AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_operons015_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944242830
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	AF0535	122	cell division protein (ftsZ-1)
#1	AF0569	300	DR-beta chain MHC class II
#2	AF0632	80	nifU protein (nifU-3)
#3	AF0633	173	isoleucyl-tRNA synthetase (ileS)
#4	AF0791	97	phosphate permease, putative
#5	AF0800	31	diaminopimelate decarboxylase (lysA)
#6	AF1215	101	cell division protein, putative
#7	AF1452	117	signal-transducing histidine kinase
#8	AF1453	37	methionyl-tRNA synthetase (metS)
#9	AF1798	87	phosphate permease, putative
#10	AF2224	38	valyl-tRNA synthetase (valS)
#11	AF2225	64	2-hydroxyhepta-2,4-diene-1,7-dioate isomerase (hpcE-2)
#12	AF2421	58	leucyl-tRNA synthetase (leuS)
#13	AF2425	85	methanol dehydrogenase regulatory protein (moxR)

Motif 1
ATCAGCTGTTGATTTTCTGCAGTTTTTATTAGTCC	1	97	1
CGCGGAATATTTTCTTAAACACTTTATCATAATAG	1	151	1
TCTGTCCTCCGATGTAGGGCAATATTTCCGGTGGA	1	272	1
CTTTAATTGTCATGTAAACCCTTATTTTTCAGCCT	3	37	1
CCAAGTGTTTTATTTATTCCCCTATCGCTCTCCAC	4	24	1
ATACGCTTTTTATTTAAACCTTTTTCCCAACTTTG	6	59	0
TCAACGCTAAGATTTAATACGCTTTTTATTTAAAC	6	75	0
          GATATATAGCCATTTATTGGATATA	9	0	1
CCATTTATTGGATATATATCCCTATCGATATTCTA	9	19	1
TATCCCTATCGATATTCTACCGTTTAAGGAAAAGG	9	35	1
TTCGAACTCTGATATATATCCTTTTCCTTAAACGG	9	54	0
ACAGAAACTTGAAATATAACTTTTTGC        	10	2	0
AACGCCAAATTTTTTAATCCCATTTATTAGCCACT	12	29	1
          *** ** * *  ***
MAP Score: 13.1385

Motif 2
AATTATAAGAATTTCTCTTCCATCAGAAGCA	0	31	1
GCATCGATCATCCTTACCTCCGGACATTTGA	1	52	1
AGATGGAGACACCAGTCCTCCATCTGTCCTC	1	250	1
CCAGTCCTCCATCTGTCCTCCGATGTAGGGC	1	261	1
TTTTTGTTTGTGTACTCCTCCTCTTTCAAAC	2	22	1
ACCTTCCCTCACTCTCCCTCC          	3	0	0
TTTTCAGCCTACTATCCCTCCTAATTTTTGC	3	62	1
TGATAACTTTTTTAATCCACCGGCTGTTCAG	3	147	1
    CTGTTTTTAATCCCTCCACACTTTTAA	5	6	1
TAAAACGTTATTTACCCCTCGCAACCTTTTC	8	11	1
CCCTCGCAACCTTTTCCCTCC          	8	26	1
TTCCCATAGCTCTAACCCTCCTACCATTCTT	13	41	1
TAACCCTCCTACCATTCTTCCAAAACACACA	13	53	1
          **** ******
MAP Score: 10.7136

Motif 3
ATTATAAGAATTTCTCTTCCATCAGAAGCACAGGAAGAGGG	0	32	1
AGTATATAAATTCTTTGTTCGCTCCGCCCTCTTCCTGTGCT	0	58	0
TTTACTCTTCTTCTTGCTCCTTCACAACCTCAAGATCTCCA	1	11	1
CAAGATCTCCAGCATCGATCATCCTTACCTCCGGACATTTG	1	41	1
CCCTCCAATTTTTGTTTGTGTACTCCTCCTCTTTCAAACCA	2	14	1
TAAAGTTTAATACCTTCCCTCACTCTCCCTCC         	3	1	0
TAAACCCTTATTTTTCAGCCTACTATCCCTCCTAATTTTTG	3	51	1
GCTGATAACTTTTTTAATCCACCGGCTGTTCAGGTTTC   	3	145	1
ACCAAGTGTTTTATTTATTCCCCTATCGCTCTCCACTCTTA	4	23	1
       CTGTTTTTAATCCCTCCACACTTTTAATTTC   	5	3	1
GGATTGCATCTGAATAATCGGCCAAATGCTTTTATTTACAA	7	70	1
  GTAAAACGTTATTTACCCCTCGCAACCTTTTCCCTCC  	8	8	1
          **  *   **  *    ****
MAP Score: 10.6246

Motif 4
CACCAACATCGAAAAAAATTATAAGAATTTCTCT	0	15	1
AATTATCAATGCAAGATAGTATATAAATTCTTTG	0	82	0
ATTCTATTATGATAAAGTGTTTAAGAAAATATTC	1	155	0
ATCCGAAAAACTTAAATATTATAATGTCGGACAA	1	187	1
TCTTTCAAACCAAAAAGCTTATTATTTCCGTCAA	2	43	1
TAATTGTCATGTAAACCCTTATTTTTCAGCCTAC	3	40	1
ATTTTGACATGCAAAAGCATATACCATCATGGTG	3	98	0
AAGGAAAGCTGATAACTTTTTTAATCCACCGGCT	3	138	1
TGCAAAGTTGGGAAAAAGGTTTAAATAAAAAGCG	6	57	1
TGAATAATCGGCCAAATGCTTTTATTTACAAAGA	7	80	1
          GTAAAACGTTATTTACCCCTCGCA	8	0	1
TACCGTTTAAGGAAAAGGATATATATCAGAGTTC	9	52	1
          GCAAAAAGTTATATTTCAAGTTTC	10	0	1
GGCGTAAGAAGGCAAAGGTTTTAAGAGTTATCTC	11	14	1
CAGGCCAAACGCCAAATTTTTTAATCCCATTTAT	12	22	1
          * ****   *****
MAP Score: 10.5993

Motif 5
TTCGCTCCGCCCTCTTCCTGTGCTTCTGATGGA	0	49	0
TCCTTCACAACCTCAAGATCTCCAGCATCGATC	1	28	1
CAGCATCGATCATCCTTACCTCCGGACATTTGA	1	50	1
AGGACTGGTGTCTCCATCTGTCCGACTTTGTCC	1	236	0
AGACACCAGTCCTCCATCTGTCCTCCGATGTAG	1	256	1
ATACCTTCCCTCACTCTCCCTCC          	3	0	0
ATTTTTCAGCCTACTATCCCTCCTAATTTTTGC	3	60	1
CTTTTTTAATCCACCGGCTGTTCAGGTTTC   	3	153	1
TATTTATTCCCCTATCGCTCTCCACTCTTACCT	4	34	1
GTTTCCCATAGCTCTAACCCTCCTACCATTCTT	13	39	1
          ****   ******
MAP Score: 9.94603

Motif 6
TTCTGCAGTTTTTATTAGTCCTTGCCAAGTA	1	111	1
ACCAAAAAGCTTATTATTTCCGTCAAGGGAA	2	51	1
AGCTGATAACTTTTTTAATCCACCGGCTGTT	3	144	1
ACCAAGTGTTTTATTTATTCCCCTATCGCTC	4	23	1
GAACCATACTTATTTTTTTCCGAGAGGTAAG	4	60	0
       CTGTTTTTAATCCCTCCACACTTT	5	3	1
AATACGCTTTTTATTTAAACCTTTTTCCCAA	6	64	0
  GTAAAACGTTATTTACCCCTCGCAACCTT	8	8	1
AAACGCCAAATTTTTTAATCCCATTTATTAG	12	28	1
          ******* ***
MAP Score: 9.31041

Motif 7
TCCTTACCTCCGGACATTTGAGCTCCTCAA	1	62	1
ATTATAATGTCGGACAATTGATACCAGCTG	1	204	1
AGGACAAAGTCGGACAGATGGAGACACCAG	1	235	1
CCTACATCGGAGGACAGATGGAGGACTGGT	1	260	0
TCTGAATAATCGGCCAAATGCTTTTATTTA	7	78	1
TTGGTCAATCAGGCCAAACGCCAAATTTTT	12	13	1
          **********
MAP Score: 6.71372

Motif 8
TCTTCCATCAGAAGCACAGGAAGAGGGCGGAGCGAA	0	46	1
ATTGATAATTGAAAAAGAAATGGGGG          	0	106	1
GCTGAAGGACAAAGTCGGACAGATGGAGACACCAGT	1	230	1
GCCCTACATCGGAGGACAGATGGAGGACTGGTGTCT	1	256	0
AGGAGTACACAAACAAAAATTGGAGGGATTT     	2	5	0
          GGAGGGAGAGTGAGGGAAGGTATTAA	3	0	1
         GAAACCTGAACAGCCGGTGGATTAAAA	3	156	0
AGGTAAGAGTGGAGAGCGATAGGGGAATAAATAAAA	4	31	0
TCGAGATTGCAAAGTTGGGAAAAAGGTTTAAATAAA	6	50	1
GGTTACCTGTAAAGCGTATTTGCTGGCGGCAGTTTT	7	27	1
   GGAGGGAAAAGGTTGCGAGGGGTAAATAACGTT	8	14	0
GTGTGTTTTGGAAGAATGGTAGGAGGGTTAGAGCTA	13	47	0
          ****   *  *** **
MAP Score: 5.19288

Motif 9
AAATTCTTTGTTCGCTCCGCCCTCTTCCTGTGCTTCTGA	0	53	0
      TTTTACTCTTCTTCTTGCTCCTTCACAACCTCA	1	4	1
GATCTCCAGCATCGATCATCCTTACCTCCGGACATTTGA	1	44	1
AGATGGAGACACCAGTCCTCCATCTGTCCTCCGATGTAG	1	250	1
TTGTTTGTGTACTCCTCCTCTTTCAAACCAAAAAGCTTA	2	25	1
AAAGTTTAATACCTTCCCTCACTCTCCCTCC        	3	2	0
GTAAACCCTTATTTTTCAGCCTACTATCCCTCCTAATTT	3	50	1
GGATTAAAAAAGTTATCAGCTTTCCTTTCCGGAATTTTG	3	126	0
TGATAACTTTTTTAATCCACCGGCTGTTCAGGTTTC   	3	147	1
AAGTGTTTTATTTATTCCCCTATCGCTCTCCACTCTTAC	4	26	1
     CTGTTTTTAATCCCTCCACACTTTTAATTTC   	5	5	1
 GTAAAACGTTATTTACCCCTCGCAACCTTTTCCCTCC 	8	9	1
   GGAGCTATTTCAGCAATCTGCTATTTGACGTTTCCC	13	7	1
TTCCCATAGCTCTAACCCTCCTACCATTCTTCCAAAACA	13	41	1
          * *   ** **  *  ***
MAP Score: 3.89602

Motif 10
TCTTCCTGTGCTTCTGATGGAAGAGAAATTC	0	39	0
TGCTGGAGATCTTGAGGTTGTGAAGGAGCAA	1	24	0
GGAGCTCAAATGTCCGGAGGTAAGGATGATC	1	57	0
CCTCAACTATTATCAGCTGTTGATTTTCTGC	1	86	1
CGACTTTGTCCTTCAGCTGGTATCAATTGTC	1	216	0
CTCCATCTGTCCTCCGATGTAGGGCAATATT	1	267	1
TAGGGCAATATTTCCGGTGGAAGG       	1	286	1
GAAACCTGAACAGCCGGTGGATTAAAAAAGT	3	152	0
AACAGCAACGCCTCAGCTTGACCG       	6	3	0
TTCAAGTTTCTGTGAGGTGGACAC       	10	24	1
   GATATCACCTCAGGCGTAGAACTTCTGA	11	46	0
          * *********
MAP Score: 2.35771

Motif 11
TAAACCCTTATTTTTCAGCCTACTATCCCTCCT	3	51	1
AGCTGATAACTTTTTTAATCCACCGGCTGTTCA	3	144	1
       CTGTTTTTAATCCCTCCACACTTTTA	5	3	1
GGCGTTGCTGTTTTTAAACTTGCCTTTATCGAG	6	22	1
  GTAAAACGTTATTTACCCCTCGCAACCTTTT	8	8	1
CAAAAAGTTATATTTCAAGTTTCTGTGAGGTGG	10	11	1
AACGCCAAATTTTTTAATCCCATTTATTAGCCA	12	29	1
AGCAATCTGCTATTTGACGTTTCCCATAGCTCT	13	21	1
          ***** * *** *
MAP Score: 1.80333