AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_operons016_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944237944
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	valS	133	Valyl tRNA Synthetase
#1	ileS	300	Isoleucyl-tRNA Synthetase
#2	pfrA	238	Peptide Chain Releasing Factor
#3	rl19	27	L19 Ribosomal Protein
#4	rnhB_1	55	Ribonuclease HII
#5	leuS	167	Leucyl tRNA Synthetase
#6	CPn0681	54	CT691 hypothetical protein
#7	murB	26	UDP-N-Acetylenolpyruvoylglucosamine Reductase
#8	CPn0989	300	CT832 hypothetical protein

Motif 1
ATGTTTATGATTTGATATTTTTTA          	0	0	0
TCTAAGTTTACAGGGTATTTCTTAGTAGAGATCA	0	90	1
CAGCCTTAGGTTCGGCATTTATTGTTTTGTTGGC	1	42	1
TATACACCCCCACAACAATTTTAGAAGCTGGTTA	1	138	1
ATTTTAGAAGCTGGTTAGCTTTTATTCAATCATC	1	155	1
TGGTCAAGTTCTAAGAACTTCTTAGAGATCTCTA	1	195	1
 CTTTTGCCTTTAGGAACATTTTGATATGAAAAC	1	277	0
TTTCCTAGGTCACGATAATTTTGAAATAGATAAC	2	122	1
CAAGGTGTTTTAGAGAATTTTTTATCTGATTCCA	2	179	1
ATACTGATTTTTCACCACTTTTTAGGGATTC   	2	217	1
TTGTCAATGTCATGGAAGTTTTTGAAGGAAAAAC	5	65	1
TACACTAAGCCTTTTTAATTTTTATATATATAAA	5	133	1
CAAGATCGTTTAGGCAAGTTATTATTGCGAAAAA	6	20	1
AGATTTTTTATATAAAAATTTTTAATTTCTAAAG	8	89	0
GAAAGAGTTGCTGGAGATTTTTTATATAAAAATT	8	103	0
CATTTTTCAACTAAGAAGTTTTTGTTGCAATTAA	8	175	1
AGGTTATCTATTAGAAAGTTTTAATTGCAACAAA	8	195	0
ATGTGTATTATTAACTATTTTTTGGTTGCTTGTC	8	276	1
          ** *  * ******
MAP Score: 13.4619

Motif 2
GGTGTATAGGTTTCGACTTGAAAATGAAGTGTTA	1	112	0
TGTAAATATGTTTTCATATCAAAATGTTCCTAAA	1	268	1
TTCTTTTAGATTTCCCATTTATAAAACCCATTCT	2	13	1
CATCTAACGTTATCTATTTCAAAATTATCGTGAC	2	130	0
TACTATAGATTATAAAAATCAAAATAAGACAATA	4	27	0
    CTTGATTAACTAATTAAAAAAGGAACACAT	5	6	1
GTCTTGTCCGTTTTTCCTTCAAAAACTTCCATGA	5	74	0
CTTTTATATATATAAAAATTAAAAAGGCTTAGTG	5	135	0
GAATAGCCTTTTTCGCAATAATAACTTGCCTAAA	6	28	0
CCTTGTCGTCTTTAGAAATTAAAAATTTTTATAT	8	80	1
AAATTAAAAATTTTTATATAAAAAATCTCCAGCA	8	95	1
CAACAAAAACTTCTTAGTTGAAAAATGTACTTTG	8	168	0
AAGAAGTTTTTGTTGCAATTAAAACTTTCTAATA	8	187	1
          ***  * ** ****
MAP Score: 13.3793

Motif 3
AAAAAGCAGCATAAAGATAATAAAATAGAACTATGC	0	47	1
GAGATCACAAATTTGGATTAAGAATT          	0	117	1
CGGGCTTGAGAGCCTGAGAATGGGTTTTATAAATGG	2	27	0
CAGGCTCTCAAGCCCGAGAATGGGTTTTTTTGTGAG	2	47	1
ACACCTTGGTATACTGATACAGGCATCTAACGTTAT	2	151	0
TATCAAATGGAATCAGATAAAAAATTCTCTAAAACA	2	184	0
TATATATATAAAAATTAAAAAGGCTTAGTGTACGTC	5	129	0
TTTAATTTTTATATATATAAAAGTTTAGAAT     	5	146	1
GCAAGTTATTATTGCGAAAAAGGCTATTCTT     	6	33	1
       TTAATTTAGACCAAGGGATTCTAAAA   	7	3	1
        CTAGAAAGAAGAAGGCTATCTTAGGGTA	8	2	1
GACAAGGATAATTATGAGAAAGGGATTTCCGTTGCT	8	51	0
TTATTTTCTGATTCAGAGAAAGAGTTGCTGGAGATT	8	118	0
AGGAGTTGTGAGAAAGAAACAAGGTTATCTATTAGA	8	214	0
          *    ** ***** **
MAP Score: 10.3584

Motif 4
CTTTATGCTGCTTTTTCTAAAAATAGGGCAT	0	32	0
AACTATGCTACTTGCTCTAAGTTTACAGGGT	0	75	1
GTTTTGTTGGCTTTTTAGGAGGCCAGCCAAC	1	65	1
CTAACGTTATCTATTTCAAAATTATCGTGAC	2	130	0
 AAGAATAGCCTTTTTCGCAATAATAACTTG	6	34	0
TTTAGAATCCCTTGGTCTAAATTAA      	7	4	0
ACGGAAATCCCTTTCTCATAATTATCCTTGT	8	55	1
TCCAGCAACTCTTTCTCTGAATCAGAAAATA	8	122	1
GCAATTAAAACTTTCTAATAGATAACCTTGT	8	201	1
AACCTTGTTTCTTTCTCACAACTCCTTAGCT	8	224	1
          ******** **
MAP Score: 8.59274

Motif 5
ACATGCCCTATTTTTAGAAAAAGCAGCATAAA	0	30	1
AATTAACACTTCATTTTCAAGTCGAAACCTAT	1	109	1
CTAAAAAACCTCTATTGTAAATATGTTTTCAT	1	253	1
GAGGGCTTTCTCTCTTGCAATAGCTTGTATAA	2	80	1
TCTAACGTTATCTATTTCAAAATTATCGTGAC	2	130	0
TGGTGAAAAATCAGTATCAAATGGAATCAGAT	2	202	0
          TCTGTAGCAAGACTTCATATTG	4	0	1
ATTTTTATAATCTATAGTAGCTT         	4	42	1
CTTGTCCGTTTTTCCTTCAAAAACTTCCATGA	5	74	0
AAGAATAGCCTTTTTCGCAATAATAACTTGCC	6	32	0
ATCCTTGTCGTCTTTAGAAATTAAAAATTTTT	8	78	1
CTGGAGATTTTTTATATAAAAATTTTTAATTT	8	95	0
ATATAAAAAATCTCCAGCAACTCTTTCTCTGA	8	110	1
CAAAAACTTCTTAGTTGAAAAATGTACTTTGT	8	167	0
CTAAGAAGTTTTTGTTGCAATTAAAACTTTCT	8	185	1
GCTAAGGACCTCTTTAGCAGTTAAATGTGTAT	8	252	1
          *** ****** *
MAP Score: 6.86707

Motif 6
CCTGTATCAGTATACCAAGGTGTTTTAGAGAATTTT	2	164	1
        TCTGTAGCAAGACTTCATATTGTCTTAT	4	2	1
TGGGGAGACGTACACTAAGCCTTTTTAATTTTTATA	5	123	1
ACAAGATCGTTTAGGCAAGTTATTATTGCGAAAAAG	6	19	1
    TTAATTTAGACCAAGGGATTCTAAAA      	7	6	1
ATAAAAAATCTCCAGCAACTCTTTCTCTGAATCAGA	8	112	1
AGTACATTTTTCAACTAAGAAGTTTTTGTTGCAATT	8	171	1
AAAGAGGTCCTTAGCTAAGGAGTTGTGAGAAAGAAA	8	231	0
          *  ******   ** *
MAP Score: 6.6716

Motif 7
TGTTTATGATTTGATATTTTTTA        	0	2	0
AGAGATCTCTAAGAAGTTCTTAGAACTTGAC	1	197	0
ATATTTACAATAGAGGTTTTTTAGGTTTTCG	1	246	0
TTCCTAGGTCACGATAATTTTGAAATAGATA	2	123	1
CAAGGTGTTTTAGAGAATTTTTTATCTGATT	2	179	1
      AAGAAAGAGAATTTTAGGTGGTATA	3	4	1
GTCAATGTCATGGAAGTTTTTGAAGGAAAAA	5	67	1
AAAGACGACAAGGATAATTATGAGAAAGGGA	8	62	0
TCTTTAGAAATTAAAAATTTTTATATAAAAA	8	88	1
AAAGAGTTGCTGGAGATTTTTTATATAAAAA	8	105	0
TTTTTCAACTAAGAAGTTTTTGTTGCAATTA	8	177	1
GGTTATCTATTAGAAAGTTTTAATTGCAACA	8	197	0
AACTTTCTAATAGATAACCTTGTTTCTTTCT	8	209	1
TTAACTGCTAAAGAGGTCCTTAGCTAAGGAG	8	245	0
          * *********
MAP Score: 5.39192

Motif 8
ATAGGGCATGTTTATGATTTGATATTTTTT	0	11	0
ATAGTTCTATTTTATTATCTTTATGCTGCT	0	51	0
TTAATCCAAATTTGTGATCTCTACTAAGAA	0	108	0
AGGTTCGGCATTTATTGTTTTGTTGGCTTT	1	49	1
AATAGAGGTTTTTTAGGTTTTCGTCCATAG	1	239	0
    AACTTCTTTTAGATTTCCCATTTATA	2	6	1
TGTATAATACGTTATGCTTTCCTAGGTCAC	2	105	1
TTTTAGAGAATTTTTTATCTGATTCCATTT	2	186	1
TATTTTGATTTTTATAATCTATAGTAGCTT	4	35	1
ACACTAAGCCTTTTTAATTTTTATATATAT	5	134	1
 ATTCTAAACTTTTATATATATAAAAATTA	5	148	0
TATATAAAAATTTTTAATTTCTAAAGACGA	8	85	0
TTATTAACTATTTTTTGGTTGCTTGTC   	8	283	1
          **********
MAP Score: 0.386155

Motif 9
TTCCCATTTATAAAACCCATTCTCAGGCTCTCA	2	24	1
GCCCTCACAAAAAAACCCATTCTCGGGCTTGAG	2	53	0
GGGTTTTTTTGTGAGGGCTTTCTCTCTTGCAAT	2	68	1
         AAGAAAGAGAATTTTAGGTGGTAT	3	1	1
ATAAGACAATATGAAGTCTTGCTACAGA     	4	5	0
TAAAAATCAAAATAAGACAATATGAAGTCTTGC	4	16	0
GGAGACGTACACTAAGCCTTTTTAATTTTTATA	5	126	1
ATTATTGCGAAAAAGGCTATTCTT         	6	40	1
 TTAATTTAGACCAAGGGATTCTAAAA      	7	9	1
  CTAGAAAGAAGAAGGCTATCTTAGGGTATTA	8	8	1
AAAAGCAACGGAAATCCCTTTCTCATAATTATC	8	48	1
AAAAATCTCCAGCAACTCTTTCTCTGAATCAGA	8	115	1
GTGAGAAAGAAACAAGGTTATCTATTAGAAAGT	8	210	0
          *  *** ******
MAP Score: 0.316982