AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_operons017_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944238030
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	lon	300	Lon ATP-dependent Protease
#1	clpB	300	Clp Protease ATPase
#2	clpC	197	ClpC Protease
#3	glyA	189	Serine Hydroxymethyltransferase
#4	clpP_2	178	CLP Protease Subunit
#5	tigA	285	Trigger Factor-peptidyl-prolyl isomerase

Motif 1
TTTAAAATTGCTCAGAGATAAGGGATTAAG	0	36	0
CTCTTTTTACCCTAGAGAAAAAGAGCCGTA	0	236	1
TGTATTTTTAGAAAGGGGAAAGAGATCCTC	1	135	1
AACGTCTAACCTAAGAGGATCTCTTTCCCC	1	149	0
CTTCTACATTCTCAGAGGAAAGTTTATAGA	1	220	1
TTCCCTTAAACTCAGAGGAATTTTACCAAA	2	90	1
AAACCTAAAAGACAGGGGTAGAACTTTCCT	2	175	0
TTTGTACCTTCAAAGGGATATATTGAAAAT	3	45	1
TCAAGAAGAACCAAGGGAAAAAGAAAAATT	3	75	0
GCCTAGCCTTCAAAGTGAAAAATGTCAATC	3	114	0
TTTTTCTGGACTTAGAGGTTCTCTCTATTA	3	148	1
    ATTTTAGTTAGAGGAAAATACTTGAC	4	6	1
CAAAGCCCTTCTCAGGGGGAAGAGACACGA	5	91	1
GCGGGTGTAGCTCAGTGGTAGAGCGTCACG	5	190	1
          **********
MAP Score: 10.541

Motif 2
AACAATGGAGTTTTTCTTAATCCCTTATCT	0	21	1
AAATCGTCTTTTTTTATTTTTTCAAAAAAA	0	83	0
AATACGGCTCTTTTTCTCTAGGGTAAAAAG	0	238	0
AAGAGGATCTCTTTCCCCTTTCTAAAAATA	1	137	0
AATCTATAAACTTTCCTCTGAGAATGTAGA	1	222	0
GTTTATAGATTTTTTATTATTCCTATGTAA	1	241	1
TTTAAAAAGGTTTTTCTTATTACATAGGAA	1	260	0
TTGTGCATAACTTTCCCTTAAACTCAGAGG	2	78	1
AGGGGTAGAACTTTCCTTAAGCATATACGA	2	162	0
ACTTAGGCAGCCTTCCTTTTACCCGAAAAG	3	14	0
TTGAAAATAATTTTTCTTTTTCCCTTGGTT	3	67	1
TGATTGACATTTTTCACTTTGAAGGCTAGG	3	113	1
GGGTCAAGTATTTTCCTCTAACTAAAAT  	4	8	0
          TTCTCCTCTGGAATAAGAGT	5	0	1
CTAAACTATTCTTTTCTTTGCGGGTGTAGC	5	171	1
TCATCACCCGCTTTTCCTTTCAAGTCTAAT	5	250	1
AAGACAACCCTTTTTATTAGACTTGAAAGG	5	265	0
          **********
MAP Score: 8.60803

Motif 3
GTCTTTTTTTATTTTTTCAAAAAAAATAGTTT	0	76	0
CTTAAACACGAGTCTTTCCTAATCTTTAATCC	0	115	1
CGAAATATGCAATCTTTTAAAATCGCTCCCTC	0	207	1
AGTTCAAGAGATCACTTCCTAATGTATTTTTA	1	113	1
ACCCTATCGAAATACTACCAAACCTAAACGTC	1	173	0
TAGAAGAGGCAACTTTATCAAACCCTATCGAA	1	194	0
AATAAGAAAAACCTTTTTAAAAAGTGCTTGGG	1	269	1
ACTAATTAAGACTGTTTCAAAAGAAGCTGAAC	2	24	1
AACTCAGAGGAATTTTACCAAATTTGCTGGTT	2	98	1
GAGTTGCATCATTATTTTAAATTTCGTATATG	2	139	1
AAAAAGAAAAATTATTTTCAATATATCCCTTT	3	56	0
ATCAATGAAAAATTTTATCAAAGCCCTTCTCA	5	73	1
CGTTGCTAAAAACTCTTCAAAAATCTAAACTA	5	147	1
          * * ********
MAP Score: 7.97574

Motif 4
AAAACTCCATTGTTTTTGAGTTTTT      	0	4	0
TGTTTAAAATTGCTCAGAGATAAGGGATTAA	0	37	0
TTCTAGATATTTTTTAGAAGTTGTATATATG	0	148	1
AAATATGCAATCTTTTAAAATCGCTCCCTCT	0	209	1
ACGGCTCTTTTTCTCTAGGGTAAAAAGAGGG	0	234	0
AGGACCAATTTCTTCACAAATCAAGGACTTA	1	58	0
AAGAAATTGGTCCTTAGGAGTTGCCGCTTTC	1	75	1
GGGAAAGAGATCCTCTTAGGTTAGACGTTTA	1	150	1
TTGGTAAAATTCCTCTGAGTTTAAGGGAAAG	2	88	0
TCTACCCCTGTCTTTTAGGTTTTT       	2	183	1
       GAGTCTTTTCGGGTAAAAGGAAGG	3	3	1
TAAGGCTTCGTCTTTAGAAGTCC        	3	176	1
       TTCTCCTCTGGAATAAGAGTGGAT	5	3	1
TGCTAAAAACTCTTCAAAAATCTAAACTATT	5	150	1
ACTATTCTTTTCTTTGCGGGTGTAGCTCAGT	5	175	1
CACCCGCTTTTCCTTTCAAGTCTAATAAAAA	5	254	1
          ****** ****
MAP Score: 7.51002

Motif 5
GGAGTTTTTCTTAATCCCTTATCTCTGAGC	0	27	1
TTCCTAATCTTTAATCCCTTCTAGATATTT	0	130	1
TCGCTCCCTCTTTTTACCCTAGAGAAAAAG	0	229	1
TAAGAGGATCTCTTTCCCCTTTCTAAAAAT	1	138	0
TTTGTGCATAACTTTCCCTTAAACTCAGAG	2	77	1
TGCCTAAGTTTTTGTACCTTCAAAGGGATA	3	35	1
TTATTTTCAATATATCCCTTTGAAGGTACA	3	47	0
ATAATTTTTCTTTTTCCCTTGGTTCTTCTT	3	73	1
TTGATTGACATTTTTCACTTTGAAGGCTAG	3	112	1
AATTCGTGTCTCTTCCCCCTGAGAAGGGCT	5	94	0
          **********
MAP Score: 6.6166

Motif 6
          AAAAACTCAAAAACAATGGAGTTTTTCTTAAT	0	0	1
ATTTTTTTTGAAAAAATAAAAAAAGACGATTTGCCTTAAACA	0	81	1
ACCAAACCTAAACGTCTAACCTAAGAGGATCTCTTTCCCCTT	1	147	0
TGTAATAAGAAAAACCTTTTTAAAAAGTGCTTGGGGTGAATT	1	266	1
TTCTTTTGAAACAGTCTTAATTAGTTTTATGTTTGTTAT   	2	7	0
CTGTTTCAAAAGAAGCTGAACTATTGTATCATATACAAAAGG	2	35	1
         AAAAACCTAAAAGACAGGGGTAGAACTTTCCTT	2	174	0
TTGAAGGTACAAAAACTTAGGCAGCCTTCCTTTTACCCGAAA	3	16	0
TTGACCCAAGAAAGTCTTAAACATAGAATTCGAGATTTTAAT	4	31	1
TACGTCAGCAACAAGCTTAGACATTAAAATCTCGAATTCTAT	4	53	0
GACAGCCTAAAAAGTCTTAGCTACGTTCCTAGGGTCATTTCG	4	95	1
AAATCAATGAAAAATTTTATCAAAGCCCTTCTCAGGGGGAAG	5	71	1
AAACTCTTCAAAAATCTAAACTATTCTTTTCTTTGCGGGTGT	5	156	1
CTTTTCCTTTCAAGTCTAATAAAAAGGGTTGTCTT       	5	260	1
          **** ** *   *      * *
MAP Score: 6.32765

Motif 7
AATCCCTTATCTCTGAGCAATTTTAAACAGTAGA	0	39	1
TCTTTAATCCCTTCTAGATATTTTTTAGAAGTTG	0	137	1
CTTCTACATTCTCAGAGGAAAGTTTATAGATTTT	1	220	1
TTAAAAAGTGCTTGGGGTGAATTTT         	1	285	1
TTTTGAAACAGTCTTAATTAGTTTTATGTTTGTT	2	12	0
TTCCCTTAAACTCAGAGGAATTTTACCAAATTTG	2	90	1
AGCCTAAAAAGTCTTAGCTACGTTCCTAGGGTCA	4	98	1
CTGAGAAGGGCTTTGATAAAATTTTTCATTGATT	5	72	0
          *** ***  * ***
MAP Score: 0.720498