AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_operons007_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944242117
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	hemL	196	Glutamate-1-semialdehyde-2,1-aminomutase
#1	dapB	176	Dihydrodipicolinate Reductase
#2	CT365_aroA	169	CT365: hypothetical protein, aroA: Phosphoshikimate 1-carboxyl vinyltransferase
#3	aroG	136	phospho-2-dehydro-3-deoxyheptonate aldolase
#4	CT382.1	182	hypothetical protein
#5	kdsA	300	KDO Synthetase
#6	CT775	298	snGlycerol 3-P Acyltransferase
#7	bioF	42	8-amino-7-oxononanoate synthase

Motif 1
CGAATCCATCATCTTTTTTTTAATGCGATCC	0	130	1
AGTTTGCGAATTTGCTTTGCTTTTCCTGTTG	1	69	1
TACTGCTGCAGTGGTTTCTTTTAGCCATTTT	1	123	1
        ATGTCTATTTTCTAAAAAGGTTA	2	2	1
GGGAAATAAGTTCTATTTTTTTGTTATGAAA	2	94	1
TCATTAAACGTTCTCTTCTCTTCAAGAGAAG	3	12	1
GAAGAGGGCGTTTTTTTCATTGAAAAATCTT	3	39	1
TGAAAAATCTTTCTATTTCTTTTCTCTTCCC	3	59	1
TCTATTTCTTTTCTCTTCCCTGTGTGTATGA	3	70	1
TGTTTTCCTTGTTTCTTCTCTTAACTCATGA	3	109	0
     TAGATTTGTTTTCCTTGTTTCTTCTC	3	120	0
TTTTGTTAAAATTTTTTCGCTATACCGCAAA	4	34	0
TTAAATTAAATTGTTTTCATTTGAATTTAAT	4	97	1
TTGAATTTAATTTTATTTTTTAAGATCTATT	4	117	1
ATTTTTTAAGATCTATTTGTTTTAGTTTTAT	4	131	1
TACCTTAGACTTCGATTTTCTGGAAGCACTC	5	43	1
CTCTTCCTTCTTCTATTCCTTGAGATGCTTG	5	71	1
AACCCATTCCTTGGATTCACTATTTCCTCTT	5	135	1
AAAAGAACTATTCTTTTCATTTATTATCAAA	6	195	0
  ACTTCCTCTTGGTTTTGTTAAAATTATTC	6	279	0
          ******** **
MAP Score: 18.6039

Motif 2
CTTTCCCCAATCTTTACAGAGATCTCTGCT	0	175	1
TATAGGATCCTCTTAGAAAATGGCTAAAAG	1	140	0
TTTTTAACCTTTTTAGAAAATAGACAT   	2	7	0
AAAATCCTTTTCATAACAAAAAAATAGAAC	2	103	0
ACAAGATTAATTATAACAACAAAATAAAAT	2	128	0
GGCGTTTTTTTCATTGAAAAATCTTTCTAT	3	45	1
ATTGCGAGGCTCTTAAAAGCA         	4	1	0
AGCGAAAAAATTTTAACAAAAGTTTTTCTT	4	44	1
ACCATTAAATTCATTGAAGACAAAGAAAAA	4	66	0
AACAAATAGATCTTAAAAAATAAAATTAAA	4	122	0
CACTATTTCCTCTTTAAAAAACCTTCTTCC	5	152	1
GATTGTTACCTCTTTGCAACCAGCGGAAAA	6	14	0
AGAGATAGTTTCTTAGCAAGAGCAGAGCTA	6	94	1
TCGTTAATAATCTTTACAGAAATCCAAGTT	6	142	0
AAAGAATAGTTCTTTTCAGAATGCAAACCT	6	210	1
GCAAGAATAATTTTAACAAAACCAAGAGGA	6	275	1
          **********
MAP Score: 13.007

Motif 3
AAGTGCAAGGCGGTTGTAAGGAGAGAAAACCTTAAAAAT	0	28	0
GATGATGGATTCGCAGACTGGAGAGGACTTGATTTCGAT	0	104	0
TGCAGCAGTATAGTATAAGTGAGTAAATAGCTCCAACAG	1	94	0
AAACGCCCTCTTCTCTTGAAGAGAAGAGAACGTTTAATG	3	13	0
GTGTATGATTTGCTGTTCATGAGTTAAGAGAAGAAACAA	3	93	1
CGCAATCATTTTGCGGTATAGCGAAAAAATTTTAACAAA	4	25	1
 AAAAGGGTATCCTTTTTTAGAGTGGAATTGTGCCTTTA	5	272	0
GCTTTTCCGCTGGTTGCAAAGAGGTAACAATCACTCATT	6	12	1
GGAGCGAATGTTGCTGTAGTGAGAGGACATCCTAACCAG	6	55	1
AGCAGAGCTATTGTAGAGTTGCGCAAATAACTTGGATTT	6	114	1
CTTTGAATGATTATAGCTATGAGGGAAATGGGTT     	7	18	1
          * ** *    ***  ** *
MAP Score: 6.78454

Motif 4
GCGATCCTGGTATACACTTCCCTTTCCCCAATCTTTACAGAGATC	0	154	1
TTTCTATTTCTTTTCTCTTCCCTGTGTGTATGATTTGCTGTTCAT	3	68	1
CACTCTTCCTTCTTCTATTCCTTGAGATGCTTGTTCAAACTGCTA	5	69	1
GCGAATTTGCTTTGCTTTTCCTGTTGGAGCTATTTACTCACTTAT	1	74	1
TCCTCTCCAGTCTGCGAATCCATCATCTTTTTTTTAATGCGATCC	0	116	1
TCCTTGCCCATAACCCATTCCTTGGATTCACTATTTCCTCTTTAA	5	124	1
GAGTGCAATATTTCCATATCCAAATTAACAGGTTTGCATTCTGAA	6	224	0
GAAGACTACATTAGCTATTCATTTTTAACCTTTTTAGAAAATAGA	2	13	0
AGTGCTGGAAGATACTATACCTTAGACTTCGATTTTCTGGAAGCA	5	26	1
          * * *  **** *          **
MAP Score: 5.5297

Motif 5
ATTTATTTAGAGAAAGAACTTTAGATGTGCAC	1	23	0
ATGTAGTCTTCGGAAGAGTTTTTTGCATGATA	2	47	1
GAAAAGAAATAGAAAGATTTTTCAATGAAAAA	3	51	0
TGCGGTATAGCGAAAAAATTTTAACAAAAGTT	4	36	1
AAAAAATTTTAACAAAAGTTTTTCTTTGTCTT	4	48	1
TCTCACAAAACACAATAGTTTCTATTATAAAA	4	156	0
GAATAGAAGAAGGAAGAGTGCTTCCAGAAAAT	5	57	0
AATGGTGTATAGTCAAATTTCTGTCAGCTGAG	5	219	1
TTGTGCCTTTAGTCAGAGTTCTTAACGATCTT	5	251	0
CTCTGACTAAAGGCACAATTCCACTCTAAAAA	5	265	1
TCCTAACCAGAGAGATAGTTTCTTAGCAAGAG	6	84	1
AATAAATGAAAAGAATAGTTCTTTTCAGAATG	6	201	1
CACCAAAGAGTGCAATATTTCCATATCCAAAT	6	244	0
TCTTTGGTGCAAGAATAATTTTAACAAAACCA	6	267	1
          ** ** ******
MAP Score: 0.706371

Motif 6
GATCGAAATCAAGTCCTCTCCAGTCTGCGAATCCATCATCTTTT	0	103	1
TCTTTTTTTTAATGCGATCCTGGTATACACTTCCCTTTCCCCAA	0	141	1
AAGCAAAGCAAATTCGCAAACTTGCTCTTTTTCCTAATTTATTT	1	47	0
GTATGATCTTAAATATCATGCAAAAAACTCTTCCGAAGACTACA	2	48	0
GATTTTCTGGAAGCACTCTTCCTTCTTCTATTCCTTGAGATGCT	5	56	1
TATTCCTTGAGATGCTTGTTCAAACTGCTAATCCGCCGAATCCT	5	84	1
CTAATCCGCCGAATCCTTGCCCATAACCCATTCCTTGGATTCAC	5	111	1
GATCGTTAAGAACTCTGACTAAAGGCACAATTCCACTCTAAAAA	5	253	1
TTCTTGCACCAAAGAGTGCAATATTTCCATATCCAAATTAACAG	6	238	0
          ** **     *      *  ****
MAP Score: 0.679609