AlignACE 3.0 10/20/99
AlignACE2 -i MJ/MJ_operons010_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944240319
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	MJ0202	56	conserved hypothetical protein
#1	MJ0203	120	phosphoribosylformylglycinamidine cyclo-ligase (purM)
#2	MJ0204	99	amidophosphoribosyltransferase (purF)
#3	MJ0831	93	conserved hypothetical protein
#4	MJ0832	259	anaerobic ribonucleoside-triphosphate reductase (nrdD)
#5	MJ0934	300	polyferredoxin (mvhB)
#6	MJ0936	94	conserved hypothetical protein
#7	MJ0937	63	phosphoribosylamine--glycine ligase (purD)
#8	MJ1116	136	asparagine synthetase (asnB)
#9	MJ1264	76	phosphoribosylformylglycinamidine synthase II (purL)
#10	MJ1265	189	nucleoside diphosphate kinase, (ndk)
#11	MJ1416	132	conserved hypothetical protein
#12	MJ1420	100	glucosamine--fructose-6-phosphate aminotransferase (isomerizing) (glmS)
#13	MJ1592	300	phosphoribosylaminoimidazolesuccinocarboxamide synthase (purC)
#14	MJ1642	300	conserved hypothetical protein
#15	MJ1644	147	M. jannaschii predicted coding region MJ1644
#16	MJ1646	24	pyrimidine biosynthesis protein, putative
#17	MJ1647	65	DNA binding protein
#18	MJ1648	143	phosphoribosylformylglycinamidine synthase I, (purQ)

Motif 1
ATAATTTTATTTTTTACTATTTTTTGGGTGAT	4	234	1
TGTTTATGGGTTTTAACTATTTATTACTTTAG	12	59	1
CGCCGGCCACTTTTTATTATTTTAAATTCTCA	5	107	1
ATTATCTTTATTTTTATTATTTTTATTTCAAA	17	22	1
TATATAAATCTTTTAAATTTTTAGTTACTATT	11	48	1
CTTTGATATATTTTTATTTTTTATTTCACTGT	13	69	1
TAAAAACCCTTTTTTAGTTTTTTAGACTTTTA	2	75	0
TTAAACCACTTTTTTACTTTTTTATTATTACA	7	15	1
ATCGCACTTATTTAAAATATTTAAGCGGAAAT	4	115	1
AATAATTCTCTTTTAAATATATTATATA    	12	6	0
TATAGTTCTTTTTAAAATATTTTGTAATAACT	13	107	1
ACCAACAATATTATCATTATTTTTAATAACTT	10	98	1
AAATTAATCCTTATCAATATTTCAACATAATA	4	16	1
TAATCTTATATTTATAATTTTTAGTTATGGTG	11	108	1
AAGAGGCTTATTTTTAGTTTATTTTTAG    	15	129	1
TAATCGATAAATTTAAATATTTTTAAAATATC	5	270	1
TATACCTTATTTTTTAATATTAGCTAACACAA	8	105	0
TAACTTTAAATTTTAATTATTAAAACTCTCAT	13	262	0
TTAATACTAATTTTAAATAATTCTCTTTTAAA	12	21	0
TATGAGCAATATTTAAATTTTTCGAGATAGAT	10	63	1
TGTTATGGCAATTTCATTTTTTATATATGAGC	10	38	1
ATAAATTATCTTTTTAATTTTACTAATTCTTC	2	12	1
AAATTGGATGTTTAAAAAATTTTTATTCCTAC	1	57	1
CAATAATGATTTTACAGTATATG         	16	1	0
TCTATAGTTCTTTTCAAAATATTTTGTAATAA	18	87	0
TCTCATTTAATTTTTAATCTTTATACTTACAA	13	236	0
TTCTTCTTTCTTTTTATTTATTTGCTAAAAGT	2	50	1
ATTTCTTTATCTTTAACTTTTTATTAAGATGG	3	59	0
TATTAGTTAATTAATATTATTTGTGGATATAC	9	44	0
ACTATCCCGCTTTTGATATTATATAATTACTA	10	166	0
GGAATAATATATTTAATAATTTCTAAAATTGA	3	29	0
ATCAAAAAGCTTTAAAGTATTAGTAATAATAA	10	134	1
          **** * *****
MAP Score: 45.6607

Motif 2
      ATAGCGGGGGGGCCACACCCGAACCCATCCC	5	4	1
CCATCCCGAACTCGGAAGTTAAGCCCCCCAGCGATGC	5	34	1
ATAAAAAGTGGCCGGCGGCGTCGCCCCTTTCCCGCCA	5	87	0
ATTACTATGCCCTGGTGGTGTAGCCCGGCCTATCATA	5	153	1
GCCTATCATACGGGACTGTCACTCCCGTGACTCGGGT	5	180	1
ACTCCCGTGACTCGGGTTCAAATCCCGGCCAGGGCGC	5	200	1
CAAGCGTTAGCGAGGCAGTGCATCCCGGATATTCCAA	15	27	1
          *  **  **  * ****
MAP Score: 7.26403

Motif 3
GATGGGTTCGGGTGTGGCCCCCCCGCTAT     	5	5	0
TAAGCCCCCCAGCGATGCCCCGAGTACTGCCATC	5	53	1
ATCTGGCGGGAAAGGGGCGACGCCGCCGGCCACT	5	84	1
ATGCCCTGGTGGTGTAGCCCGGCCTATCATACGG	5	159	1
TCTAAAATAAAAAGAAGCCCGGCAAATGGCGCCC	5	231	0
GAACCCTTTAAGGGAGGCACATCGAAATCTTTGA	13	41	1
CCTATCTTCGAGCGTAGCAAGGAGAGTTAATGAA	14	73	0
GCTCGAAGATAGGGAGGCGGCGAGACAAACATTA	14	94	1
TGCTTTATTGAGGGTAGCTCTGACTCTGCCCGAT	14	154	1
      GGTTTAAGAGGCACTGCCAAGCGTTAGC	15	4	1
GCCAAGCGTTAGCGAGGCAGTGCATCCCGGATAT	15	25	1
CGGATATTCCAATAGGGCAGAGCCCTATGGTGTG	15	52	1
          ** * *** * ***
MAP Score: 2.94162

Motif 4
CGCCGTATTGTTTAAGAGTTTGAAGATTTAT	0	16	1
AAATTGGATGTTTAAAAAATTTTTATTCCTA	1	57	1
ATTCCATCTTAATAAAAAGTTAAAGATAAAG	3	56	1
TATATACTATTTTAAAAGATTATCGCACTTA	4	94	1
ATCGCACTTATTTAAAATATTTAAGCGGAAA	4	115	1
TAGATAGTGTTATAAAATATTCTCCATTATA	6	52	1
TTTAATCTTTATTAAGATATTTAAATTAAAA	8	44	1
AGATATTTAAATTAAAATTTTGCAAATATTT	8	58	1
AAATATTTAGCATAAAATGTTAAGTTGTGTT	8	81	1
         GCATAAAGGTTTAATAACACAT	9	1	1
ATGAGCAATATTTAAATTTTTCGAGATAGAT	10	64	1
ATCAAAAAGCTTTAAAGTATTAGTAATAATA	10	134	1
TATTGACATATATAAATCTTTTAAATTTTTA	11	40	1
TATAGTTCTTTTTAAAATATTTTGTAATAAC	13	107	1
TGAAAAGAACTATAAATTTTTTATATTACAT	13	206	1
TTATTTTTATTTCAAAAATTTTTGGAGGTAT	17	38	1
          ******* ***
MAP Score: 2.42524

Motif 5
          ATAGCGGGGGGGCCACACCCGAACCCA	5	0	1
TTAACTTCCGAGTTCGGGATGGGTTCGGGTGTGGCCC	5	19	0
TAATAAAAAGTGGCCGGCGGCGTCGCCCCTTTCCCGC	5	89	0
CAGTCCCGTATGATAGGCCGGGCTACACCACCAGGGC	5	161	0
TCGGGTTCAAATCCCGGCCAGGGCGCCATTTGCCGGG	5	211	1
TGTGCCTCCCTTAAAGGGTTCGGCACATCGTAAGAAC	13	25	0
TCCAAGCTTTAGCTCGGAGAGGATTCAGATGAAATCC	14	29	1
GCTCGAAGATAGGGAGGCGGCGAGACAAACATTAGTT	14	94	1
GATAGGTCACAGGGCAGGTTGGTGTCATCGGGCAGAG	14	177	0
GCCAAGCGTTAGCGAGGCAGTGCATCCCGGATATTCC	15	25	1
          **  ****  **   **
MAP Score: 1.57906