AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_operons010_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944237667
 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	vacB	270	ribonuclease family
#7	oppA_5	21	Oligopeptide Binding Lipoprotein
#8	CPn0600	300	hypothetical protein

Motif 1
CCCCCATACTATAAAAGGCAACGTTTTCTT	0	50	1
 AAAAAACCAAGAAAAGAAAACGTTGCCTT	0	64	0
GTTTGCGAGATTAAAAGAGGTG        	1	2	0
AGAAGAGCAGTCAGAAGGAAACGAGGTGCC	1	73	0
GAAATCTTATTCTAAAGAAAGGTCTTTT  	1	132	1
          ACAAAAGAAGTCTTTGGTAA	3	0	1
GGTTTTTTTTATTGAAGAGACCTTTCTTCA	3	32	1
TATTGTATCTTTATAAGAAGTTTCTTCTGT	3	71	1
CAATTTATATACAGAAGAAACTTCTTATAA	3	81	0
GTTCATATGGATTGAAGACATGGGAGGTCG	3	225	0
TAGACAATCTTGAAAAGAGAATTAAAAATT	4	38	1
       AAGTCATAAGAAAAAAAGAAGCA	5	3	1
ATTCCCATCCTCATAAGAGGATGGGAAACT	6	36	1
TGTTTTCTGTTTATAAGGAAGTTTCCCATC	6	55	0
AGCCAATTGTACTAAAGAAGCTCTGTTATT	6	119	0
CAAAACCCACTTAAAAGGGAAAATTTTGTT	6	179	1
AGAAGGCGGTTCTGAAGAGAATACTGCTGA	8	51	1
TTTTTAGTTTTTAAAAGACAAACAAGAGGG	8	85	1
CAAAATTTTAATATAAGAGAGTTGTGAGTA	8	166	0
TCAAGAAATTTCAGAAGAGAGGGATAAGGA	8	248	0
          **********
MAP Score: 15.6444

Motif 2
ACTTCCTTATAAACAGAAAACAGTTCCATTCTCT	6	63	1
AGAGAAACTTAAATTGAAAATTTTGA        	6	2	0
AGCGACACTCAAACTGAAAAAGATGAAGAAGGCG	8	25	1
AGATTTATAGAAAAATAAAAGTCTTCCTTCCCAA	4	163	1
CCGAAATGGAAAAATTAAAAATTTTATAGACAAT	4	12	1
AAAAAACCAAGAAAAGAAAACGTTGCCTTTTATA	0	59	0
TGTCTTTTAAAAACTAAAAACTATTCAGCAGTAT	8	71	0
ACTATAATTTAAATTAAAAATTTTTAATTCTCTT	4	52	0
AACCCACTTAAAAGGGAAAATTTTGTTGAGCCAC	6	182	1
AACTTCTTATAAAGATACAATAGTATACTGGTGA	3	59	0
TTCTATCCTGAAAGATACAATAATCTCATTCCCC	3	166	1
GAAGATGACTAAAAATGAAAGTATAATGACTTAA	4	212	1
CGCATCCCTAAAAGTTGAAATCTTATTCTAAAGA	1	116	1
AAGTCATAAGAAAAAAAGAAGCATAAACTT    	5	10	1
ATGAGGATGGGAATAGAGAAACTTAAATTGAAAA	6	16	0
CAATTGTTAAAAAAATAAGAGATTTATAGAAAAA	4	144	1
          *** ******   *
MAP Score: 15.147

Motif 3
TCAAGAACTGAATCTTATACTAAACTGGGTGCCT	1	35	1
TAAAAGTTGAAATCTTATTCTAAAGAAAGGTCTT	1	124	1
TTAGACTTAAAATTCGATAGTAAATTTATTAAAG	2	20	1
TGGTAAGGGGTTTTTTTTATTGAAGAGACCTTTC	3	24	1
TATACTATTGTATCTTTATAAGAAGTTTCTTCTG	3	66	1
ATAAGAAGTTTCTTCTGTATATAAATTGCTATAT	3	83	1
TCCTTAAGGTATTTCTATCCTGAAAGATACAATA	3	154	1
TATAGTACTCAATTTGCTACTTAATATTACGTTC	3	251	0
AAAAATTAAAAATTTTATAGACAATCTTGAAAAG	4	21	1
AAAAATTTTTAATTCTCTTTTCAAGATTGTCTAT	4	37	0
GAGAATTAAAAATTTTTAATTTAAATTATAGTTG	4	54	1
ATAAATCTCTTATTTTTTTAACAATTGCATTTCA	4	137	0
GGAAGACTTTTATTTTTCTATAAATCTCTTATTT	4	156	0
TCCCAACGCATTTTTTGTATTGAAGATGACTAAA	4	191	1
CCTATTAAGCATTTCTACCTTGAAGTAGACCTCA	4	258	0
      TCAAAATTTTCAATTTAAGTTTCTCTAT	6	4	1
AATGGAACTGTTTTCTGTTTATAAGGAAGTTTCC	6	59	0
TCCATTCTCTTATTCTCTGATCAAGGAGTTGCAA	6	87	1
TATTCAGCAGTATTCTCTTCAGAACCGCCTTCTT	8	50	0
TACTCACAACTCTCTTATATTAAAATTTTGGAGA	8	166	1
          ****** *  * **
MAP Score: 12.7599

Motif 4
CAAGAGGGTGAAAGCCCTCTATTTGTCTTTTTCC	8	107	1
        TCAAAATTTTCAATTTAAGTTTCTCT	6	2	1
ATTTTTCTATAAATCTCTTATTTTTTTAACAATT	4	145	0
GTGGCTCAACAAAATTTTCCCTTTTAAGTGGGTT	6	182	0
ATAGAAAAATAAAAGTCTTCCTTCCCAACGCATT	4	169	1
         AAAAGACCTTTCTTTAGAATAAGAT	1	135	0
AAGAGAATTAAAAATTTTTAATTTAAATTATAGT	4	52	1
GATTGTCTATAAAATTTTTAATTTTTCCATTTCG	4	13	0
TATAAACAGAAAACAGTTCCATTCTCTTATTCTC	6	70	1
TTTTCAATTTAAGTTTCTCTATTCCCATCCTCAT	6	16	1
CAAGAAAAGAAAACGTTGCCTTTTATAGTATGGG	0	52	0
ATTGAACGAGAAATCCCGTAGTTTCACTCGTGAA	6	220	0
TTTGAATTTGAGACTGCTCCTTTCATAATCACAA	6	148	1
AGTCTTTGGTAAGGGGTTTTTTTTATTGAAGAGA	3	18	1
TTTTTATTGAAGAGACCTTTCTTCACCAGTATAC	3	37	1
ACCCCTTACCAAAGACTTCTTTTGT         	3	1	0
          ***  ****  ***
MAP Score: 10.9467

Motif 5
AGACAATCTTGAAAAGAGAATTAAAAATTTTT	4	39	1
TTGTTAAAAAAATAAGAGATTTATAGAAAAAT	4	147	1
AACAGTAAGTAATAGGAGCATTAGGATACGCC	3	122	1
AAATAATTTCTAAAAGAGTCTTTGCTCCTTAT	8	223	1
AATGCGTTGGGAAGGAAGACTTTTATTTTTCT	4	171	0
AACCCACTTAAAAGGGAAAATTTTGTTGAGCC	6	182	1
        ACAAAAGAAGTCTTTGGTAAGGGG	3	2	1
AAAATTTTAATATAAGAGAGTTGTGAGTATGG	8	163	0
CTCATAAGAGGATGGGAAACTTCCTTATAAAC	6	45	1
GTATACTGGTGAAGAAAGGTCTCTTCAATAAA	3	39	0
AGGCGGTTCTGAAGAGAATACTGCTGAATAGT	8	54	1
ATCTTATTCTAAAGAAAGGTCTTTT       	1	135	1
AGAAATTTCAGAAGAGAGGGATAAGGAGCAAA	8	243	0
TTGTGATTATGAAAGGAGCAGTCTCAAATTCA	6	150	0
AAAACCAAGAAAAGAAAACGTTGCCTTTTATA	0	59	0
ATTGTATCTTTATAAGAAGTTTCTTCTGTATA	3	72	1
    ATCCGAAATGGAAAAATTAAAAATTTTA	4	6	1
CCAATTGTACTAAAGAAGCTCTGTTATTGCAA	6	115	0
GTCATAAGAAAAAAAGAAGCATAAACTT    	5	12	1
          ********  **
MAP Score: 8.57568

Motif 6
CCCCATACTATAAAAGGCAACGTTTTCTTTTCTTGGTTTT	0	51	1
ATCCGAAATGGAAAAATTAAAAATTTTATAGACAATCTTG	4	10	1
AGACAATCTTGAAAAGAGAATTAAAAATTTTTAATTTAAA	4	39	1
TGCAATTGTTAAAAAAATAAGAGATTTATAGAAAAATAAA	4	142	1
GAGATTTATAGAAAAATAAAAGTCTTCCTTCCCAACGCAT	4	162	1
AAGTCATAAGAAAAAAAGAAGCATAAACTT          	5	10	1
ACTTCCTTATAAACAGAAAACAGTTCCATTCTCTTATTCT	6	63	1
AAAACCCACTTAAAAGGGAAAATTTTGTTGAGCCACTCAG	6	180	1
TTAGGACATTGAACGAGAAATCCCGTAGTTTCACTCGTGA	6	221	0
CTCAAACTGAAAAAGATGAAGAAGGCGGTTCTGAAGAGAA	8	32	1
TTTAGTTTTTAAAAGACAAACAAGAGGGTGAAAGCCCTCT	8	87	1
TCATGGGGGAAAAAGACAAATAGAGGGCTTTCACCCTCTT	8	108	0
          ******  **        **
MAP Score: 1.80417

Motif 7
AATATGAGCAAGTAAAAGTTACATGGGGTT	0	13	0
GTTTAGTATAAGATTCAGTTCTTGACAAGT	1	30	0
         GAGAAAAAGTTTAGACTTAAA	2	1	1
CTTCTTATAAAGATACAATAGTATACTGGT	3	61	0
TGCTATATGAAGAAACAGTAAGTAATAGGA	3	109	1
CTATCCTGAAAGATACAATAATCTCATTCC	3	168	1
CGTAATATTAAGTAGCAAATTGAGTACTAT	3	254	1
TTTAAATTATAGTTGCAATTGAAAACGCCC	4	73	1
CATTTCACGTAGATTCAGTAGTTAGGGGCC	4	114	0
AATCTACGTGAAATGCAATTGTTAAAAAAA	4	129	1
     TCAAAATTTTCAATTTAAGTTTCTC	6	5	1
CTGATCAAGGAGTTGCAATAACAGAGCTTC	6	103	1
          **********
MAP Score: 0.137776