AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_operons034_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944238528
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	valS	133	Valyl tRNA Synthetase
#1	CPn0095	62	S/T Protein Kinase
#2	pfrA	238	Peptide Chain Releasing Factor
#3	rl19	27	L19 Ribosomal Protein
#4	rnhB_1	55	Ribonuclease HII
#5	rpe	300	Ribulose-P Epimerase
#6	CPn0397	300	PP2C phosphatase family

Motif 1
TTGAGAGCCTGAGAATGGGTTTTATAAATGGG	2	26	0
TCTCAAGCCCGAGAATGGGTTTTTTTGTGAGG	2	52	1
GATTCCATTTGATACTGATTTTTCACCACTTT	2	206	1
TGCATTTGGAGATAAGGATTATGATATAGCAA	5	32	0
TTTCACTAATGAAAATGCATTTGGAGATAAGG	5	47	0
TGTATAAAAAGAAAAGAATTTTTAATAAGAAA	5	103	1
TGTATGAATAGAAAATGAATACGGACTACTAC	5	175	0
TTCATACAATGAGTAGGAGTTCATGAATACAT	5	199	1
TAATAGTAAAGAGAATGCTTTTTTCATTATTC	6	68	1
TATGAAATTAGAGAATGTCTATAGGGGCGGAC	6	242	1
          *******  ***
MAP Score: 10.8058

Motif 2
CCCTATTTTTAGAAAAAGCAGCATAAAGAT	0	35	1
AAAAAGCAGCATAAAGATAATAAAATAGAA	0	47	1
TAAAAAGTGGTGAAAAATCAGTATCAAATG	2	211	0
         AAGAAAGAGAATTTTAGGTGG	3	1	1
ACTATAGATTATAAAAATCAAAATAAGACA	4	30	0
GTTTCACTAATGAAAATGCATTTGGAGATA	5	50	0
TTAGTGAAACAGAAAGATTAATCTTGGGAT	5	70	1
GGATTTTTGTATAAAAAGAAAAGAATTTTT	5	96	1
TTGTATGAATAGAAAATGAATACGGACTAC	5	178	0
TATAAATAGTAGAAAGTTAAAGCTCACTCT	5	242	1
CAAGATAATAGTAAAGAGAATGCTTTTTTC	6	63	1
GATGAATAATGAAAAAAGCATTCTCTTTAC	6	73	0
GAGCTAGGCTGGAAAGGTCAATTAACCTAA	6	104	0
GATTTCGTCAGGAAAATTCAATTCTTTATA	6	205	1
          **********
MAP Score: 10.0602

Motif 3
CAGCATAAAGATAATAAAATAGAACTATGCTACTT	0	53	1
CAAATTTGTGATCTCTACTAAGAAATACCCTGTAA	0	97	0
TATACAAGCTATTGCAAGAGAGAAAGCCCTCACAA	2	76	0
TTTCAAAATTATCGTGACCTAGGAAAGCATAACGT	2	113	0
GGTCACGATAATTTTGAAATAGATAACGTTAGATG	2	129	1
ACACCTTGGTATACTGATACAGGCATCTAACGTTA	2	152	0
GGAGATAAGGATTATGATATAGCAAATATATTGTG	5	22	0
TGCATTTTCATTAGTGAAACAGAAAGATTAATCTT	5	60	1
CTTGGGATTTTTGTATAAAAAGAAAAGAATTTTTA	5	92	1
AAAGAAAAGAATTTTTAATAAGAAATGTTCAATGG	5	110	1
AGAGCTAACAATACTAAACAAGATAATAGTAAAGA	6	45	1
CGCATGATCATTAATTACAAAGAAAAATTTGATAA	6	146	0
ATTTCATATCATTATTATAAAGAATTGAATTTTCC	6	215	0
GCGGACTCTATTTGTGATCCAGGATCTCTTTAGGA	6	268	1
          **  * * * *****
MAP Score: 8.67242

Motif 4
GCATAGTTCTATTTTATTATCTTTATGCTGC	0	52	0
TCTTAATCCAAATTTGTGATCTCTACTAAGA	0	109	0
          AATTCTTAATCCAAATTTGTG	0	122	0
TGTTTTAGAGAATTTTTTATCTGATTCCATT	2	184	1
CTTATTTTGATTTTTATAATCTATAGTAGCT	4	33	1
AAAAGAAAAGAATTTTTAATAAGAAATGTTC	5	109	1
GCTCTAGGGCGATTATTTATCAAATTTTTCT	6	130	1
TTTTCTTTGTAATTAATGATCATGCGACCAT	6	155	1
TTTATCGCTAAATTAATGGTCGCATGATCAT	6	170	0
AGGAAAATTCAATTCTTTATAATAATGATAT	6	214	1
GACATTCTCTAATTTCATATCATTATTATAA	6	230	0
GGGCGGACTCTATTTGTGATCCAGGATCTCT	6	266	1
          ***** *****
MAP Score: 6.25042

Motif 5
TTCTAAAAATAGGGCATGTTTATGATTTGATATTTTTTA     	0	5	0
AAGTAGCATAGTTCTATTTTATTATCTTTATGCTGCTTTTTCTA	0	44	0
CTCTCTTGCAATAGCTTGTATAATACGTTATGCTTTCCTAGGTC	2	89	1
TCAGTATACCAAGGTGTTTTAGAGAATTTTTTATCTGATTCCAT	2	170	1
TCCATTTGATACTGATTTTTCACCACTTTTTAGGGATTC     	2	209	1
GCAAGACTTCATATTGTCTTATTTTGATTTTTATAATCTATAGT	4	16	1
GGTTAGAATCACAATATATTTGCTATATCATAATCCTTATCTCC	5	13	1
TATAAAAAGAAAAGAATTTTTAATAAGAAATGTTCAATGGTTCT	5	105	1
AGAAATGTTCAATGGTTCTTTGAAATATATTCGTTCTGTATTAT	5	130	1
TTATGGTAGTAGTCCGTATTCATTTTCTATTCATACAATGAGTA	5	170	1
TAGTAAAGAGAATGCTTTTTTCATTATTCATCCTTAGGTTAATT	6	71	1
CTAGCTCTAGGGCGATTATTTATCAAATTTTTCTTTGTAATTAA	6	127	1
ATTATAAAGAATTGAATTTTCCTGACGAAATCATAATTTATCGC	6	193	0
          *  *  * **    *  * **  *
MAP Score: 5.85376

Motif 6
ACTTAGAGCAAGTAGCATAGTTCTATTTTATTATCTTTATG	0	56	0
CAACGATCTTTGGAGCGCTATGATATTGTTAGAATTATTGG	1	21	1
TATGCTTTCCTAGGTCACGATAATTTTGAAATAGATAACGT	2	117	1
TAGAGAATTTTTTATCTGATTCCATTTGATACTGATTTTTC	2	189	1
AAGACTTCATATTGTCTTATTTTGATTTTTATAATCTATAG	4	18	1
   GGAGGTTAGAATCACAATATATTTGCTATATCATAATC	5	7	1
AGTAGAAAGTTAAAGCTCACTCTACTTTAAATTTAGCGTAG	5	249	1
CTACTTTAAATTTAGCGTAGTGAAGTTGAGATAGGCTGAG 	5	270	1
TTATTCATCCTTAGGTTAATTGACCTTTCCAGCCTAGCTCT	6	94	1
AGGGCGATTATTTATCAAATTTTTCTTTGTAATTAATGATC	6	135	1
GAATGTCTATAGGGGCGGACTCTATTTGTGATCCAGGATCT	6	254	1
          *  ***  * *    ***  *
MAP Score: 3.85895

Motif 7
AAGTTTACAGGGTATTTCTTAGTAGAGATCACAAA	0	93	1
TGATATTGTTAGAATTATTGGAAAGGGAGGC    	1	41	1
GCCCGAGAATGGGTTTTTTTGTGAGGGCTTTCTCT	2	58	1
CTAGGTCACGATAATTTTGAAATAGATAACGTTAG	2	126	1
GGTGTTTTAGAGAATTTTTTATCTGATTCCATTTG	2	182	1
TTTGGAGATAAGGATTATGATATAGCAAATATATT	5	25	0
GATTAATCTTGGGATTTTTGTATAAAAAGAAAAGA	5	85	1
TAAAAAGAAAAGAATTTTTAATAAGAAATGTTCAA	5	107	1
TAGCTCTAGGGCGATTATTTATCAAATTTTTCTTT	6	128	1
CTAATTTCATATCATTATTATAAAGAATTGAATTT	6	218	0
          ** ******    **
MAP Score: 0.332369