AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_operons009_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944237604
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	ybaB	64	YbaB family hypothetical protein
#1	dnaX_1	300	DNA Polymerase III Gamma and Tau
#2	uvrA	240	Excinuclease ABC Subunit A
#3	CPn0276	263	CT191 hypothetical protein
#4	recR	94	Recombination Protein
#5	yaeT	300	Omp85 Analog
#6	CPn0301	94	(OmpH-Like Outer Membrane Protein)
#7	lpxD	21	UDP Glucosamine N-Acyltransferase
#8	ndk	71	Nucleoside-2-P Kinase
#9	ruvC	142	Crossover Junction Endonuclease
#10	lpxC	29	Myristoyl GlcNac Deacetylase
#11	yciA	130	acyl-CoA Thioesterase
#12	minD	32	chromosome partitioning ATPase
#13	thrS	199	Threonyl tRNA Synthetase

Motif 1
ATTTTATTCAAAGAGATTCATTTTCCTTCTAAA	1	133	1
AGAATACCCTATAAAAATCCTTTCGGTAGAGTC	11	103	1
GATTTTCATAAGAAAATTCTTTTCGCAGAGATG	1	205	0
TTTAAATAGCAGGAAATTTTTTTCTAGAAACCG	9	36	1
TGAGTTAATAAAGAGAATTTTTTAATATTTTTT	2	74	0
TAAGTATATTACGAGAATTCTTT          	2	227	1
AGGTCTTGTTAAAAAACTTCTTTGTCCCTATTT	5	220	1
GTATTAAAAAATAAAAGTTTTTTTATAAAAAAA	13	100	1
GAATGTGTATAGAAAGCTCATTTTCTCATTTAA	1	264	0
CTGTGGATATAAGAAGTTTCTTTTGATGCAGCA	3	114	1
TGATCAAAGCAAGAAGCTTTTTTTTATAAAAAA	13	118	0
TTCCCTAGATAGAAAGCTTGTTTATCAGATAAT	5	266	0
CTATTTTAGAAGGAAAATCATTCCATCTCTGCG	1	182	1
AATTCTTATGATAAAAATCCCTTTTAGGGGCTG	3	52	0
TTTCTCATTTAAGAGATTTTTTCTTGAAGACCT	1	243	0
          AGAAAACTCCTTAAACTTGGA  	7	8	0
TAATATACTTAGAAAGGTCTCTTACCTAACCTT	2	205	0
TGTTGTTTTCAGAAAAGGCTTTTGGTACCCTTT	6	43	1
TATTTGAGCGACAAGGTTTATTAAGCTTTTTAA	5	60	1
GATTTTTATCATAAGAATTCCTCTTCGTCTTAT	3	66	1
CTTTCCTCTCATGAAATTTTCTAAGAGGTTCTT	0	12	0
AAGACGAGACATAAAGGTCTCTCAATTTGATAA	3	195	1
CAGATAGTATAAAAGATGTTTTTATTAGTTCCA	13	39	1
ATCTCCTTTAAATAAAATCGTTTTATTTTAGGA	8	37	0
CCATGTAATCAGTAGAGTTATTTGAGCGACAAG	5	42	1
TATGAAAATCAGAAAAGGTCTTCAAGAAAAAAT	1	228	1
          * **** ** ***
MAP Score: 31.7407

Motif 2
AAATAGCAGGAAATTTTTTTCTAGAAACCGAGAATT	9	39	1
TTAAAAAATAAAAGTTTTTTTATAAAAAAAAGCTTC	13	103	1
AAATATTAAAAAATTCTCTTTATTAACTCAAACTCT	2	77	1
TCCTAAAATAAAACGATTTTATTTAAAGGAGATATG	8	37	1
TTTCATAAGAAAATTCTTTTCGCAGAGATGGAATGA	1	199	0
TGAAAATCAGAAAAGGTCTTCAAGAAAAAATCTCTT	1	230	1
TCTTCAAGAAAAAATCTCTTAAATGAGAAAATGAGC	1	246	1
AAACACAATTTAAATTTCTTTAGAAATACAAAAATA	5	172	1
ATAGGGACAAAGAAGTTTTTTAACAAGACCTTACTA	5	215	0
GAAATATTTTATATTCTTTTTTGAAAAAATATTAAA	2	51	1
CTACTAATATATAGTATTTTATTCAAAGAGATTCAT	1	118	1
CATGTTATTAAAACTTTATTTAAAAACTGATCATAA	3	145	1
AAGAATTCACAAATTCTATTTTAGAAGGAAAATCAT	1	167	1
AAGGGTACCAAAAGCCTTTTCTGAAAACAACAAAGA	6	39	0
CTGAAATTTTTGATTATTTTTTAGAAATCGAAGTGC	11	10	0
      TTGCTAAGGATTTTTGAGGATACGCATCAA	12	4	1
AGAAAATCTATGATTTTCTTTCATAAGTTACTGAAA	11	40	0
CAAGGTTTATTAAGCTTTTTAAGGAAGCAAAAAACC	5	71	1
       GCAAGAACCTCTTAGAAAATTTCATGAGA	0	3	1
TGTTAGCATTTTAGTGTTTTTTTTGATCAAAGCAAG	13	138	0
GAGACCTTTCTAAGTATATTACGAGAATTCTTT   	2	217	1
TATACTTAGAAAGGTCTCTTACCTAACCTTGAGAAA	2	199	0
          *** * ****    **
MAP Score: 20.6493

Motif 3
ATTCAAAGAGATTCATTTTCCTTCTAAAGAAGAATTCAC	1	138	1
GCAGAGATGGAATGATTTTCCTTCTAAAATAGAATTTGT	1	175	0
ATCTCTGCGAAAAGAATTTTCTTATGAAAATCAGAAAAG	1	206	1
TTTTCTCATTTAAGAGATTTTTTCTTGAAGACCTTTTCT	1	238	0
CATTATACCATGAGTTTTTCATTGAATAGACAATAGGAC	2	13	0
TAATGAAATATTTTATATTCTTTTTTGAAAAAATATTAA	2	47	1
AAAAAATATTAAAAAATTCTCTTTATTAACTCAAACTCT	2	74	1
CAGCATGTTATTAAAACTTTATTTAAAAACTGATCATAA	3	142	1
TTCGGCGGGTTTTTTGCTTCCTTAAAAAGCTTAATAAAC	5	75	0
ATCAAACACAATTTAAATTTCTTTAGAAATACAAAAATA	5	169	1
CTTCCCTAGATAGAAAGCTTGTTTATCAGATAATGAGGT	5	261	0
TCGAAGGAAATCTTTGTTGTTTTCAGAAAAGGCTTTTGG	6	29	1
   GGTGTATACATATCTCCTTTAAATAAAATCGTTTTA	8	45	0
TTTAAATAGCAGGAAATTTTTTTCTAGAAACCGAGAATT	9	36	1
AAATACTTTGAACTTATTGTCTTTAAAAGATGATCCTAA	9	101	0
TACTGAAATTTTTGATTATTTTTTAGAAATCGAAGTGC 	11	9	0
AAAGAAAATCTATGATTTTCTTTCATAAGTTACTGAAAT	11	39	0
CAAACCAGTTTGTAATGTTTATTAAGCAGATAGTATAAA	13	13	1
GCAGATAGTATAAAAGATGTTTTTATTAGTTCCAATCTA	13	38	1
CCTGGCGCTTTGGAACTTGTATTAAAAAATAAAAGTTTT	13	82	1
TATTAAAAAATAAAAGTTTTTTTATAAAAAAAAGCTTCT	13	101	1
TATAAAAAAAAGCTTCTTGCTTTGATCAAAAAAAACACT	13	123	1
          *   *  *** ** *  **
MAP Score: 12.3269

Motif 4
CTTTAGAAGGAAAATGAATCTCTTTGAATAAAATA	1	132	0
CATCTCTGCGAAAAGAATTTTCTTATGAAAATCAG	1	205	1
AAAAGAATATAAAATATTTCATTATACCATGAGTT	2	36	0
GAAAAAATATTAAAAAATTCTCTTTATTAACTCAA	2	73	1
TACAGCCCCTAAAAGGGATTTTTATCATAAGAATT	3	50	1
TTCTGTGGATATAAGAAGTTTCTTTTGATGCAGCA	3	112	1
CTCAATTTGATAAATCTGTGTTTTTGTGATATGCG	3	215	1
AGGTCTTGTTAAAAAACTTCTTTGTCCCTATTTTT	5	220	1
CTCCTAAAATAAAACGATTTTATTTAAAGGAGATA	8	36	1
CAACTGAAAGAAAATCTATGATTTTCTTTCATAAG	11	49	0
CAGATAGTATAAAAGATGTTTTTATTAGTTCCAAT	13	39	1
TTTTTATAAAAAAACTTTTATTTTTTAATACAAGT	13	96	0
          ****    * *****
MAP Score: 3.5189

Motif 5
AGAAAATTTCATGAGAGGAAAGATCAATATTTCACCTA	0	23	1
ATGAATCTCTTTGAATAAAATACTATATATTAGTAGCT	1	116	0
CAAATTCTATTTTAGAAGGAAAATCATTCCATCTCTGC	1	176	1
TTTCTGATTTTCATAAGAAAATTCTTTTCGCAGAGATG	1	205	0
GAAAAGGTCTTCAAGAAAAAATCTCTTAAATGAGAAAA	1	239	1
CAAGAGAATGTGTATAGAAAGCTCATTTTCTCATTTAA	1	264	0
AAACTCATGGTATAATGAAATATTTTATATTCTTTTTT	2	35	1
TTTTATATTCTTTTTTGAAAAAATATTAAAAAATTCTC	2	57	1
AGAGTTTGAGTTAATAAAGAGAATTTTTTAATATTTTT	2	75	0
TCTCGTAATATACTTAGAAAGGTCTCTTACCTAACCTT	2	205	0
AGAGGAATTCTTATGATAAAAATCCCTTTTAGGGGCTG	3	52	0
ACATGCTGCATCAAAAGAAACTTCTTATATCCACAGAA	3	112	0
TGATGCAGCATGTTATTAAAACTTTATTTAAAAACTGA	3	137	1
AAACTGATCATAAAGAAAAACAGAGAAAAGACGAGACA	3	168	1
CACAGCGCATATCACAAAAACACAGATTTATCAAATTG	3	217	0
         GTAAAGAAAAAAGCTAGTATACTATTCAG	4	1	1
GACCCGAATGTAAAAATAAAATTCACATCACT      	4	72	1
GTTTTTTGCTTCCTTAAAAAGCTTAATAAACCTTGTCG	5	68	0
TTTTTGTATTTCTAAAGAAATTTAAATTGTGTTTGATT	5	168	0
TAGTAAGGTCTTGTTAAAAAACTTCTTTGTCCCTATTT	5	215	1
GAGTCTTCCCTAGATAGAAAGCTTGTTTATCAGATAAT	5	266	0
ATCTTTGTTGTTTTCAGAAAAGGCTTTTGGTACCCTTT	6	38	1
CATATCTCCTTTAAATAAAATCGTTTTATTTTAGGAGG	8	35	0
GCACTTCGATTTCTAAAAAATAATCAAAAATTTCAGTA	11	10	1
TTTCAGTAACTTATGAAAGAAAATCATAGATTTTCTTT	11	40	1
AGCTTTTTTTTATAAAAAAACTTTTATTTTTTAATACA	13	99	0
CTTCTTGCTTTGATCAAAAAAAACACTAAAATGCTAAC	13	135	1
          *  * *****   *  **
MAP Score: 1.69861