AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_operons002_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241868
 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
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: 13.7882

Motif 3
AGAGAAATTCTTATAATTTTTTTCGATGTTGG	0	17	0
       CCCCCATTTCTTTTTCAATTATCAA	0	107	0
TGGGCAACATTTTTAACTTTTCTGACAGTTTG	1	16	0
      AAATTTATTCCTTTTTTTCTCTTGCT	2	4	1
ACCTTTAAACTTTTTGATTTTTACCGGAGCAA	2	31	0
GAGTATTAGACAAAACATTTTTAACTAACAAC	3	24	0
ATATGCAAAATTTTAAATTTTCGGTTACATCA	4	89	0
TCAGCTGATTTAAAACGTTTTTCCGTT     	5	5	0
TATCTCCTCCTTTCTGGTTTTTCGTTAAATCC	7	32	0
          CTTTATTTTTTTGGTGGTCTC 	8	0	1
ATAAGAGGAATTAAAACGTTTCCCCTTCTGTC	9	21	1
GTCATCTCACCTTTCTCTTTTTGCAGATTTCA	10	10	0
GCGATTTGGGCTAATACTTTTTATCACCCCAC	11	22	1
   CCTATCACCAAAAGTTTTTGAGGAAGTCT	12	7	1
CTACGAAAGACTATTATTTTTCTCCTCGCCCA	12	68	0
GTAGTGTTTATTAAAAGTTTTTTTTATATATC	12	96	1
          *****  *****
MAP Score: 7.99582

Motif 4
 CCTTTCACCAACATCGAAAAAAATTATAAGAA	0	9	1
ATCTTGCATTGATAATTGAAAAAGAAATGGGGG	0	99	1
ATTTTTAACTAACAACTACAAAACAAATAC   	3	7	0
AAAAACCTTTGACGTCATCAAAGCTAAACCGCA	4	32	1
TGCATATACCCACTTCTTAAAAAGGAGGTTAAG	4	114	1
        GAGACCACCAAAAAAATAAAG    	8	6	0
TCAGAGAACCGATAACTTAAAATACCTCTCCAC	9	88	1
         TGAAATCTGCAAAAAGAGAAAGGT	10	1	1
TATTTGTTAAGACTTCCTCAAAAACTTTTGGTG	12	15	0
AAGCGCGCTGGATATATAAAAAAAACTTTTAAT	12	105	0
       TTAAACTTTGCCAAAAGCGCGCTGGA	12	126	0
          *** **  *****
MAP Score: 4.87274

Motif 5
ATCTTGCATTGATAATTGAAAAAGAAATGGGGG	0	99	1
CAAACTGTCAGAAAAGTTAAAAATGTTGCCCAA	1	16	1
TTTTACCGGAGCAAGAGAAAAAAAGGAATAAAT	2	12	0
CTTGCTCCGGTAAAAATCAAAAAGTTTAAAGGT	2	30	1
GTTTTGTAGTTGTTAGTTAAAAATGTTTTGTCT	3	16	1
ATTGTTAAAATCTATTTTAAAAAACTTGCGAAA	3	113	0
GATATATTTATTTATTGTTAAAATCTATTTTAA	3	126	0
GGAATGATGATGTAACCGAAAATTTAAAATTTT	4	82	1
TTAAGAAGTGGGTATATGCAAAATTTTAAATTT	4	101	0
GAGTTAATCAGCTGATTTAAAACGTTTTTCCGT	5	11	0
TCCTAATGGATTTAACGAAAAACCAGAAAGGAG	7	25	1
AGATAAAATTTCAAAATTAAAAAGCACAGACAG	9	48	0
TCAGAGAACCGATAACTTAAAATACCTCTCCAC	9	88	1
         TGAAATCTGCAAAAAGAGAAAGGT	10	1	1
AAGCGCGCTGGATATATAAAAAAAACTTTTAAT	12	105	0
          * *** * *****
MAP Score: 2.31604