AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_operons002_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241859
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	AF0535	122	cell division protein (ftsZ-1)
#1	AF0592	44	translation initiation factor eIF-2, subunit gamma (eif2G)
#2	AF0676	72	adenylate kinase (adk)
#3	AF0677	165	acetyl-CoA synthetase (acs-3)
#4	AF0914	144	conserved hypothetical protein
#5	AF0932	41	conserved hypothetical protein
#6	AF0933	22	branched-chain amino acid aminotransferase (ilvE)
#7	AF0937	57	translation elongation factor EF-1, subunit alpha (tuf)
#8	AF0938	21	SSU ribosomal protein S10P (rps10P)
#9	AF1490	166	LSU ribosomal protein L1P (rpl1P)
#10	AF1886	32	DNA-directed RNA polymerase, subunit B'' (rpoB2)
#11	AF1926	57	conserved hypothetical protein
#12	AF1927	142	conserved hypothetical protein

Motif 1
GTCAGAAAAGTTAAAAATGTTGCCCAAAGCTC	1	22	1
TCCGGTAAAAATCAAAAAGTTTAAAGGTGTAA	2	35	1
TAGTTGTTAGTTAAAAATGTTTTGTCTAATAC	3	22	1
AAAATCTATTTTAAAAAACTTGCGAAAGCGTG	3	108	0
ATACGAGGGGTTAAAAACCTTTGACGTCATCA	4	20	1
TAACCGAAAATTTAAAATTTTGCATATACCCA	4	94	1
AATCAGCTGATTTAAAACGTTTTTCCGTT   	5	7	0
TATAAGAGGAATTAAAACGTTTCCCCTTCTGT	9	20	1
GTGTGGGGTGATAAAAAGTATTAGCCCAAATC	11	24	0
TAAGACTTCCTCAAAAACTTTTGGTGATAGG 	12	9	0
CGTAGTGTTTATTAAAAGTTTTTTTTATATAT	12	95	1
          ** **** ****
MAP Score: 16.4126

Motif 2
CTGTGCTTCTGATGGAAGAGAAATTCTTATAAT	0	32	0
CAGGAAGAGGGCGGAGCGAACAAAGAATTTATA	0	62	1
ATCAATGCAAGATAGTATATAAATTCTTTGTTC	0	79	0
ATCTTGCATTGATAATTGAAAAAGAAATGGGGG	0	99	1
CAAACTGTCAGAAAAGTTAAAAATGTTGCCCAA	1	16	1
TTTTACCGGAGCAAGAGAAAAAAAGGAATAAAT	2	12	0
TTGATTATACGAGGGGTTAAAAACCTTTGACGT	4	14	1
GTGGGTATATGCAAAATTTTAAATTTTCGGTTA	4	94	0
GAGTTAATCAGCTGATTTAAAACGTTTTTCCGT	5	11	0
AATCCATTAGGAGGATATATAAACCTT      	7	4	0
TGGATTTAACGAAAAACCAGAAAGGAGGAGATA	7	31	1
CAGTTTATAAGAGGAATTAAAACGTTTCCCCTT	9	15	1
GCCCATTTCAGAGAACCGATAACTTAAAATACC	9	81	1
  TGAAATCTGCAAAAAGAGAAAGGTGAGATGA	10	8	1
GCTTAATTGTGTGGGGTGATAAAAAGTATTAGC	11	31	0
CGCCCAAAAAGAGAACGGTTAAATAGTATTTGT	12	41	0
CTCTTTTTGGGCGAGGAGAAAAATAATAGTCTT	12	61	1
          *****  ** ***
MAP Score: 13.5991

Motif 3
AGAGAAATTCTTATAATTTTTTTCGATGTTGGTG	0	15	0
TTTGTTCGCTCCGCCCTCTTCCTGTGCTTCTGAT	0	52	0
TGGGCAACATTTTTAACTTTTCTGACAGTTTGTC	1	14	0
     AAATTTATTCCTTTTTTTCTCTTGCTCCG	2	5	1
GCAGTTACACCTTTAAACTTTTTGATTTTTACCG	2	37	0
TGATTTATCTCAGCACGCTTTCGCAAGTTTTTTA	3	95	1
ATATGCAAAATTTTAAATTTTCGGTTACATCATC	4	87	0
     TTTCACCCTTCATTTCTGGTTG       	6	5	1
    ACCTATCTCCTCCTTTCTGGTTTTTCGTTA	7	37	0
          CTTTATTTTTTTGGTGGTCTC   	8	0	1
GGAATTAAAACGTTTCCCCTTCTGTCTGTGCTTT	9	27	1
 GTCATCTCACCTTTCTCTTTTTGCAGATTTCA 	10	9	0
TACTATTTAACCGTTCTCTTTTTGGGCGAGGAGA	12	46	1
CTACGAAAGACTATTATTTTTCTCCTCGCCCAAA	12	66	0
TTTATATATCCAGCGCGCTTTTGGCAAAGTTTAA	12	118	1
          *  * * *******
MAP Score: 10.9224

Motif 4
ACCAACATCGAAAAAAATTATAAGAATTTCTCT	0	16	1
GCGGAGCGAACAAAGAATTTATATACTATCTTG	0	72	1
TATCTTGCATTGATAATTGAAAAAGAAATGGGG	0	98	1
ACAAACTGTCAGAAAAGTTAAAAATGTTGCCCA	1	15	1
CGGTAAAAATCAAAAAGTTTAAAGGTGTAACTG	2	37	1
CACGCTTTCGCAAGTTTTTTAAAATAGATTTTA	3	108	1
ATTGATTATACGAGGGGTTAAAAACCTTTGACG	4	13	1
ATGATGTAACCGAAAATTTAAAATTTTGCATAT	4	88	1
TTGCATATACCCACTTCTTAAAAAGGAGGTTAA	4	113	1
    AACGGAAAAACGTTTTAAATCAGCTGATT	5	6	1
GCAGTTTATAAGAGGAATTAAAACGTTTCCCCT	9	14	1
TTCAGAGAACCGATAACTTAAAATACCTCTCCA	9	87	1
          ***  * ******
MAP Score: 5.12203

Motif 5
CAACATCGAAAAAAATTATAAGAATTTCTCT	0	18	1
CAAACTGTCAGAAAAGTTAAAAATGTTGCCC	1	16	1
AGCAAGAGAAAAAAAGGAATAAATTT     	2	5	0
GGTAAAAATCAAAAAGTTTAAAGGTGTAACT	2	38	1
CGAGGGGTTAAAAACCTTTGACGTCATCAAA	4	23	1
TGATGTAACCGAAAATTTAAAATTTTGCATA	4	89	1
    AACGGAAAAACGTTTTAAATCAGCTGA	5	6	1
GACAGAAGGGGAAACGTTTTAATTCCTCTTA	9	22	0
GTGGGGTGATAAAAAGTATTAGCCCAAATCG	11	23	0
GAGAACGGTTAAATAGTATTTGTTAAGACTT	12	33	0
ATATATAAAAAAAACTTTTAATAAACACTAC	12	96	0
          ********* *
MAP Score: 3.95265

Motif 6
TTTGTTCGCTCCGCCCTCTTCCTGTGCTTCTG	0	54	0
       CCCCCATTTCTTTTTCAATTATCAA	0	107	0
  AAATTTATTCCTTTTTTTCTCTTGCTCCGG	2	8	1
GGTTACATCATCATTCCCTGCTTTGCATAGGC	4	67	0
     TTTCACCCTTCATTTCTGGTTG     	6	5	1
    ACCTATCTCCTCCTTTCTGGTTTTTCGT	7	39	0
TAAAACGTTTCCCCTTCTGTCTGTGCTTTTTA	9	32	1
 GTCATCTCACCTTTCTCTTTTTGCAGATTTC	10	11	0
TACTATTTAACCGTTCTCTTTTTGGGCGAGGA	12	46	1
          ** *** *****
MAP Score: 0.109347