AlignACE 3.0 10/20/99
AlignACE2 -i EC_operons130_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943443936
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	caiC	58	probable crotonobetaine/carnitine-CoA ligase
#1	caiB	128	l-carnitine dehydratase
#2	caiA	30	probable carnitine operon oxidoreductase
#3	caiT	300	probable carnitine transporter
#4	lacA	65	thiogalactoside acetyltransferase
#5	lacY	51	galactoside permease (M protein)
#6	lacZ	122	beta-D-galactosidase
#7	lacI	76	transcriptional repressor of the lac operon
#8	mhpR	76	transcriptional regulator for mhp operon
#9	ydbO	284	orf, hypothetical protein
#10	b1398	26	orf, hypothetical protein
#11	b1399	100	orf, hypothetical protein
#12	yrdA	300	putative transferase

Motif 1
        ACGCGTGGCGTCAGTCGGCTTGCCTG	0	2	1
AGACGCATCAGCGTCGCATCAGGCAGCGCACGGA	1	11	0
CGACGCTGATGCGTCTTATCAGGCCTACGGGAGC	1	29	1
TGCGGCGTAAACGCTTTATCCGGCCTACATTCGT	1	63	0
TAAAGCGTTTACGCCGCATCCGGCAGTCATGCGC	1	79	1
TAAGGCGCTCGCGCCGCATCCGACATTGATTGC 	4	9	0
TGCGGCGCGAGCGCCTTATCCGACCAACATATCA	4	25	1
GGATTTCCTTACGCGAAATACGGGCAGACATGGC	5	24	0
ATGTCGTTGCGCGCACAGTACAGCGCAACTTATT	8	35	1
TAAAAATAGGGTGCGAAATCCGTCACAGTTCAAA	9	155	1
TCTGGCCCTGGCGCTTTACCCCACCAGGGCCAGA	11	17	0
   GCCGCCAGCGTTCAATCTGAGCCATGATCAA	12	7	1
AAAGAGGAAAGCGTAATATACGCCACCTCGCGAC	12	222	0
          ****   ***** *
MAP Score: 26.7494

Motif 2
GCATCAGCGTCGCATCAGGCAGCGCACGGA	1	11	0
CCTGATAAGACGCATCAGCGTCGCATCAGG	1	22	0
GCTGATGCGTCTTATCAGGCCTACGGGAGC	1	33	1
GCGTAAACGCTTTATCCGGCCTACATTCGT	1	63	0
GCGTTTACGCCGCATCCGGCAGTCATGCGC	1	83	1
GCGCTCGCGCCGCATCCGACATTGATTGC 	4	9	0
GCGCGAGCGCCTTATCCGACCAACATATCA	4	29	1
AGTTAGCTCACTCATTAGGCACCCCAGGCT	6	29	1
TTACACTTTATGCTTCCGGCTCGTATGTTG	6	59	1
TGAATTGACTCTCTTCCGGGCGCTATCATG	7	45	0
         TCGCTTCAGTCTGTTGTTATT	11	89	0
TCAGATTGAACGCTGGCGGC          	12	0	0
TACGTGTTCACTCTTGAGACTTGGTATTCA	12	92	1
TCTTTAACAATTTATCAGACAATCTGTGTG	12	164	0
          **********
MAP Score: 16.8435

Motif 3
AGACGCATCAGCGTCGCATCAGGCAGCGCACG	1	13	0
CGACGCTGATGCGTCTTATCAGGCCTACGGGA	1	29	1
GCCTACATTCGTGCTCCCGTAGGCCTGATAAG	1	43	0
GCCGGATAAAGCGTTTACGCCGCATCCGGCAG	1	73	1
AGCCATTAACGCGTCCACGAGGTTAATAATAA	3	203	1
TATTTATTTTGCGTTCCCGTTTGTTTTATTTT	3	253	0
AAATAAATATTCGTTTTCACAGTGGAATTAAC	3	276	1
TAAGGCGCTCGCGCCGCATCCGACATTGATTG	4	11	0
TGCGGCGCGAGCGCCTTATCCGACCAACATAT	4	25	1
         TGCGATCACTCCGTTATGATATG	4	52	0
      TGTAGGGTACTCGCAGGTTGATATGC	10	10	0
   GCCGCCAGCGTTCAATCTGAGCCATGATC	12	7	1
AATGAATTACGTGTTCACTCTTGAGACTTGGT	12	85	1
GTATCTTCGAGTGCCCACACAGATTGTCTGAT	12	149	1
GCTGAAAGCCGCGTCGCAACTGCTCTTTAACA	12	185	0
CTGAAATTCAGGGTTGACTCTGAAAGAGGAAA	12	246	0
          ****** *** *
MAP Score: 10.2647

Motif 4
TGCCTGACTAGCGCCCGCCCAATAACAAAC	0	30	1
GCATCAGGCAGCGCACGGAC          	1	0	0
CATCAGCGTCGCATCAGGCAGCGCACGGAC	1	10	0
CTGATAAGACGCATCAGCGTCGCATCAGGC	1	21	0
GCCGGATGCGGCGTAAACGCTTTATCCGGC	1	73	0
CGTTTACGCCGCATCCGGCAGTCATGCGCT	1	84	1
AGCCATTAACGCGTCCACGAGGTTAATAAT	3	203	1
GTCGGATGCGGCGCGAGCGCCTTATCCGAC	4	19	1
CCCGTATTTCGCGTAAGGAAATCCATT   	5	34	1
          GCGCAACGCAATTAATGTGA	6	0	1
TGGCATGATAGCGCCCGGAAGAGAGTCAAT	7	42	1
TGTACTGTGCGCGCAACGACATTTTGTCCG	8	27	0
GCGCTTTACCCCACCAGGGCCAGACGATAC	11	11	0
GTGGGGTAAAGCGCCAGGGCCAGAAGTCGA	11	27	1
         GCCGCCAGCGTTCAATCTGAG	12	1	1
          **********
MAP Score: 10.2433

Motif 5
        ACGCGTGGCGTCAGTCGGCTTGCCTG	0	2	1
AGACGCATCAGCGTCGCATCAGGCAGCGCACGGA	1	11	0
CGACGCTGATGCGTCTTATCAGGCCTACGGGAGC	1	29	1
TAAAGCGTTTACGCCGCATCCGGCAGTCATGCGC	1	79	1
AATGTCGGATGCGGCGCGAGCGCCTTATCCGACC	4	16	1
AAGAGCAGTTGCGACGCGGCTTTCAGCTCACTGT	12	190	1
          *** **** * * *
MAP Score: 6.60404

Motif 6
TTGTTATTGGGCGGGCGCTAGTCAGGCAAG	0	28	0
GCATCAGGCAGCGCACGGAC          	1	0	0
TATCAGGCCTACGGGAGCACGAATGTAGGC	1	45	1
AATAAAACAAACGGGAACGCAAAATAAATA	3	255	1
GTCGGATGCGGCGCGAGCGCCTTATCCGAC	4	19	1
    TAATAACCGGGCAGGCCATGTCTGCC	5	6	1
TACGCGAAATACGGGCAGACATGGCCTGCC	5	19	0
TGACTCTCTTCCGGGCGCTATCATGCCATA	7	40	0
AAATGTCGTTGCGCGCACAGTACAGCGCAA	8	33	1
GTGGGGTAAAGCGCCAGGGCCAGAAGTCGA	11	27	1
          **********
MAP Score: 2.97225

Motif 7
TGCCTGACTAGCGCCCGCCCAATAACAAAC	0	30	1
AGCGTCGCATCAGGCAGCGCACGGAC    	1	6	0
AATAAAACAAACGGGAACGCAAAATAAATA	3	255	1
GTCGGATGCGGCGCGAGCGCCTTATCCGAC	4	19	1
    TAATAACCGGGCAGGCCATGTCTGCC	5	6	1
AAAACCTTTCGCGGTATGGCATGATAGCGC	7	26	1
GCGCTTTACCCCACCAGGGCCAGACGATAC	11	11	0
GTGGGGTAAAGCGCCAGGGCCAGAAGTCGA	11	27	1
         GCCGCCAGCGTTCAATCTGAG	12	1	1
          **********
MAP Score: 2.59333

Motif 8
TTCTGTGATTGGTATCACATTTTTGTTTCGGG	3	142	0
TGTTTTATTTTTGTTAACATTTAATATAATTA	3	232	0
ATAAATATTCGTTTTCACAGTGGAATTAACTC	3	278	1
AGGCACCCCAGGCTTTACACTTTATGCTTCCG	6	45	1
GAATTGTGAGCGGATAACAATTTCACACAGGA	6	93	1
ACTCTCCAGATGTTTCACATTTCTGTTGCTAA	9	14	1
TATGATTCGCGATTTAACTATTAGCAACAGAA	9	34	0
ACAGATCGCATAGTTAACATTTCGTTAAAAGA	9	78	0
GGGTGCGAAATCCGTCACAGTTCAAACATACA	9	163	1
TTTGTGATTTTACTTAACTATTGTGTAACTTT	9	198	1
AATGAATTACGTGTTCACTCTTGAGACTTGGT	12	85	1
TCGCAACTGCTCTTTAACAATTTATCAGACAA	12	172	0
          * ******* **
MAP Score: 2.26322

Motif 9
   ACGCGTGGCGTCAGTCGGCTTGCCTGACT	0	7	1
CAGTCGGCTTGCCTGACTAGCGCCCGCCCAAT	0	21	1
TCCGTGCGCTGCCTGATGCGACGCTGATGCGT	1	11	1
ACGAATGTAGGCCGGATAAAGCGTTTACGCCG	1	63	1
AAGCGTTTACGCCGCATCCGGCAGTCATGCGC	1	81	1
AGGCGCTCGCGCCGCATCCGACATTGATTGC 	4	9	0
CGGCGCGAGCGCCTTATCCGACCAACATATCA	4	27	1
CATGATAGCGCCCGGAAGAGAGTCAATTCAGG	7	45	1
          ******  ****
MAP Score: 1.54027

Motif 10
CGCCCGCCCAATAACAAACGAACAAAA        	0	41	1
GGTGATCCATAAAACAATATTGAAAATTTCTTTTT	3	16	0
ACAACAGAGCATAACAAACTGATTATTAATCAAAA	3	82	1
TTCACCCGAAACAAAAATGTGATACCAATCACAGA	3	138	1
CACGAGGTTAATAATAATTATATTAAATGTTAACA	3	218	1
TTAAATGTTAACAAAAATAAAACAAACGGGAACGC	3	240	1
TTGTGAGCGGATAACAATTTCACACAGGAAACAGC	6	96	1
GCAACTGCGGAAAACATTAATGCACTGATAAATAA	9	113	1
ATAATGATTTATAAAAATAGGGTGCGAAATCCGTC	9	144	1
TAACTTTCATAAAACAATGTGATTCGTGTTTTTAA	9	223	1
TTCATAAATCACAACAATAACAACAGACTGAAGCG	11	74	1
CAACGAAGAGAAAAAAATCCTGAAATTCAGGGTTG	12	262	0
          * ******   ** *
MAP Score: 1.43788

Motif 11
AGACGCATCAGCGTCGCATCAGGCAGCGCA	1	15	0
TAAAGCGTTTACGCCGCATCCGGCAGTCAT	1	79	1
CGGCAGTCATGCGCTACATAAATTTTTCAG	1	99	1
ACAAACGGGAACGCAAAATAAATATTCGTT	3	261	1
TAAGGCGCTCGCGCCGCATCCGACATTGAT	4	13	0
TGCGGCGCGAGCGCCTTATCCGACCAACAT	4	25	1
          GCGCAACGCAATTAATGTGA	6	0	1
GGAATTGTGAGCGGATAACAATTTCACACA	6	92	1
CCATCGAATGGCGCAAAACCTTTCGCGGTA	7	12	1
TGTACTGTGCGCGCAACGACATTTTGTCCG	8	27	0
GCACAGTACAGCGCAACTTATTTTGTTAAA	8	47	1
TAGTTAAATCGCGAATCATAAAAAGCAAAG	9	46	1
TATAGCAACTGCGGAAAACATTAATGCACT	9	109	1
TCTGGCCCTGGCGCTTTACCCCACCAGGGC	11	21	0
          **********
MAP Score: 0.987759