATTCGAACCCTCGGTACCC	3	62	0
ACAGTTGCAAGATGAGAAACCGTTTGAGCG	3	191	1
CTCATGGACAGACAAGAACCATATATTAGG	4	272	1
          **********
MAP Score: 2.85588

Motif 12
ATGAGATTTCGAATTCTTCGCCTCTCTTTTTGC	0	138	1
TCGCTACATCGAAGCACTCTCTTGAGAAATACT	0	179	0
GAAGCTCTAGGAAGTCCTTGCTCTAATTGACTT	1	67	0
AAGGTAAAGAGAATTCCACTTTTTTGTTTTGAC	1	199	1
GATATGTTAAGTACCCTGCCCTTTAGGGCGGGG	2	61	1
AGCTTTTGAAGTATTCCTCTTTTCTTAATAGAA	2	128	0
CCGAGGGTTCGAATCCCTCTCTTTCCGAATAAC	3	67	1
CCGTTTGAGCGAACTCTATGCTTGTTTGTAGAT	3	210	1
          *** *** * ***
MAP Score: 0.979451

Motif 13
GAATTCTTCGCCTCTCTTTTTGCTATTAAGGA	0	148	1
AAAGAGAATTCCACTTTTTTGTTTTGACGAGA	1	204	1
TGACGAGAAACCTCTCTGAGAGATAAAAAAGT	1	228	1
GAAAGCATGAGCTCTCATTCTGATATGTTAAG	2	40	1
GTACTTTCGACCACTCAGTCATCT        	3	2	0
GGTTCGAATCCCTCTCTTTCCGAATAACCTCT	3	72	1
TCAGTGCTTTCCTCTTAGTAAGGCACTCATCT	4	242	1
          *********  *
MAP Score: 0.961301