AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_operons007_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944242096
 numcols =     	10
 undersample = 	1
 oversample = 	1

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

Motif 1
TGTTTGACGCTTATTTCTCTCTAAGTGCAA	0	59	0
GAATCCATCATCTTTTTTTTAATGCGATCC	0	131	1
ATCCTGGTATACACTTCCCTTTCCCCAATC	0	157	1
GCAAACTTGCTCTTTTTCCTAATTTATTTA	1	46	0
GGAAATAAGTTCTATTTTTTTGTTATGAAA	2	64	0
AAAATAGAACTTATTTCCCTCGTATGATCT	2	76	1
       ATGTCTATTTTCTAAAAAGGTTA	2	156	0
CATTAAACGTTCTCTTCTCTTCAAGAGAAG	3	13	1
AAAAAAACGCCCTCTTCTCTTGAAGAGAAG	3	26	0
GAAAAATCTTTCTATTTCTTTTCTCTTCCC	3	60	1
CTATTTCTTTTCTCTTCCCTGTGTGTATGA	3	71	1
GTTTTCCTTGTTTCTTCTCTTAACTCATGA	3	109	0
TTCTGGAAGCACTCTTCCTTCTTCTATTCC	4	60	1
TCTTCCTTCTTCTATTCCTTGAGATGCTTG	4	72	1
CCTTGGATTCACTATTTCCTCTTTAAAAAA	4	143	1
TCTGAAAAGAACTATTCTTTTCATTTATTA	5	200	0
       AACCCATTTCCCTCATAGCTATA	6	29	0
          **********
MAP Score: 19.7333

Motif 2
TCTGAGATCGAAATCAAGTCCTCTCCAGTCTGCGAA	0	98	1
CCAGTCTGCGAATCCATCATCTTTTTTTTAATGCGA	0	122	1
CGATCCTGGTATACACTTCCCTTTCCCCAATCTTTA	0	155	1
TCAGGTGCACATCTAAAGTTCTTTCTCTAAATAAAT	1	19	1
       AAAAAAACATAAAATCTTTCAACAAGATT	2	3	1
TATAACAACAAAATAAAATCCTTTTCATAACAAAAA	2	42	1
CTTAAATATCATGCAAAAAACTCTTCCGAAGACTAC	2	104	1
      CATCATTAAACGTTCTCTTCTCTTCAAGAG	3	4	1
TTTTCAATGAAAAAAACGCCCTCTTCTCTTGAAGAG	3	29	0
CGTTTTTTTCATTGAAAAATCTTTCTATTTCTTTTC	3	47	1
TTTCCTCTTTAAAAAACCTTCTTCCTAGGATTTTAT	4	157	1
TGCTCTTGCTAAGAAACTATCTCTCTGGTTAGGATG	5	82	0
GAGTTGCGCAAATAACTTGGATTTCTGTAAAGATTA	5	129	1
GAAAAATATGAAGCCACGATATCTTTTTGATAATAA	5	170	1
GCATTCTGAAAAGAACTATTCTTTTCATTTATTATC	5	198	0
TTGGATATGGAAATATTGCACTCTTTGGTGCAAGAA	5	246	1
          **  **    ******
MAP Score: 10.6252

Motif 3
ATTTTTAAGGTTTTCTCTCCTTACAACCGCCT	0	28	1
GCGAATTTGCTTTGCTTTTCCTGTTGGAGCTA	1	74	1
AAAAGGATTTTATTTTGTTGTTATAATTAATC	2	35	0
AAATAAGTTCTATTTTTTTGTTATGAAAAGGA	2	60	0
GAAGACTACATTAGCTATTCATTTTTAACCTT	2	131	1
TTAAACGTTCTCTTCTCTTCAAGAGAAGAGGG	3	15	1
TTTCTATTTCTTTTCTCTTCCCTGTGTGTATG	3	68	1
GTGTGTATGATTTGCTGTTCATGAGTTAAGAG	3	91	1
      TAGATTTGTTTTCCTTGTTTCTTCTC	3	120	0
CACTCTTCCTTCTTCTATTCCTTGAGATGCTT	4	69	1
CTATACACCATTTGCGTTTGATTGGTACGAGA	4	199	0
CTACAATAGCTCTGCTCTTGCTAAGAAACTAT	5	98	0
TGAAAAGAACTATTCTTTTCATTTATTATCAA	5	196	0
          ****** *** *
MAP Score: 9.5527

Motif 4
GATGATGGATTCGCAGACTGGAGAGGACTTGATTTCG	0	106	0
GGAGCGAATGTTGCTGTAGTGAGAGGACATCCTAACC	5	55	1
GTTTCTTTTAGCCATTTTCTAAGAGGATCCTATAGGT	1	136	1
CGCCCTCTTCTCTTGAAGAGAAGAGAACGTTTAATGA	3	12	0
TGATTTGCTGTTCATGAGTTAAGAGAAGAAACAAGGA	3	98	1
AGTTCTATTTTTTTGTTATGAAAAGGATTTTATTTTG	2	50	0
AGAATAATTTTAACAAAACCAAGAGGAAGT       	5	278	1
 AAAAGGGTATCCTTTTTTAGAGTGGAATTGTGCCTT	4	274	0
TAACAATCACTCATTATAGGGAGCGAATGTTGCTGTA	5	36	1
ATTAACAGGTTTGCATTCTGAAAAGAACTATTCTTTT	5	209	0
CAGAGAGATAGTTTCTTAGCAAGAGCAGAGCTATTGT	5	91	1
TAGTCAAATTTCTGTCAGCTGAGAAGATCGTTAAGAA	4	228	1
CTCATAGCTATAATCATTCAAAGAGCAGTCC      	6	4	0
TTTTTCCTAATTTATTTAGAGAAAGAACTTTAGATGT	1	27	0
AAGCTTTTCCGCTGGTTGCAAAGAGGTAACAATCACT	5	10	1
ACCATTTGCGTTTGATTGGTACGAGAAACCTTATAAA	4	188	0
AGCAAATCATACACACAGGGAAGAGAAAAGAAATAGA	3	70	0
TATACCAGGATCGCATTAAAAAAAAGATGATGGATTC	0	131	0
CACGATATCTTTTTGATAATAAATGAAAAGAATAGTT	5	184	1
          **    *   *******
MAP Score: 4.06166

Motif 5
TTCCAGCACTATGGAAGTGTTTCCTT      	4	4	0
AATGTAGTCTTCGGAAGAGTTTTTTGCATGAT	2	111	0
AGAAAAGAAATAGAAAGATTTTTCAATGAAAA	3	52	0
ATTAATCTTGTTGAAAGATTTTATGTTTTTTT	2	10	0
TCTTCAAGAGAAGAGGGCGTTTTTTTCATTGA	3	30	1
AAATCCTAGGAAGAAGGTTTTTTAAAGAGGAA	4	158	0
GATTGGGGAAAGGGAAGTGTATACCAGGATCG	0	155	0
AGTGAATCCAAGGAATGGGTTATGGGCAAGGA	4	124	0
TCTTGAAGAGAAGAGAACGTTTAATGATG   	3	7	0
GGACTGCTCTTTGAATGATTATAGCTATGAGG	6	10	1
TCTTTGGTGCAAGAATAATTTTAACAAAACCA	5	267	1
          * ***** ****
MAP Score: 2.09672