AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_operons020_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944243093
 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	AF2328	116	Glu-tRNA amidotransferase, subunit C (gatC)

Motif 1
ACTTTTTGGAAAAGCTTAAATACAAGTGCA	0	22	0
TTATGAGTACAAACCTTTGGTACAATTTCA	0	58	1
TATTATGGTAAAAGCATTGCAACTTAGTTG	0	88	1
CAATCAAACTAAACAATTAACTGTTTAAGA	0	118	1
GATATTCGGAAAATCTTAAACAGTTAATTG	0	131	0
CATCATCTCCAAAACATAAATACATTTGCG	1	17	1
TTTCTATCATAAACCTTAAAGTTTAAATTG	2	13	1
GATGATGCGTAAACAATTTAAACTTTAAGG	2	26	0
    TTTTAAAAAACTTTGACCCAATCTAT	3	6	1
GAAACACTTTAAAACATTTCTACTACTCAG	5	13	0
CAGAGATATTAAACAATTAATTGAGGTGGT	5	45	1
AATGTACAACAAACCAAAAATC        	6	2	0
AAAACTAGAAAAACCATTTATTACCCACCC	6	83	1
          **********
MAP Score: 13.323

Motif 2
AAGCTTTTCCAAAAAGTTACCAGTTATGAGT	0	35	1
TTATGAGTACAAACCTTTGGTACAATTTCAT	0	58	1
CAATCAAACTAAACAATTAACTGTTTAAGAT	0	118	1
GATGATGCGTAAACAATTTAAACTTTAAGGT	2	25	0
    TTTTAAAAAACTTTGACCCAATCTATC	3	6	1
GAAACACTTTAAAACATTTCTACTACTCAGC	5	12	0
CAGAGATATTAAACAATTAATTGAGGTGGTT	5	45	1
AAAACTAGAAAAACCATTTATTACCCACCCT	6	83	1
          ******** **
MAP Score: 4.17388

Motif 3
         GTGCTATTAAGATGCACTTGTATT	0	1	1
AAGATGCACTTGTATTTAAGCTTTTCCAAAAAG	0	18	1
AATATGAAATTGTACCAAAGGTTTGTACTCATA	0	59	0
TTAGTTTGATTGCAACTAAGTTGCAATGCTTTT	0	97	0
TTATAAATGTTGCTGTCGAGGCGGGGGC     	0	162	1
AATGTATTTATGTTTTGGAGATGATGGCAGAGC	1	10	0
GTAGTAGAAATGTTTTAAAGTGTTTCTTCAGAG	5	17	1
          **** * *** **
MAP Score: 3.51802

Motif 4
AAAGGTTTGTACTCATAACTGGTAACTTTT	0	46	0
ATCAAACTAAACAATTAACTGTTTAAGATT	0	120	1
TGCGGTAAGAATTAATAACCTCTGCACAAA	1	43	1
  GTCTTTCTATCATAAACCTTAAAGTTTA	2	8	1
GAGATATTAAACAATTAATTGAGGTGGTTA	5	47	1
TGTACAACAAACCAAAAATC          	6	0	0
TTTATTACCCACCCTTAACCACCCTTC   	6	99	1
          **********
MAP Score: 0.126757