AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_profile005_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944239013
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	kdsB	175	deoxyoctulonosic Acid Synthetase
#1	zwf	85	Glucose-6-P Dehyrogenase
#2	acpP	155	Acyl Carrier Protein
#3	rs1	300	S1 Ribosomal Protein
#4	CPn0767	101	CT645 hypothetical protein
#5	pcnB_1	29	Poly A Polymerase
#6	clpP_2	178	CLP Protease Subunit
#7	rsbV_2	47	Sigma Regulatory Factor
#8	pcnB_2	300	Poly A Polymerase

Motif 1
CCCTTCGAGATTTTTATTTTGTAAAATAAA	0	52	1
CGCAATATTTTTTTTATTTTTCTGAAAAAA	0	88	0
CTTGTTTTGTTTTTTAGTTTATT       	0	3	0
TTTTAGAAACTTTTTACTTTTTGTTATTTT	1	34	1
AACTACGGGATTTTAATTTTAGAAACTTTT	1	18	1
CATCTTTTGTTTTTCATTTTTATCCTTGAA	8	180	1
AAGGCCTCTTTTTTAACTTTTCTATATTAC	3	132	0
AACTAGATATTTTTTATTCCATGCTTTTTA	8	30	1
       CTCTTTTTAGTTCCTATTTTAGG	5	3	1
CTTCCAAGACTTTTAACTCTTAATAACTAT	8	276	1
TTTTTACTTTTTGTTATTTTCGCAAGTGCG	1	44	1
AAAAAATCATTTTTTATTCGACGGTTACTT	2	56	0
TAGCTAAGACTTTTTAGGCTGTCTACGTCA	6	88	0
       TTATTGTTATTCTCCTAAAAACT	3	287	0
AAAAAAAAGTATTTTATTTTACAAAATAAA	0	64	0
GTCTTGCCTTTTTTAAGGTTTATATTTACA	3	238	1
AATAGCTGCCTTTATATTTTAAGAATTCTT	4	15	0
       TATATTTTACTCTCTTAATTATA	4	88	0
CCTCTTCAATTTTTAATTATATATGGATCA	8	135	0
GAATTCGAGATTTTAATGTCTAAGCTTGTT	6	56	1
CATCAAATAATTTTCAGTTGTGTCCATACG	6	147	0
ACACTGTCTTTTTTGACTTTGTAGTTTTTA	3	265	1
          **********
MAP Score: 21.037

Motif 2
GATTTTTATTTTGTAAAATAAAATACTTTTTTTTCAGAAAAA	0	60	1
TTCAGAAAAATAAAAAAAATATTGCGTTTTATAAAATGCATC	0	92	1
ATCCTGGTAGTCTTAAACACATAAGTTTTTGTTAGGTATCTC	0	140	1
       TCATCAAAAACTACGGGATTTTAATTTTAGAAACT	1	3	1
GATTTTAATTTTAGAAACTTTTTACTTTTTGTTATTTTCGCA	1	26	1
AGAATTAGTATCGCAAAAAATCATTTTTTATTCGACGGTTAC	2	58	0
GGGGTGCTTATGAAAAAAACGATATGTTTTCTATGCGCCAAA	3	25	1
TTGAATTCTGTCAGAAACTAGATATTTTTTATTCCATGCTTT	8	15	1
GGAATCTCTATAGAAAACATCTTTTGTTTTTCATTTTTATCC	8	163	1
ATTTTTATCCTTGAAAACTTCCCTAGTTTTGCTATGTTGGGA	8	195	1
          *   ****        **** *
MAP Score: 14.9986

Motif 3
ATAATATCCCTTCGAGATTTTTATTTTGTAA	0	45	1
CATCAAAAACTACGGGATTTTAATTTTAGAA	1	11	1
        GGGACGAGAATTTATGGGGTGCT	3	2	1
TTTTCTATATTACCAGATTTTATAAAATACG	3	114	0
AGAACGGAAGTATAGGATTTTACGATTAATT	3	172	1
GAATTCTATGTTTAAGACTTTCTTGGGTCAA	6	31	0
AAACATAGAATTCGAGATTTTAATGTCTAAG	6	49	1
TAGGAACGTAGCTAAGACTTTTTAGGCTGTC	6	95	0
GTTTTGCTATGTTGGGATTTTAAAATGGAAG	8	220	1
CTCTTTTTCTTCCAAGACTTTTAACTCTTAA	8	268	1
          * *********
MAP Score: 10.0719

Motif 4
          AATAAACTAAAAAACAAAACAAGATAACT	0	0	1
AAAAGTATTTTATTTTACAAAATAAAAATCTCGAAGGGA	0	51	0
TATTTTTTTTATTTTTCTGAAAAAAAAGTATTTTATTTT	0	74	0
ATAATCCTGGTAGTCTTAAACACATAAGTTTTTGTTAGG	0	137	1
AAAAAGTAAAAAGTTTCTAAAATTAAAATCCCGTAGTTT	1	17	0
  GACAATAGAAGAAAGGGATTTGAAAATTTCTCTTCGA	2	8	1
TTCGAGAACTAATTAAGTAACCGTCGAATAAAAAATGAT	2	42	1
TGAAGTATTGTATAGTTTAAATAGTAAAAGGATATAAGC	2	125	1
TAAAATCTGGTAATATAGAAAAGTTAAAAAAGAGGCCTT	3	123	1
TGTAAATATAAACCTTAAAAAAGGCAAGACCTCCCTTGC	3	229	0
TATTCTCCTAAAAACTACAAAGTCAAAAAAGACAGTGTA	3	264	0
  AGCTCAAGAATTCTTAAAATATAAAGGCAGCTATTTT	4	8	1
 GACACCCCTAAAATAGGAACTAAAAAGAG         	5	1	0
AAGGATGTAAAAAGCATGGAATAAAAAATATCTAGTTTC	8	28	0
ATGATCCATATATAATTAAAAATTGAAGAGGAATCTCTA	8	134	1
TTTCAAGGATAAAAATGAAAAACAAAAGATGTTTTCTAT	8	172	0
TAAGAGTTAAAAGTCTTGGAAGAAAAAGAGTGTGTAGTT	8	259	0
          **   *  ***    ****
MAP Score: 3.44632