AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_operons012_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944242676
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	AF0062	52	conserved hypothetical protein
#1	AF0063	27	A. fulgidus predicted coding region AF0063
#2	AF0111	115	conserved hypothetical protein
#3	AF0209	112	conserved hypothetical protein
#4	AF0332	122	conserved hypothetical protein
#5	AF0743	283	conserved hypothetical protein
#6	AF0847	112	inosine monophosphate dehydrogenase (guaB-1)
#7	AF0848	24	conserved hypothetical protein
#8	AF0971	101	conserved hypothetical protein
#9	AF1186	139	conserved hypothetical protein
#10	AF1259	36	inosine monophosphate dehydrogenase, putative
#11	AF1260	207	phosphoribosylformylglycinamidine synthase I (purQ)
#12	AF1388	48	DNA helicase, putative
#13	AF1415	203	chloride channel, putative
#14	AF1960	242	DNA helicase, putative

Motif 1
GTGAGAGATATTTATAATTTTCTGACACAGGA	2	50	0
CCACCTCCAATTTTTAATTTTAATATTCTTTA	2	88	0
ATCGGAAAATTTTTTATTTTTTCAAAAGTAAA	4	19	0
AATAAAAAATTTTCCGATTTTTTGAATCTAAC	4	33	1
TTTAAGAGCTTTTCAGAATTTTTCACGAAAAC	5	35	1
ATAGTGGCTATTTTGAGTTTTCGTGAAAAATT	5	51	0
AAATCCGAGTTTTAAAATTTTCAATACAAAAT	5	216	0
CGAATACTTTTTTATAAATTTCCGAACGAAGT	5	256	1
TTGTCTGCAATTTTGAAATTTCATGAACATCA	6	45	1
ATTAAAAGCTTTTTTGATGTTCATGAAATTTC	6	59	0
         ATTTAAATTTTTTCATTTATGAA	8	1	1
TATATAAACTTTTGTAATGTTTGAGCTGCTTT	9	96	0
GCTTTGAAAGTTTAGGTTTTTCTTTTTTTACT	11	26	1
GGTTTTTCTTTTTTTACTTTTCCCTAGACAGG	11	40	1
ACCGCAATCTTTTAAGCTTTTTCCGTGTCGGC	11	172	0
          TTTTTGTTTTTTATTTCATAAA	13	0	1
AAAATTGCCATTTCGAATTTTTGTGCTGCCAG	13	120	0
          ***  *******
MAP Score: 23.1025

Motif 2
CTTATTTATTTTTAAAAGCTTTTCTTTAATA	2	18	1
ATAAATTTTTTTGAAAAGAATTGGCAGTTAG	3	41	0
CGCCCCAAGGTAAAAAAGTTTTATTGGTTTA	3	81	0
TTTGAAAAAATAAAAAATTTTCCGATTTTTT	4	25	1
CGAGAGGCGATTAAAAAGTTT          	5	0	0
CTCTCGCCTTTTTAAGAGCTTTTCAGAATTT	5	25	1
AAATCCGAGTTTTAAAATTTTCAATACAAAA	5	217	0
CGGAAATTTATAAAAAAGTATTCGTTTGCGG	5	249	0
TCATGAACATCAAAAAAGCTTTTAATTCACC	6	65	1
TGAGTGTATCTGCAAAAGCTTTATATTGCCA	8	61	1
GCTCAAACATTACAAAAGTTTATATACCTCA	9	102	1
ATCTGCCAGCTTTGAAAGTTTAGGTTTTTCT	11	18	1
CGGCATCAATTTGAAAAGAATTCTTTTAGCT	11	107	0
ACGGAAAAAGCTTAAAAGATTGCGGTTGATT	11	178	1
TCAGCCCAACTTTCAAAGTTTACTTCTTTGC	13	34	1
TACTTCTTTGCTCCAAAGCTTCAATTGACAC	13	54	1
          TTGAAGAGCTTGTTGAAATTC	14	0	1
          ** ********
MAP Score: 17.2305

Motif 3
TGACACAGGAATATTAAAGAAAAGCTTTTAAAAAT	2	25	0
AAAGACATAAATTTTTTTGAAAAGAATTGGCAGTT	3	43	0
AAACTTTTTTACCTTGGGGCGAGGAGGAGCG    	3	91	1
GTTTTCGTGAAAAATTCTGAAAAGCTCTTAAAAAG	5	32	0
TTTCAATACAAAATTAAATCAAAGATTCCATGCAA	5	195	0
TATAATAAAAATAATATTGCCAAGAA         	9	1	0
GGATTGAGATAAGATTGAGCAAAGAAGTGTGATAT	9	33	0
AGACAGGACGATCTTAGAGAAAGGAATCAGACCAG	11	65	1
TAGTAACGGCATCAATTTGAAAAGAATTCTTTTAG	11	109	0
GTCAATTGAAGCTTTGGAGCAAAGAAGTAAACTTT	13	48	0
GAGCTTGTTGAAATTCTGGACAGGATTGAGAAGGC	14	15	1
TATTCTGCCGAACTTTTGGCAAGGAGAGGAGAAAT	14	81	1
          *  **   *******
MAP Score: 7.22446

Motif 4
AACCTTACTGTGCTGGAAATGAAGGACATTCTGCA	5	115	1
AATGCCTACCTGCTGGCTGTGAAGGAA        	14	225	1
AAGGACATTCTGCAGAATCTGAACAGGTGGCTAAT	5	136	1
CACTAAAGAGTGCAGAACATCAACGCTGCCGACAC	11	145	1
ACATCAACGCTGCCGACACGGAAAAAGCTTAAAAG	11	161	1
AACTCGGATTTGCCGCAAACGAATACTTTTTTATA	5	237	1
ATTAAAGATCTGCCAGCTTTGAAAGTTTAGGTTTT	11	11	1
GAAGCGCTGTTGCTGAGGTTGAGGGCGATGCAGCG	14	151	1
ATGCAGAAGATGCTGAAGAGGGACATCTATTCTGC	14	54	1
CTCAATCCTGTCCAGAATTTCAACAAGCTCTTCAA	14	10	0
TCTAAGATCGTCCTGTCTAGGGAAAAGTAAAAAAA	11	48	0
          *** * *  **** *
MAP Score: 6.5745

Motif 5
GATGAGTTGGATTTAGATGCCCCCATAACTTTGTT	0	22	1
TTCCGATTTTTTGAATCTAACTCCAAAGCAAGTTC	4	44	1
GTGCTTTTATAAATACCTAACCTCAGTTGACATTC	4	82	0
TATAAAGCTTTTGCAGATACACTCATTTTAAATAT	8	51	0
CACTTCTTTGCTCAATCTTATCTCAATCCTTAAGA	9	39	1
ACCAACAGTAATTTAAAGCAGCTCAAACATTACAA	9	82	1
ACAAAAGTTTATATACCTCAGCCCACTTCACATTA	9	113	1
AATCTCACTTATTAACCTTCCCCCAACTAAGGCT 	12	24	1
TTTTTATTTCATAAAACTCAGCCCAACTTTCAAAG	13	17	1
GTTGAGGGCGATGCAGCGTATCCCATCGGCTGGGT	14	168	1
          **  * ** * ****
MAP Score: 4.92004

Motif 6
GGGCATCTAAATCCAACTCATCGTCAGGTTGATT    	0	6	0
AATAAAACTTTTTTACCTTGGGGCGAGGAGGAGCG   	3	87	1
TGAACAGGTGGCTAATCTGATTGCAGGGTTCTCATCAA	5	155	1
        TGTACCACCTCATGGTTTGGTCTTCAGGTG	6	92	0
CCCTAGACAGGACGATCTTAGAGAAAGGAATCAGACCA	11	61	1
AAAAGAATTCTTTTAGCTGGTGGGGCTGGTCTGATTCC	11	87	0
TGAAGAGCTTGTTGAAATTCTGGACAGGATTGAGAAGG	14	11	1
CATCTATTCTGCCGAACTTTTGGCAAGGAGAGGAGAAA	14	77	1
ATACGGAAATGCCTACCTGCTGGCTGTGAAGGAA    	14	218	1
          * * * **  ***   **
MAP Score: 4.51755

Motif 7
TTCTTATTTATTTTTAAAAGCTTTTCTTTAA	2	16	1
ACATAAATTTTTTTGAAAAGAATTGGCAGTT	3	43	0
CTTTTTTACCTTGGGGCGAGGAGGAGCG   	3	94	1
TCGTGAAAAATTCTGAAAAGCTCTTAAAAAG	5	32	0
GCACGGAATTTTCTTGACAGCGTAAACCTTA	5	91	1
ATTCTGCAGAATCTGAACAGGTGGCTAATCT	5	142	1
         AATGTGGAAAGGCTGTACGAAA	6	1	1
AACGGCATCAATTTGAAAAGAATTCTTTTAG	11	109	0
  AGCCTTAGTTGGGGGAAGGTTAATAAGTG	12	29	0
ATTTTGTAAGTTGGTGACAGAATCTGAAAGA	13	147	1
CTTGTTGAAATTCTGGACAGGATTGAGAAGG	14	18	1
TCTGCCGAACTTTTGGCAAGGAGAGGAGAAA	14	84	1
          ** ********
MAP Score: 1.9477

Motif 8
ACCAACAGTAATTTAAAGCAGCTCAAACATTACAA	9	82	1
ACAAAAGTTTATATACCTCAGCCCACTTCACATTA	9	113	1
CTAAACTTTCAAAGCTGGCAGATCTTTAATT    	11	6	0
GATCTTAGAGAAAGGAATCAGACCAGCCCCACCAG	11	74	1
TACTAGCACTAAAGAGTGCAGAACATCAACGCTGC	11	139	1
TTTTTATTTCATAAAACTCAGCCCAACTTTCAAAG	13	17	1
TTATCCTCCTACTGCTGGCAGCACAAAAATTCGAA	13	106	1
          * **   ***** **
MAP Score: 1.36474

Motif 9
       CGCTCCTCCTCGCCCCAAGGTAAAAAAGT	3	93	0
CCAAAGCAAGTTCACAGAATGTCAACTGAGGTTAGG	4	66	1
CATTACAAAAGTTTATATACCTCAGCCCACTTCACA	9	109	1
        AATTAAAGATCTGCCAGCTTTGAAAGTT	11	2	1
GAGAAAGGAATCAGACCAGCCCCACCAGCTAAAAGA	11	81	1
TTTTAAGCTTTTTCCGTGTCGGCAGCGTTGATGTTC	11	159	0
ATCTCACTTATTAACCTTCCCCCAACTAAGGCT   	12	25	1
TTGTTTTTTATTTCATAAAACTCAGCCCAACTTTCA	13	13	1
AGCTTTATCCTCCTACTGCTGGCAGCACAAAAATTC	13	102	1
GAAAAATATATCATCACTCCCCCAGCAAAAACGAAG	13	176	1
CTCTTCAGCATCTTCTGCATCGCAGCCTTCTCAATC	14	38	0
TCCTTATGAATCCCGATGAGCGCAGCACGGCAATTT	14	112	0
GTATCGCCTCGCATCAACGACCCAGCCGATGGGATA	14	186	0
          TTCCTTCACAGCCAGCAGGTAGGCAT	14	226	0
          *** *     ******
MAP Score: 0.0527907