AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_operons028_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944243000
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	kdsB	300	CMP-2-keto-3-deoxyoctulosonic acid synthetase
#1	accA	132	AcCoA Carboxylase/Transferase Alpha
#2	CT266	117	hypothetical protein
#3	himD	219	Integration Host Factor Alpha
#4	murE	300	UDP-N-acetylmuramoylalanylglutamyl DAP Ligase

Motif 1
GAGAGCCTATGAGAAGGCTTGTAAATATCTA	0	46	0
CCAATAAGTTAAGAAAGCTAGTAGCTCTGTG	0	137	1
GTAGCTCTGTGAATAATCTTGATTGTTAACG	0	157	1
CTAGTCATATGAATATGTTTGGTAAGGGCCT	0	228	1
CCTACTGTATAAGAAGTTTTGCTTCTTAGGT	0	256	1
AAGAGAAATTAAAATTGTTTGCGTGAAACAA	1	19	1
GCTTCAGCGTAAGCAAGCTTGACTCTAAATT	2	53	1
CAATGGCAAAAAATAATCTTGAGGAAATTTA	2	78	0
ATTCGTAGTGGAGAAGGTTTCGGTTGAGTGC	3	58	1
GAAAAGATAAAAAAAGTCTTGAATCCAAAGG	3	118	1
ATGGAGCAAAGAAATGTTTTGTTTGTGAGAT	4	110	0
GTAAAAAGACGAGTTCTCTTGTCTTTGCTCT	4	167	1
GTAGTTAGTCGACAAAGCTTGACAACGAATA	4	214	1
TAAACTATTTGAGAAAGCTTTTTGAAGCCCT	4	254	1
          ***** *****
MAP Score: 11.4873

Motif 2
GAAATTAAAATTGTTTGCGTGAAACAAAGG	1	23	1
TGGTTTTTGGTTGTTTTTGATTATTGTTTG	1	71	1
TTTTTGATTATTGTTTGTATTAAAATAACT	1	84	1
TTTCCCGGCTTTGCTTTCGATCGTAGAGTC	2	21	1
CTCAAGATTATTTTTTGCCATTGGACGTCT	2	86	1
CGTGGGTAGATTTTGTGCGTTCATGGAAAA	3	93	1
AAGAAATGTTTTGTTTGTGAGATGTAATTA	4	103	0
AAGAGTTACTTTTTTTGTGAAAGAGTAAAA	4	143	1
TTTGAAGCCCTTGTGTGCGTGTCTTAGGGA	4	274	1
          **********
MAP Score: 7.74629

Motif 3
TTTATGATGTTATTTACTATTTTTC       	0	3	0
TTGGATAATGTATTTGATTATTTTTCACGAAT	0	109	0
CTACTAGCTTTCTTAACTTATTGGATAATGTA	0	129	0
TGTATAAGAAGTTTTGCTTCTTAGGTGGGACG	0	261	1
TATAATCAAATAGTTGGTTTTTGGTTGTTTTT	1	57	1
TTTTTGGTTGTTTTTGATTATTGTTTGTATTA	1	74	1
ATTCAAGACTTTTTTTATCTTTTCCATGAACG	3	110	0
ATGAAATTGCTCTTTTCTTTATTATTAGTTTC	4	72	0
ACAAAACATTTCTTTGCTCCATATAAGAGTTA	4	119	1
CTCCATATAAGAGTTACTTTTTTTGTGAAAGA	4	135	1
AGAACTCGTCTTTTTACTCTTTCACAAAAAAA	4	152	0
AGTTCTCTTGTCTTTGCTCTTTCTCTGACAGA	4	178	1
          * ******* **
MAP Score: 5.08576

Motif 4
CGAATATAGGAACGAAGAGAGCCTATGAGA	0	63	0
CCCGACCATCCTAACAAGGAGATCGTTAAC	0	181	0
TTTAATTTCTCTTAAAAAGAAA        	1	2	0
ACCTTTGTTTCACGCAAACAATTTTAATTT	1	24	0
ACAAACAATAATCAAAAACAACCAAAAACC	1	72	0
GAGTTATTTTAATACAAACAATAATCAAAA	1	85	0
CTCCCTTCTTATAAAAAAGAGTTATTTTAA	1	103	0
TGACTCTACGATCGAAAGCAAAGCCGGGAA	2	22	0
      AGTTAATAAAAAGACGTCCAATGG	2	103	0
CCTTTAAGTGCTCGAAAGGATATTCGTAGT	3	37	1
TTGTGCGTTCATGGAAAAGATAAAAAAAGT	3	105	1
AAAGTCTTGAATCCAAAGGATGAATGCATA	3	130	1
AACTAATAATAAAGAAAAGAGCAATTTCAT	4	74	1
ATAATTACATCTCACAAACAAAACATTTCT	4	102	1
TTTGTGAAAGAGTAAAAAGACGAGTTCTCT	4	156	1
TGTCAGAGAAAGAGCAAAGACAAGAGAACT	4	178	0
          **********
MAP Score: 4.48563

Motif 5
TGATTTATGATGTTATTTACTATTTTTC      	0	4	0
TCATAGGCTCTCTTCGTTCCTATATTCGACACCT	0	65	1
GATGGTCGGGTTCTGTGTACTAGATCCCTAGTCA	0	201	1
         TTTCTTTTTAAGAGAAATTAAAATT	1	1	1
GAGAAATTAAAATTGTTTGCGTGAAACAAAGGTC	1	21	1
TGTTTTTGATTATTGTTTGTATTAAAATAACTCT	1	82	1
TTAAAATAACTCTTTTTTATAAGAAGGGAGCGTG	1	103	1
TCCTCAAGATTATTTTTTGCCATTGGACGTCTTT	2	84	1
AGACTTTTTTTATCTTTTCCATGAACGCACAAAA	3	103	0
ATTATGAAATTGCTCTTTTCTTTATTATTAGTTT	4	73	0
CAAAGAAATGTTTTGTTTGTGAGATGTAATTATG	4	101	0
ATATAAGAGTTACTTTTTTTGTGAAAGAGTAAAA	4	139	1
CTCTTGTCTTTGCTCTTTCTCTGACAGATGACGT	4	182	1
          * ** *** * ***
MAP Score: 4.18278

Motif 6
TAAAGCCCTCCCTCCCCCGGA         	3	1	0
TTATTAGTTTCCTCTCCCGCTTTCCTTATG	4	53	0
ATATTCGACACCTCCCGCGTTTCATTCGTG	0	86	1
 TCTTCTTCCCTTTTCCCGGCTTTGCTTTC	2	9	1
CTACGAATATCCTTTCGAGCACTTAAAGGT	3	36	0
          **********
MAP Score: 2.1719

Motif 7
AAGAGAGCCTATGAGAAGGCTTGTAAATAT	0	49	0
ATCCAATAAGTTAAGAAAGCTAGTAGCTCT	0	135	1
TCCCACCTAAGAAGCAAAACTTCTTATACA	0	261	0
TTGTTTGCGTGAAACAAAGGTCATTATAAT	1	33	1
TCCCTTCTTATAAAAAAGAGTTATTTTAAT	1	102	0
ACTCTTTTTTATAAGAAGGGAGCGTGCTAC	1	111	1
TCTACGATCGAAAGCAAAGCCGGGAAAAGG	2	18	0
     AGTTAATAAAAAGACGTCCAATGGC	2	102	0
AGGGAGGGCTTTAACAAGACCTTTAAGTGC	3	18	1
CATGGAAAAGATAAAAAAAGTCTTGAATCC	3	114	1
CAGCCTGGCATAAGGAAAGCGGGAGAGGAA	4	45	1
AAACTAATAATAAAGAAAAGAGCAATTTCA	4	73	1
TTGTGAAAGAGTAAAAAGACGAGTTCTCTT	4	157	1
AGTAAACTATTTGAGAAAGCTTTTTGAAGC	4	252	1
          **********
MAP Score: 0.807381

Motif 8
GTTAGGATGGTCGGGTTCTGTGTACTAGATCC	0	196	1
TTCATATGACTAGGGATCTAGTACACAGAACC	0	209	0
          TCCGGGGGAGGGAGGGCTTTAA	3	0	1
TGGAGAAGGTTTCGGTTGAGTGCAACTCGTGG	3	66	1
    AATGTGTTGAGGTCTGTTGCTTTGGGAT	4	6	1
GTCTGTTGCTTTGGGATGAGTGTGCAGCCTGG	4	21	1
GTGCGTGTCTTAGGGATCTGGT          	4	288	1
          * *** ******
MAP Score: 0.515851

Motif 9
ATGTATTTGATTATTTTTCACGAATGAAACGCGGGAG	0	97	0
ATAAGAAGTTTTGCTTCTTAGGTGGGACGTCATTAAT	0	264	1
          TTTCTTTTTAAGAGAAATTAAAATTGT	1	0	1
TTTTTGATTATTGTTTGTATTAAAATAACTCTTTTTT	1	84	1
AAAATAACTCTTTTTTATAAGAAGGGAGCGTGCTACG	1	105	1
AAGAAATGTTTTGTTTGTGAGATGTAATTATGAAATT	4	96	0
CATATAAGAGTTACTTTTTTTGTGAAAGAGTAAAAAG	4	138	1
          ** *** *   ***  *
MAP Score: 0.199318