AlignACE 3.0 10/20/99
AlignACE2 -i EC_sum_all136_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943445263
 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
TACGTGTTCACTCTTGAGACTTGGTATTCA	12	92	1
TCTTTAACAATTTATCAGACAATCTGTGTG	12	164	0
          **********
MAP Score: 16.9341

Motif 3
GTCGCATCAGGCAGCGCACGGAC       	1	3	0
AGACGCATCAGCGTCGCATCAGGCAGCGCA	1	15	0
ACTGCCGGATGCGGCGTAAACGCTTTATCC	1	76	0
AAAAATTTATGTAGCGCATGACTGCCGGAT	1	96	0
TAAGGCGCTCGCGCCGCATCCGACATTGAT	4	13	0
 CACCATCGAATGGCGCAAAACCTTTCGCG	7	9	1
CGCGCACAGTACAGCGCAACTTATTTTGTT	8	44	1
CGGATTCTTAACGTCGCAAGACGAAAAATG	12	120	0
GCTGAAAGCCGCGTCGCAACTGCTCTTTAA	12	187	0
CTGTCGCGAGGTGGCGTATATTACGCTTTC	12	220	1
          **********
MAP Score: 7.81664

Motif 4
GCATCAGCGTCGCATCAGGCAGCGCACGGAC	1	10	0
GCGTTTACGCCGCATCCGGCAGTCATGCGCT	1	83	1
GGCAGTCATGCGCTACATAAATTTTTCAGGA	1	100	1
       CGTAGCAAAAAGAAATTTTCAATA	3	3	1
CTCACAACAGAGCATAACAAACTGATTATTA	3	79	1
TCTATTCACCCGAAACAAAAATGTGATACCA	3	134	1
CAAACGGGAACGCAAAATAAATATTCGTTTT	3	262	1
GCGCTCGCGCCGCATCCGACATTGATTGC  	4	8	0
GCCCGTATTTCGCGTAAGGAAATCCATT   	5	33	1
TTTAACTATTAGCAACAGAAATGTGAAACAT	9	23	0
AGTTAAATCGCGAATCATAAAAAGCAAAGGA	9	47	1
CGTCGCAAGACGAAAAATGAATACCAAGTCT	12	108	0
          ******* ***
MAP Score: 7.7531

Motif 5
GGCAAGCCGACTGACGCCACGCGT        	0	2	0
CGTGCGCTGCCTGATGCGACGCTGATGCGTCT	1	13	1
GCATGACTGCCGGATGCGGCGTAAACGCTTTA	1	79	0
CAATCAATGTCGGATGCGGCGCGAGCGCCTTA	4	11	1
TATCGACTTCTGGCCCTGGCGCTTTACCCCAC	11	27	0
TTCATTTTTCGTCTTGCGACGTTAAGAATCCG	12	118	1
TGTTAAAGAGCAGTTGCGACGCGGCTTTCAGC	12	185	1
TTTCAGCTCACTGTCGCGAGGTGGCGTATATT	12	210	1
          * * ********
MAP Score: 7.27455

Motif 6
TCAGGCAAGCCGACTGACGCCACGCGT      	0	4	0
GTCCGTGCGCTGCCTGATGCGACGCTGATGCGT	1	10	1
GACGCTGATGCGTCTTATCAGGCCTACGGGAGC	1	30	1
GCGGCGTAAACGCTTTATCCGGCCTACATTCGT	1	63	0
AAAGCGTTTACGCCGCATCCGGCAGTCATGCGC	1	80	1
TATGAGTTAGCCATTAACGCGTCCACGAGGTTA	3	195	1
  GCAATCAATGTCGGATGCGGCGCGAGCGCCT	4	8	1
GCGGCGCGAGCGCCTTATCCGACCAACATATCA	4	26	1
CCAGGCTTTACACTTTATGCTTCCGGCTCGTAT	6	52	1
     TTCAGTACCTCACGACTCGGACAAAATG	8	5	1
CTGGCCCTGGCGCTTTACCCCACCAGGGCCAGA	11	17	0
CAGGTCGTATCGACTTCTGGCCCTGGCGCTTTA	11	33	0
GTTATTGTTGTGATTTATGAATCATAGCACAGG	11	62	0
TGCTCTTTAACAATTTATCAGACAATCTGTGTG	12	164	0
          ** ** ***** *
MAP Score: 5.97228

Motif 7
TCAGGCAAGCCGACTGACGCCACGCGT        	0	2	0
GTCCGTGCGCTGCCTGATGCGACGCTGATGCGTCT	1	10	1
TGCTCCCGTAGGCCTGATAAGACGCATCAGCGTCG	1	29	0
TTTTCAATATTGTTTTATGGATCACCAATATTGAA	3	25	1
GAAACAAAAATGTGATACCAATCACAGAATACAGC	3	145	1
  GCAATCAATGTCGGATGCGGCGCGAGCGCCTTA	4	8	1
        AATGGATTTCCTTACGCGAAATACGGG	5	34	0
ACGCAATTAATGTGAGTTAGCTCACTCATTAGGCA	6	15	1
CATCGAATGGCGCAAAACCTTTCGCGGTATGGCAT	7	13	1
AAATAAGTTGCGCTGTACTGTGCGCGCAACGACAT	8	35	0
TTTCCGCAGTTGCTATACAGATCGCATAGTTAACA	9	91	0
GTTTGAACTGTGACGGATTTCGCACCCTATTTTTA	9	155	0
ACCTGTGCTATGATTCATAAATCACAACAATAACA	11	61	1
GACAGTGAGCTGAAAGCCGCGTCGCAACTGCTCTT	12	190	0
TGTCGCGAGGTGGCGTATATTACGCTTTCCTCTTT	12	221	1
          **  ****   ****
MAP Score: 3.5164

Motif 8
TTTTCAATATTGTTTTATGGATCACCAATATTGAA	3	25	1
AAGTCAGATGTTATTTTTTACTCACAACAGAGCAT	3	59	1
GAAACAAAAATGTGATACCAATCACAGAATACAGC	3	145	1
ACGCAATTAATGTGAGTTAGCTCACTCATTAGGCA	6	15	1
CTGTGTGAAATTGTTATCCGCTCACAATTCCACAC	6	88	0
   CGCTACTCTCCAGATGTTTCACATTTCTGTTG	9	7	1
AGATCCTTTGCTTTTTATGATTCGCGATTTAACTA	9	46	0
TTTCCGCAGTTGCTATACAGATCGCATAGTTAACA	9	91	0
AAAAATAGGGTGCGAAATCCGTCACAGTTCAAACA	9	156	1
TGATTCGTGTTTTTAATTAATTCACGAAAACTGGA	9	242	1
ACCTGTGCTATGATTCATAAATCACAACAATAACA	11	61	1
AGTTGCGACGCGGCTTTCAGCTCACTGTCGCGAGG	12	196	1
          ** ** **   ****
MAP Score: 2.95973

Motif 9
CTGATAAGACGCATCAGCGTCGCATCAGGCAGCGCA	1	15	0
GCCGGATAAAGCGTTTACGCCGCATCCGGCAGTCAT	1	73	1
GTCGGATAAGGCGCTCGCGCCGCATCCGACATTGAT	4	13	0
GCCCTGGTGGGGTAAAGCGCCAGGGCCAGAAGTCGA	11	21	1
TTGTTAAAGAGCAGTTGCGACGCGGCTTTCAGCTCA	12	184	1
CTTTCAGCTCACTGTCGCGAGGTGGCGTATATTACG	12	209	1
          **    *** ** ***
MAP Score: 2.44614

Motif 10
AAACAATGTGATTCGTGTTTTTAATTAATTC	9	234	1
ATTTTTTTCTCTTCGTTGTTCCGACCATCCT	12	279	1
GCTTTTTATGATTCGCGATTTAACTATTAGC	9	41	0
AACATACAAAATTTGTGATTTTACTTAACTA	9	187	1
AGGCTTTACACTTTATGCTTCCGGCTCGTAT	6	54	1
TCCGGCCTACATTCGTGCTCCCGTAGGCCTG	1	48	0
  GTCATCACCTTTACGATTCCAGTTTTCGT	9	265	0
GAGACTTGGTATTCATTTTTCGTCTTGCGAC	12	107	1
TTGGTATCACATTTTTGTTTCGGGTGAATAG	3	135	0
TTAAAAGATCCTTTGCTTTTTATGATTCGCG	9	55	0
GACTTTCAATATTGGTGATCCATAAAACAAT	3	33	0
          ******* ***
MAP Score: 1.31009

Motif 11
GTCATGCGCTACATAAATTTTTCAGGAGCAAATA   	1	104	1
   CGTAGCAAAAAGAAATTTTCAATATTGTTTTATG	3	7	1
AGAGCATAACAAACTGATTATTAATCAAAATTAACGA	3	87	1
CAATCACAGAATACAGCTTATTGAATACCCATTATGA	3	163	1
AATAATAATTATATTAAATGTTAACAAAAATAAAACA	3	227	1
TTCCACTGTGAAAACGAATATTTATTTTGCGTTCCCG	3	266	0
AAGGATCTTTTAACGAAATGTTAACTATGCGATCTGT	9	73	1
GCACTGATAAATAATGATTTATAAAAATAGGGTGCGA	9	134	1
GCACTCGAAGATACGGATTCTTAACGTCGCAAGACGA	12	126	0
ACAGATTGTCTGATAAATTGTTAAAGAGCAGTTGCGA	12	167	1
          * *  **** ** *  *
MAP Score: 1.28205