AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_operons020_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944243098
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	AF0528	180	cytochrome-c3 hydrogenase, subunit gamma
#1	AF0883	71	argininosuccinate lyase (argH)
#2	AF1442	54	conserved hypothetical protein
#3	AF1553	28	conserved hypothetical protein
#4	AF1554	21	thioredoxin reductase (trxB)
#5	AF1954	68	Glu-tRNA amidotransferase, subunit A (gatA-1)
#6	AF2327	72	shikimate 5-dehydrogenase (aroE)
#7	AF2328	116	Glu-tRNA amidotransferase, subunit C (gatC)

Motif 1
ACTTTTTGGAAAAGCTTAAATACAAGTGCATCT	0	19	0
TTATGAGTACAAACCTTTGGTACAATTTCATAT	0	58	1
TATTATGGTAAAAGCATTGCAACTTAGTTGCAA	0	88	1
CATCATCTCCAAAACATAAATACATTTGCGGTA	1	17	1
GATGATGCGTAAACAATTTAAACTTTAAGGTTT	2	23	0
    TTTTAAAAAACTTTGACCCAATCTATCT 	3	6	1
        GCAACCCCTACTTCCCCATGG    	4	6	0
GAAACACTTTAAAACATTTCTACTACTCAGCTT	5	10	0
CCGCTCCGAAAACCCTTTTTTACTGCATGACCA	6	40	1
AAACTAGAAAAACCATTTATTACCCACCCTTAA	7	84	1
ATTTATTACCCACCCTTAACCACCCTTC     	7	98	1
          ***** **  ***
MAP Score: 13.5663

Motif 2
CCTTAAAGTTTAAATTGTTTACGCATCATC	2	26	1
AGAAATGTTTTAAAGTGTTTCTTCAGAGAT	5	22	1
TCTTAAACAGTTAATTGTTTAGTTTGATTG	0	118	0
ACCACCTCAATTAATTGTTTAATATCTCTG	5	45	0
GGGTGGGTAATAAATGGTTTTTCTAGTTTT	7	83	0
CATGCAGTAAAAAAGGGTTTTCGGAGCGGT	6	39	0
GAATATCTTTATAAATGTTGCTGTCGAGGC	0	154	1
GCTGAGTAGTAGAAATGTTTTAAAGTGTTT	5	12	1
CAATTTAAACTTTAAGGTTTATGATAGAAA	2	13	0
          **********
MAP Score: 9.71768

Motif 3
TGCACTTGTATTTAAGCTTTTCCAAAAAGTTACCAGTTA	0	22	1
CAGTTATGAGTACAAACCTTTGGTACAATTTCATATTAT	0	55	1
CATATTATGGTAAAAGCATTGCAACTTAGTTGCAATCAA	0	86	1
CAATTAACTGTTTAAGATTTTCCGAATATCTTTATAAAT	0	131	1
CGAATATCTTTATAAATGTTGCTGTCGAGGCGGGGGC  	0	153	1
CTCCAAAACATAAATACATTTGCGGTAAGAATTAATAAC	1	23	1
       TTTTAAAAAACTTTGACCCAATCTATCT    	3	3	1
TAGAAATGTTTTAAAGTGTTTCTTCAGAGATATTAAACA	5	21	1
          *  ***  ****     **
MAP Score: 7.93678

Motif 4
         GCCCCCGCCTCGACAGCAACATTTATAAA	0	161	0
         GCTCTGCCATCATCTCCAAAACATAAATA	1	1	1
CGGTAAGAATTAATAACCTCTGCACAAACTGAGTGC  	1	45	1
      GTCTTTCTATCATAAACCTTAAAGTTTAAATT	2	4	1
TTTGGATAAATACTTACCGCTCCGAAAACCCTTTTTTA	6	24	1
CATCATGGAATAATTCCCTCATCTAAAGGCACACCCCC	7	38	1
TCTAAAGGCACACCCCCAGCCCCCAAAACTAGAAAAAC	7	59	1
          * **  ****  *   **
MAP Score: 3.25876