AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_operons003_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944237218
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	rnc	105	Ribonuclease III
#1	lepB	196	Signal Peptidase I
#2	pfrA	238	Peptide Chain Releasing Factor
#3	rl19	27	L19 Ribosomal Protein
#4	rnhB_1	55	Ribonuclease HII
#5	CPn0574	33	hypothetical protein
#6	yhhY	300	Amino Group Acetyl Transferase
#7	CPn0720	109	CT659 hypothetical protein
#8	CPn0906	101	CT763 hypothetical protein
#9	ftsY_sucC	70	ftsY: Cell Division Protein FtsY, sucC: Succinyl-CoA Synthetase, Beta
#10	htrA	283	DO Serine Protease

Motif 1
CTATAGACTTTAAGCTTTTTTCCGCCTATA	0	43	1
TTCTAGCGTATTAGATTTTTCGATCCAAAA	1	36	0
CGAGGATTGTTTTGATTTTTCATTTAGGTC	1	85	1
  AACTTCTTTTAGATTTCCCATTTATAAA	2	8	1
TATAATACGTTATGCTTTCCTAGGTCACGA	2	107	1
ATTGTCTTATTTTGATTTTTATAATCTATA	4	28	1
CCCCAAGCAATTTCCTTTTTATCTTTGCGA	6	130	0
CGCTTGGACATTTCCTGTTTCATGTCCCGT	6	215	0
TAAAATTGAATTTCATTTTTTAACATCTCT	7	55	1
ACATTGACTTTTTCATTTTGAATATCTATC	8	10	1
TTTGAATATCTATCCTTTCTTCAGGAACTT	8	26	1
AACATAGAGTTATGTTTTTTTCTTTCTATA	8	60	1
 AAATAACTCTTTGCTTTTTCCTTCTTATC	9	9	1
TCTTATCTTGTATCATTTCTTTTACTTCAA	9	32	1
TCACATATGATTTGTTTTTCGTAATTACTA	10	188	1
          **********
MAP Score: 13.2273

Motif 2
AATCAAAACAATCCTCGAGCTAAATTCGTAA	1	71	0
AGAAAGTCAGATTCTATCTCTTTAGATTGAT	1	160	0
TATAAAACCCATTCTCAGGCTCTCAAGCCCG	2	32	1
AAAAAAACCCATTCTCGGGCTTGAGAGCCTG	2	47	0
GTTTTAGAGAATTTTTTATCTGATTCCATTT	2	185	1
ACCACCTAAAATTCTCTTTCTT         	3	1	0
GGATGTCTAAAACCTCTTTCTGCGCT     	5	5	0
AGCTCTCACGATTCTGTATCTGACTACGTTC	6	29	0
GAGTTATGTTTTTTTCTTTCTATATCTCAAT	8	66	1
AGAAGAGAGGATCTTCAAGCTCAAAGTCTCC	10	65	1
ATCATGAAGTATTCTCAATCTAAAGATATAA	10	133	1
CTACAAAGGGATTTTATATCTTTAGATTGAG	10	146	0
          ******* ***
MAP Score: 9.31514

Motif 3
     AAAGATCTAACAATATAGCAAAATAAT	1	5	1
TAATTTTGGATCGAAAAATCTAATACGCTAGA	1	33	1
GAAGACCTAAATGAAAAATCAAAACAATCCTC	1	86	0
CTATAATCAATCTAAAGAGATAGAATCTGACT	1	155	1
CACGATAATTTTGAAATAGATAACGTTAGATG	2	132	1
TACTATAGATTATAAAAATCAAAATAAGACAA	4	29	0
AACATCTCTTTTTAAAGACAACGCGAATTAGT	7	76	1
CTTCAGGAACTTTAAAAACATAGAGTTATGTT	8	44	1
AATTGAGATATAGAAAGAAAAAAACATAACTC	8	66	0
CAAGATAAGAAGGAAAAAGCAAAGAGTTATTT	9	10	0
GTATTCTCAATCTAAAGATATAAAATCCCTTT	10	141	1
CCTAGTAATTACGAAAAACAAATCATATGTGA	10	188	0
TTCTGCTTCATCGAAAGACAACCTTCTTGAGG	10	254	1
          * ****** ***
MAP Score: 4.81876

Motif 4
GCCGTTCTATAATCAATCTAAAGAGATAGAATCTGA	1	149	1
      AAAGATACTGGGGTAAGAAAGTCAGATTCT	1	176	0
AAAAAAACCCATTCTCGGGCTTGAGAGCCTGAGAAT	2	42	0
CGTATTATACAAGCTATTGCAAGAGAGAAAGCCCTC	2	80	0
ATCAGTATACCAAGGTGTTTTAGAGAATTTTTTATC	2	169	1
ACTGATTTTTCACCACTTTTTAGGGATTC       	2	219	1
ACGTAGTCAGATACAGAATCGTGAGAGCTGTATGAA	6	31	1
GCAGGTTTTACAAGAACGTTTAGAGAAGCAATCTCT	6	91	1
TCCTTTTTATCTTTGCGATCAAGAGATTGCTTCTCT	6	112	0
TTTCAGCCCTATACTCTTGTTAAAGATGTACGTACG	6	182	1
CATTTTTTAACATCTCTTTTTAAAGACAACGCGAAT	7	68	1
TTGAATATCTATCCTTTCTTCAGGAACTTTAAAAAC	8	27	1
AGCTCAAAGTCTCCGGATTTGAGCGATGTTTCCCTC	10	82	1
ATCATGAAGTATTCTCAATCTAAAGATATAAAATCC	10	133	1
CGATGGTATTCTGCTTCATCGAAAGACAACCTTCTT	10	246	1
CATCGAAAGACAACCTTCTTGAGGGATAGAT     	10	262	1
          ** *    ** *****
MAP Score: 4.45086

Motif 5
CGTATCCGAATAAGATAACAAATCCAAAAGCACT	0	11	1
AAGACCTAAATGAAAAATCAAAACAATCCTCGAG	1	83	0
CCATTAGCTCTAAAGTATCCAATGCAGCCGTTCT	1	123	1
TAATCAATCTAAAGAGATAGAATCTGACTTTCTT	1	158	1
AATGGGTTTTATAAATGGGAAATCTAAAAGAAGT	2	11	0
TCAAATGGAATCAGATAAAAAATTCTCTAAAACA	2	184	0
GAAAGAGGTTTTAGACATCCTATCGTT       	5	16	1
ATGAACGTAGTCAGATACAGAATCGTGAGAGCTG	6	27	1
ACAAGAACGTTTAGAGAAGCAATCTCTTGATCGC	6	100	1
TCTCTTGATCGCAAAGATAAAAAGGAAATTGCTT	6	122	1
GTACGGGACATGAAACAGGAAATGTCCAAGCGAT	6	213	1
AAAGAGATGTTAAAAAATGAAATTCAATTTTAAT	7	53	0
ATATTCAAAATGAAAAAGTCAATGT         	8	1	0
ATTGAGATATAGAAAGAAAAAAACATAACTCTAT	8	63	0
TTCTCAATCTAAAGATATAAAATCCCTTTGTAGT	10	144	1
          * *** *  *****
MAP Score: 2.96476

Motif 6
CATAACGTATTATACAAGCTATTGCAAGAG	2	91	0
        AATATACCACCTAAAATTCTCT	3	15	0
  TCTGTAGCAAGACTTCATATTGTCTTAT	4	8	1
AAAGAGGTTTTAGACATCCTATCGTT    	5	17	1
TTAAGGTAACAAGACATCCTCGCAGTAGAA	10	39	1
TTAGATTGAGAATACTTCATGATGTAGAAT	10	126	0
AATACCATCGTATACTAGCTAACACAGGTT	10	226	0
GCTTCATCGAAAGACAACCTTCTTGAGGGA	10	258	1
          **********
MAP Score: 1.98924

Motif 7
AATAATTTTGGATCGAAAAATCTAATACGCTA	1	31	1
TACAAGATAAGAAGGAAAAAGCAAAGAGTTAT	9	12	0
ATTAAAGTTTGAGGGAAACATCGCTCAAATCC	10	96	0
CTGAAGACCTAAATGAAAAATCAAAACAATCC	1	88	0
ATTTTTATAGGCGGAAAAAAGCTTAAAGTCTA	0	46	0
AATCATATGTGACGAAAACATTACTACAAAGG	10	168	0
AATGGAATCAGATAAAAAATTCTCTAAAACAC	2	183	0
GATATAGAAAGAAAAAAACATAACTCTATGTT	8	60	0
TAGATATTCAAAATGAAAAAGTCAATGT    	8	6	0
TAGTAATTACGAAAAACAAATCATATGTGACG	10	186	0
          **  ********
MAP Score: 1.50548

Motif 8
TATCCAATGCAGCCGTTCTATAATCAATCT	1	138	1
CATTTATAAAACCCATTCTCAGGCTCTCAA	2	28	1
TCACAAAAAAACCCATTCTCGGGCTTGAGA	2	52	0
AAGAGGTTTTAGACATCCTATCGTT     	5	18	1
GAAATGTCCAAGCGATGCTCGACGGCGAGC	6	231	1
TAAGGTAACAAGACATCCTCGCAGTAGAAG	10	40	1
          **********
MAP Score: 0.855944