AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_operons013_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944237860
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	ydaO	256	PP-Loop Superfamily ATPase
#1	CPn0379	153	CT053 hypothetical protein
#2	CPn0755	260	CT616 hypothetical protein
#3	rpoD	158	RNA Polymerase Sigma-66
#4	folX	53	Dihydroneopterin Aldolase
#5	CPn0767	101	CT645 hypothetical protein
#6	alaS	232	Alanyl tRNA Synthetase
#7	pssA	300	Glycerol-Serine Phosphatidyltransferase
#8	mesJ	118	PP-loop superfamily ATPase
#9	ftsH	187	ATP-dependent zinc protease

Motif 1
ATTATTCATTAAGTTTTTCTTCTTTTTATTAACGAGT	0	120	0
AAAAAAAAAAAAATCTTTGTTTTTTTTCTGCAGTTGA	1	72	1
TGTTGGCATAAAACTTTTTTTATTTCTCATAAATTCT	2	128	0
TATGAAGAGCAATTTATTCTTATTTTTGTTGATATAA	2	220	1
CTTATGTTTAAAGGCGTTTTTCTTTCTACTTTTTAAT	7	40	0
TTTTAGTTAAAAAACTTTCCTGTTTATTATTGAGATT	6	123	0
TATTCAATATAACATATTTTTTATTATTTTGTTTTAG	9	123	0
AGAGGACTGCAAAAACTTGTTGATTTTAGAAGAATCC	7	236	1
TCTGCTTCATAGCAAATTTTTATTTTTCAAAAAAAAA	1	44	1
GCAGGTGCATAGCATTTTTTTGTTTTTTCAACTGCAG	1	99	0
AGAGAAAGGAAAGCTTTTTCTTATTTTCGATACACAT	2	78	1
TCTTTGAGTAAAAGGTTCGTTTTTTATAGCCTTGTAT	4	10	1
CAAATGCAAAAACCTATTGCTTTTTTCTTTAACCTTG	0	74	1
TTTTCAAGAAAAACACATATTAATTATAATTAAGAGA	5	64	1
         CAGAGCAATATTTTTTATACAAGGCTAT	4	35	0
         AAAGTATATACTCATTATCTTCTCTATA	9	1	1
GTATTTTTTTAAGACCATTCTTATTGTTATGTTGGCA	2	157	0
TTTTAAAGAAAAATCCTTCTTATGTTTAAAGGCGTTT	7	58	0
ATGGATGGTTAAAGGAATATTATTCTTAAGAAATCGC	0	218	0
ACAAGGTAAGAGTTCCTTGCTTTTTGCTTGGGGATTT	6	54	0
TATTTCTCATAAATTCTCTTTTTTCTTAATATGTGTA	2	108	0
AATTGTTGGTAAGATATTGATTTTCGTCAGCGTATAA	3	44	1
          **    ** ** *** *
MAP Score: 28.9475

Motif 2
AACAAAGATTTTTTTTTTTTTGAAAAATAAA	1	62	0
CATAGCATTTTTTTGTTTTTTCAACTGCAGA	1	98	0
AAAAAAAAATCTTTGTTTTTTTTCTGCAGTT	1	76	1
TTCTCATAAATTCTCTTTTTTCTTAATATGT	2	111	0
TTCATTAAGTTTTTCTTCTTTTTATTAACGA	0	122	0
ATAACATATTTTTTATTATTTTGTTTTAGAA	9	121	0
AAGGAAAGCTTTTTCTTATTTTCGATACACA	2	83	1
GGCATAAAACTTTTTTTATTTCTCATAAATT	2	130	0
ACCTAGTGTTCTCTCTTTTTTTCACATATAG	9	33	0
TGATATAAGGATTTATTTTTT          	2	249	1
AAACCTATTGCTTTTTTCTTTAACCTTGGAA	0	83	1
GCCTGTTCATATTTTTTATTTGGCTGTTATA	9	76	1
TCATAGCAAATTTTTATTTTTCAAAAAAAAA	1	50	1
AAATAGCTGCCTTTATATTTTAAGAATTCTT	5	15	0
GAGCAATTTATTCTTATTTTTGTTGATATAA	2	226	1
TATAGGAGAGTTCTTTATTTTCGTCTCTATC	6	166	0
AGGCGTTTTTCTTTCTACTTTTTAATTATAA	7	35	0
          **** ******
MAP Score: 24.7404

Motif 3
TTATTTTTCAAAAAAAAAAAAATCTTTGTTTTTTT	1	63	1
GATAGAGACGAAAATAAAGAACTCTCCTATAATGG	6	166	1
AATTCTTTCAAAAACAAATGAATTTTCGATCAAAT	6	91	1
GGGTTTTTTAAAGAAAAATCCTTCTTATGTTTAAA	7	65	0
CCCCAAGCAAAAAGCAAGGAACTCTTACCTTGTAA	6	58	1
TTTAAGATTTAAAATAAACTGCTATTAATTGCAGA	2	34	1
        AAAAAATAAATCCTTATATCAACAAAA	2	243	0
ATTGAGAGAGAAAGGAAAGCTTTTTCTTATTTTCG	2	72	1
AATGGTCTTAAAAAAATACTTTTCTAATCAAATAG	2	175	1
AGCCTTGTATAAAAAATATTGCTCTG         	4	37	1
TACTTGGAATAAAACAAGGGGATTTCTAGCCTTAG	3	127	0
GGTTAAAGAAAAAAGCAATAGGTTTTTGCATTTGA	0	73	0
AAAAAGTAGAAAGAAAAACGCCTTTAAACATAAGA	7	43	1
GGATTCTTCTAAAATCAACAAGTTTTTGCAGTCCT	7	238	0
TAATTATAACAAAGGAAAAAGTACTCCAATATTT 	7	9	0
AACAAAAATAAGAATAAATTGCTCTTCATAGCCAT	2	215	0
CTCGTTAATAAAAAGAAGAAAAACTTAATGAATAA	0	121	1
GCTCTTTTTCAAGAAAAACACATATTAATTATAAT	5	59	1
GTCAGCGTATAAGATAAAAATCCCTAGATTTCCTA	3	69	1
CCTTCTATGTAAAAGCAGCAACTATAGGAAATCCC	6	26	1
TGGATGGTTAAAGGAATATTATTCTTAAGAAATCG	0	219	0
CTTAAAATATAAAGGCAGCTATTTTAATGGATAGA	5	22	1
ATATGTGAAAAAAAGAGAGAACACTAGGTCATTGT	9	35	1
TACACATATTAAGAAAAAAGAGAATTTATGAGAAA	2	108	1
CAAGGCTATAAAAAACGAACCTTTTACTCAAAGA 	4	9	0
          **** ***    ***
MAP Score: 22.2937

Motif 4
TTTTTATTTTTCAAAAAAAAAAAAATCTTTGTT	1	60	1
GATACACATATTAAGAAAAAAGAGAATTTATGA	2	106	1
CTAAAACAAAATAATAAAAAATATGTTATATTG	9	123	1
CGATCAAATCTCAATAATAAACAGGAAAGTTTT	6	117	1
CTAGTACTCGTTAATAAAAAGAAGAAAAACTTA	0	115	1
ATGTGTATCGAAAATAAGAAAAAGCTTTCCTTT	2	82	0
CTTTCCTCATAGAAGAAGAAATAGTA       	3	3	0
ATTATTTTGTTTTAGAAAAAATATTTTAAACTA	9	105	0
TTTATAGCCTTGTATAAAAAATATTGCTCTG  	4	32	1
AGAGAATTTATGAGAAATAAAAAAAGTTTTATG	2	126	1
TTATGCCAACATAACAATAAGAATGGTCTTAAA	2	154	1
CCTTATATCAACAAAAATAAGAATAAATTGCTC	2	226	0
TAATTATAACAAAGGAAAAAGTACTCCAATATT	7	11	0
TTCCAAGGTTAAAGAAAAAAGCAATAGGTTTTT	0	81	0
CTTCTCTATATGTGAAAAAAAGAGAGAACACTA	9	28	1
CTATAACAGCCAAATAAAAAATATGAACAGGCA	9	75	0
TCCTTTGTTATAATTAAAAAGTAGAAAGAAAAA	7	28	1
ATAAGAATGGTCTTAAAAAAATACTTTTCTAAT	2	170	1
TTTTTTCTGCAGTTGAAAAAACAAAAAAATGCT	1	93	1
ATATTGGGTTTTTTAAAGAAAAATCCTTCTTAT	7	72	0
AGAGGGCTCTTTTTCAAGAAAAACACATATTAA	5	54	1
AGGAAATCCCCAAGCAAAAAGCAAGGAACTCTT	6	51	1
          * ** ****** *
MAP Score: 21.0075

Motif 5
ATTGAGAGAGAAAGGAAAGCTTTTTCTTATTTTC	2	72	1
TCAATAATAAACAGGAAAGTTTTTTAACTAAAAA	6	127	1
GCCTTTAAACATAAGAAGGATTTTTCTTTAAAAA	7	62	1
         CAGAGCAATATTTTTTATACAAGGC	4	38	0
CCTTGCCATTATAGGAGAGTTCTTTATTTTCGTC	6	172	0
CTATTTGATTAGAAAAGTATTTTTTTAAGACCAT	2	176	0
TTTATGAGAAATAAAAAAAGTTTTATGCCAACAT	2	132	1
ATTTTGTTTTAGAAAAAATATTTTAAACTATAAC	9	101	0
ATCCTCTTCCACACAAGATCTTTTAGAAAAGTCT	0	13	1
TTTACCGAGAAAGGGAGCATTTTTCAATTGCAGG	7	156	0
TGCAGAAAAAAAACAAAGATTTTTTTTTTTTTGA	1	70	0
CAACATAACAATAAGAATGGTCTTAAAAAAATAC	2	160	1
TTAAAATATAAAGGCAGCTATTTTAATGGATAGA	5	23	1
AGAACTCTCAACGGCAGCGGTTTTGCAGATTCCT	6	203	0
TCTGCAATTAATAGCAGTTTATTTTAAATCTTAA	2	35	0
AAAATCATTGAAAAGAATAGTGTTGCTAGGGATT	8	78	0
TGTCTGCTTCATAGCAAATTTTTATTTTTCAAAA	1	42	1
AGGCTATAAAAAACGAACCTTTTACTCAAAGA  	4	8	0
ACATATTAAGAAAAAAGAGAATTTATGAGAAATA	2	111	1
      AAATATTGGAGTACTTTTTCCTTTGTTA	7	4	1
ATGGATGGTTAAAGGAATATTATTCTTAAGAAAT	0	221	0
ACTTGGAATAAAACAAGGGGATTTCTAGCCTTAG	3	127	0
TCTCCAGACAAGACAAGAACTTTAAGATTTAAAA	2	14	1
AAACAAAATAATAAAAAATATGTTATATTGAATA	9	126	1
ATTCTTTCAAAAACAAATGAATTTTCGATCAAAT	6	92	1
TTTTTCTTGAAAAAGAGCCCTCTATCCATTAAAA	5	43	0
TGTTGATTTTAGAAGAATCCATTATGCTACGAGC	7	253	1
          * *****   ****
MAP Score: 20.6201

Motif 6
ACAAAGATTTTTTTTTTTTTGAAAAATAAAAATTTG	1	56	0
AATTAATATGTGTTTTTCTTGAAAAAGAGCCCTCTA	5	53	0
TAGTTTAAAATATTTTTTCTAAAACAAAATAATAAA	9	105	1
AATTTATTCTTATTTTTGTTGATATAAGGATTTATT	2	230	1
TAGAGTATGATATTTTTACCGAGAAAGGGAGCATTT	7	168	0
ACATAAGAAGGATTTTTCTTTAAAAAACCCAATATG	7	70	1
AAACAGGAAAGTTTTTTAACTAAAAATTAGGGATAG	6	135	1
GTTAAAGGAATATTATTCTTAAGAAATCGCTGTTAA	0	212	0
ATAAAACTTTTTTTATTTCTCATAAATTCTCTTTTT	2	122	0
GAAAGCTTTTTCTTATTTTCGATACACATATTAAGA	2	86	1
TGTTGCTAGGGATTTTTCAAAACAGATCGTGACTCT	8	56	0
AATAAAAAAAGTTTTATGCCAACATAACAATAAGAA	2	141	1
AACGTTATGCGCTTATCTACCATATATAGGAATTGT	7	112	1
TCTTTCTACTTTTTAATTATAACAAAGGAAAAAGTA	7	21	0
AGCCATAAGTTCTATTTGATTAGAAAAGTATTTTTT	2	185	0
TGTTCTCTCTTTTTTTCACATATAGAGAAGATAATG	9	22	0
AAACTTTCCTGTTTATTATTGAGATTTGATCGAAAA	6	113	0
          * *****  * * * *
MAP Score: 17.5469

Motif 7
GGTTAAAGAAAAAAGCAATAGGTTTTTGCATTTGACTTTG	0	68	0
AATGTCTGCTTCATAGCAAATTTTTATTTTTCAAAAAAAA	1	40	1
GCAGAAAAAAAACAAAGATTTTTTTTTTTTTGAAAAATAA	1	63	0
ATTGATCTGCAATTAATAGCAGTTTATTTTAAATCTTAAA	2	34	0
CAATTGAGAGAGAAAGGAAAGCTTTTTCTTATTTTCGATA	2	70	1
GTTCTATTTGATTAGAAAAGTATTTTTTTAAGACCATTCT	2	173	0
TTATTTTTGTTGATATAAGGATTTATTTTTT         	2	239	1
TCTTAATTATAATTAATATGTGTTTTTCTTGAAAAAGAGC	5	59	0
GATTTGATCGAAAATTCATTTGTTTTTGAAAGAATTACAA	6	87	0
        AAATATTGGAGTACTTTTTCCTTTGTTATAAT	7	2	1
AATCCTTCTTATGTTTAAAGGCGTTTTTCTTTCTACTTTT	7	44	0
GGATTCTTCTAAAATCAACAAGTTTTTGCAGTCCTCTTGT	7	233	0
GCAACACTATTCTTTTCAATGATTTTTATATAGGCGTATA	8	86	1
TTGGCTGTTATAGTTTAAAATATTTTTTCTAAAACAAAAT	9	95	1
ATTATTCAATATAACATATTTTTTATTATTTTGTTTTAGA	9	122	0
          *  *   *    ***** **
MAP Score: 0.87349