AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_operons010_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944237694
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	gcp_2	83	O-Sialoglycoprotein Endopeptidase
#1	oppA_2	150	Oligopeptide Binding Protein
#2	oppA_3	55	Oligopeptide Binding Protein
#3	oppA_4	283	Oligopeptide Binding Protein
#4	oppB_1	292	Oligopeptide Permease
#5	oppC_1	30	Oligopeptide Permease
#6	proS	299	Prolyl tRNA Synthetase
#7	hrcA	91	HTH Transcriptional Repressor
#8	dnaK	29	Heat Shock Protein-70
#9	vacB	270	ribonuclease family
#10	oppA_5	21	Oligopeptide Binding Lipoprotein
#11	CPn0600	300	hypothetical protein

Motif 1
TCCGAAATGGAAAAATTAAAAATTTTATAGACAATC	4	11	1
AAATTTCTAAATAAAAACAAAAATATAATTAAAATA	6	73	1
TTTGTCTTTTAAAAACTAAAAACTATTCAGCAGTAT	11	71	0
AGAGATTTATAGAAAAATAAAAGTCTTCCTTCCCAA	4	161	1
AATCTTGAAAAGAGAATTAAAAATTTTTAATTTAAA	4	43	1
GTTTTTATTTAGAAATTTAATAATCTCAACTTATAA	6	55	0
ATAGAGAAACTTAAATTGAAAATTTTGA        	9	2	0
AAACTTCCTTATAAACAGAAAACAGTTCCATTCTCT	9	61	1
AAAACCCACTTAAAAGGGAAAATTTTGTTGAGCCAC	9	180	1
TACTACAATTACAAAAATAAAAGATTAATAAGTATA	6	12	1
AACTTCTTATAAAGATACAATAGTATACTGGTGAAG	3	57	0
TTGTCGCTACATAGAACAAAAACAATCTCCAAAATT	11	189	0
TTCTATCCTGAAAGATACAATAATCTCATTCCCCCA	3	166	1
GAGAAAAAGTTTAGACTTAAAATTCGATAGTAAATT	2	10	1
ATAGCGACACTCAAACTGAAAAAGATGAAGAAGGCG	11	23	1
TGCAATTGTTAAAAAAATAAGAGATTTATAGAAAAA	4	142	1
          * ***   **** * *
MAP Score: 19.8688

Motif 2
AGATTTATAGAAAAATAAAAGTCTTCCTTCCCAAC	4	163	1
TCCGAAATGGAAAAATTAAAAATTTTATAGACAAT	4	11	1
GAAGATGACTAAAAATGAAAGTATAATGACTTAAA	4	212	1
AAGTCATAAGAAAAAAAGAAGCATAAACTT     	5	10	1
CTACAATTACAAAAATAAAAGATTAATAAGTATAC	6	14	1
ATTTCTAAATAAAAACAAAAATATAATTAAAATAA	6	75	1
TTTGTCTTTTAAAAACTAAAAACTATTCAGCAGTA	11	72	0
CCCTCCTCGTAAAAAAGTTAGCATTCATTCAATTC	7	24	1
       GAGAAAAAGTTTAGACTTAAAATTCGAT	2	3	1
CCGCATCCCTAAAAGTTGAAATCTTATTCTAAAGA	1	115	1
AAACCCACTTAAAAGGGAAAATTTTGTTGAGCCAC	9	181	1
AGTCTATAGAAAAAATTACAGGCTATTGCGATTTT	6	237	0
TGCAATTGTTAAAAAAATAAGAGATTTATAGAAAA	4	142	1
 AAAAAACCAAGAAAAGAAAACGTTGCCTTTTATA	0	59	0
CTCATGGGGGAAAAAGACAAATAGAGGGCTTTCAC	11	114	0
ATTGATCTAGAAAAATCCCTGTGTTAAGATACCTC	6	157	1
AAAGAGAATTAAAAATTTTTAATTTAAATTATAGT	4	51	1
          *****   ***  **
MAP Score: 14.7664

Motif 3
TTTCCTTCTGACTGCTCTTCTCTCTCTACTC	1	82	1
CTTACCAAAGACTTCTTTTGT          	3	0	0
GGCGTATCCTAATGCTCCTATTACTTACTGT	3	123	0
AAAAATTTTTAATTCTCTTTTCAAGATTGTC	4	40	0
ATTTTTCTATAAATCTCTTATTTTTTTAACA	4	148	0
TCGAGTGCTAAATTCTCTTGACCTTCTCGGG	7	57	1
GGAAGTTTCCCATCCTCTTATGAGGATGGGA	9	38	0
AAAACAGTTCCATTCTCTTATTCTCTGATCA	9	79	1
TGAATTTGAGACTGCTCCTTTCATAATCACA	9	150	1
AGAGGGCTTTCACCCTCTTGTTTGTCTTTTA	11	96	0
CCATACTCACAACTCTCTTATATTAAAATTT	11	163	1
TGCTCCTTATCCCTCTCTTCTGAAATTTCTT	11	245	1
          ********* *
MAP Score: 10.6398

Motif 4
  AGTACTACAATTACAAAAATAAAAGATTAATAA	6	8	1
GAGATTATTAAATTTCTAAATAAAAACAAAAATAT	6	64	1
CAATCTCCAAAATTTTAATATAAGAGAGTTGTGAG	11	168	0
TTTACTATCGAATTTTAAGTCTAAACTTTTTCTC 	2	9	0
GAGAATTAAAAATTTTTAATTTAAATTATAGTTGC	4	54	1
GTATACACTTAATTATAAGTTGAGATTATTAAATT	6	43	1
CTGATCAAGGAGTTGCAATAACAGAGCTTCTTTAG	9	103	1
TTTAAATTATAGTTGCAATTGAAAACGCCCCTAAG	4	73	1
TCTGTATATAAATTGCTATATGAAGAAACAGTAAG	3	96	1
TTTTATAGACAATCTTGAAAAGAGAATTAAAAATT	4	33	1
AGCGACAAATAATTTCTAAAAGAGTCTTTGCTCCT	11	217	1
         AAGTCATAAGAAAAAAAGAAGCATAA	5	1	1
CGTGAAATGCAATTGTTAAAAAAATAAGAGATTTA	4	135	1
      TCAAAATTTTCAATTTAAGTTTCTCTATT	9	4	1
TGAAAGGAGCAGTCTCAAATTCAAAGCCAATTGTA	9	138	0
ATGGGTCAAGAAATTTCAGAAGAGAGGGATAAGGA	11	248	0
    TTTAAAAATTACTTTAATAAATTTACTATCG	2	34	0
CTAAAAGTTGAAATCTTATTCTAAAGAAAGGTCTT	1	123	1
AATAGCCTGTAATTTTTTCTATAGACTCTTGACGA	6	245	1
          **** * * *  ***
MAP Score: 9.52218

Motif 5
AAAAGAAAACGTTGCCTTTTATAGTATGGG	0	52	0
AAAAGGCAACGTTTTCTTTTCTTGGTTTTT	0	62	1
AAATTTTTAATTTTTCCATTTCGGAT    	4	6	0
TCTTTTCAAGATTGTCTATAAAATTTTTAA	4	26	0
AAAATTTTTAATTCTCTTTTCAAGATTGTC	4	40	0
AAGACTTTTATTTTTCTATAAATCTCTTAT	4	158	0
CCCAACGCATTTTTTGTATTGAAGATGACT	4	192	1
TATGCTTCTTTTTTTCTTATGACTT     	5	5	0
TAATCTTTTATTTTTGTAATTGTAGTACT 	6	9	0
TTTAATTATATTTTTGTTTTTATTTAGAAA	6	76	0
AGCCTGTAATTTTTTCTATAGACTCTTGAC	6	248	1
TCTCGGGTTCTTTTCCTATA          	7	81	1
TCAATTTAAGTTTCTCTATTCCCATCCTCA	9	19	1
ATGGAACTGTTTTCTGTTTATAAGGAAGTT	9	62	0
AAACAGTTCCATTCTCTTATTCTCTGATCA	9	80	1
TCAACAAAATTTTCCCTTTTAAGTGGGTTT	9	181	0
CACCCTCTTGTTTGTCTTTTAAAAACTAAA	11	87	0
AAGCCCTCTATTTGTCTTTTTCCCCCATGA	11	118	1
          **********
MAP Score: 9.17792

Motif 6
GTGCCTTTGTGGCACCTCGTTTCCTTCTGACTGCT	1	63	1
GTTTCCTTCTGACTGCTCTTCTCTCTCTACTCAAC	1	81	1
TTTTATTGAAGAGACCTTTCTTCACCAGTATACTA	3	38	1
AATCCACCACGGACTCCGACCTCCCATGTCTTCAA	3	209	1
TCAGTAGTTAGGGGCCCCGATTCTTAGGGGCGTTT	4	95	0
TAGAAAAATAAAAGTCTTCCTTCCCAACGCATTTT	4	170	1
CCCTGTGTTAAGATACCTCCTTCATAGCTAAACTA	6	173	1
    CTCTTTGATCGCTGCCCTCCTCGTAAAAAAG	7	6	1
TTTCAATTTAAGTTTCTCTATTCCCATCCTCATAA	9	17	1
TTGAATTTGAGACTGCTCCTTTCATAATCACAAAA	9	149	1
AATTTTGTTGAGCCACTCAGTTCACGAGTGAAACT	9	200	1
TTCTCTTCAGAACCGCCTTCTTCATCTTTTTCAGT	11	37	0
AATTTCTAAAAGAGTCTTTGCTCCTTATCCCTCTC	11	227	1
          **   ***  *****
MAP Score: 2.36846

Motif 7
GTAAAAGTTACATGGGGTTTTT        	0	2	0
AAAATTACTTTAATAAATTTACTATCGAAT	2	31	0
AAGTCTTTGGTAAGGGGTTTTTTTTATTGA	3	17	1
TGTATCTTTATAAGAAGTTTCTTCTGTATA	3	74	1
TACGCCTCCTTAAGGTATTTCTATCCTGAA	3	148	1
CCCCGATTCTTAGGGGCGTTTTCAATTGCA	4	86	0
GTTAAAAAAATAAGAGATTTATAGAAAAAT	4	149	1
TAGAAATGCTTAATAGGGTTGTCTCTC   	4	275	1
TCTTTTAAGCTAGTAGATTTAGTTTAGCTA	6	197	0
CCGAGAAGGTCAAGAGAATTTAGCACTCGA	7	57	0
CCCATCCTCTTATGAGGATGGGAATAGAGA	9	31	0
TTTCTGTTTATAAGGAAGTTTCCCATCCTC	9	52	0
GATCAGAGAATAAGAGAATGGAACTGTTTT	9	79	0
ATTCTCTGATCAAGGAGTTGCAATAACAGA	9	98	1
CGAGTGAAACTACGGGATTTCTCGTTCAAT	9	224	1
AAAAGACAAACAAGAGGGTGAAAGCCCTCT	11	97	1
AATTTTAATATAAGAGAGTTGTGAGTATGG	11	163	0
ATGAATGGGTCAAGAAATTTCAGAAGAGAG	11	257	0
          **********
MAP Score: 0.877048