AlignACE 3.0 10/20/99
AlignACE2 -i AG/AG_operons015_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944242851
 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	AF1446	63	A. fulgidus predicted coding region AF1446
#8	AF1448	114	transcriptional regulatory protein, AsnC family
#9	AF1449	33	pyruvate formate-lyase 2 (pflD)
#10	AF1451	88	thermosome, subunit beta (thsB)
#11	AF1452	117	signal-transducing histidine kinase
#12	AF1453	37	methionyl-tRNA synthetase (metS)
#13	AF1798	87	phosphate permease, putative
#14	AF2224	38	valyl-tRNA synthetase (valS)
#15	AF2225	64	2-hydroxyhepta-2,4-diene-1,7-dioate isomerase (hpcE-2)
#16	AF2421	58	leucyl-tRNA synthetase (leuS)
#17	AF2425	85	methanol dehydrogenase regulatory protein (moxR)

Motif 1
GATGGAAGAGAAATTCTTATAATTTTTTTCGATG	0	21	0
ATATTTTCTTAAACACTTTATCATAATAGAATCC	1	157	1
ATAGAATCCGAAAAACTTAAATATTATAATGTCG	1	182	1
TTTCAAACCAAAAAGCTTATTATTTCCGTCAAGG	2	45	1
ATTGTCATGTAAACCCTTATTTTTCAGCCTACTA	3	42	1
CCATGATGGTATATGCTTTTGCATGTCAAAATTC	3	100	1
TCAGTTAAACCAAGTGTTTTATTTATTCCCCTAT	4	15	1
TTGAATTGAACCATACTTATTTTTTTCCGAGAGG	4	64	0
TTTAATCCCTCCACACTTTTAATTTC        	5	15	1
CTAAGATTTAATACGCTTTTTATTTAAACCTTTT	6	70	0
     TAATGACAGTCTTTTCTTTGTAATTGAAG	8	5	1
TTCATTGTAAATAAAGTTTACCTTATAAACTGAC	8	73	0
GTATTTCTATATAAGCTTTTCTATCACGAATTTA	10	28	0
ATAATCGGCCAAATGCTTTTATTTACAAAGATAG	11	83	1
ACTCTGATATATATCCTTTTCCTTAAACGGTAGA	13	50	0
        GCAAAAAGTTATATTTCAAGTTTCTG	14	2	1
GATAACTCTTAAAACCTTTGCCTTCTTACGCCAC	15	12	0
          ***  *****  **
MAP Score: 18.5479

Motif 2
AATTATAAGAATTTCTCTTCCATCAGAAGCACAG	0	31	1
AAATTCTTTGTTCGCTCCGCCCTCTTCCTGTGCT	0	58	0
CACAACCTCAAGATCTCCAGCATCGATCATCCTT	1	33	1
AGCTGGTATCAATTGTCCGACATTATAATATTTA	1	199	0
TGGTGTCTCCATCTGTCCGACTTTGTCCTTCAGC	1	230	0
AGATGGAGACACCAGTCCTCCATCTGTCCTCCGA	1	250	1
        AAATCCCTCCAATTTTTGTTTGTGTA	2	2	1
TTGTTTGTGTACTCCTCCTCTTTCAAACCAAAAA	2	25	1
         AAAATCTCTTCCCTTGACGGAAATA	2	65	0
TCAGCCTACTATCCCTCCTAATTTTTGCTGCCCC	3	65	1
TTATTCCCCTATCGCTCTCCACTCTTACCTCTCG	4	37	1
 CTGTTTTTAATCCCTCCACACTTTTAATTTC  	5	9	1
          TCTGCTCCACCTTCGAAGTAATTG	7	49	0
CCATACTGCATGCTCTCCAACGTCAGTTTATAAG	8	52	1
CCATAGCTCTAACCCTCCTACCATTCTTCCAAAA	17	44	1
          * * **** ** **
MAP Score: 16.1735

Motif 3
CACCAACATCGAAAAAAATTATAAGAATTTCTCT	0	15	1
ATTCTATTATGATAAAGTGTTTAAGAAAATATTC	1	155	0
ATCCGAAAAACTTAAATATTATAATGTCGGACAA	1	187	1
TCTTTCAAACCAAAAAGCTTATTATTTCCGTCAA	2	43	1
TAATTGTCATGTAAACCCTTATTTTTCAGCCTAC	3	40	1
AAGGAAAGCTGATAACTTTTTTAATCCACCGGCT	3	138	1
TGCAAAGTTGGGAAAAAGGTTTAAATAAAAAGCG	6	57	1
GTGTGTACTGGTGAAAGTTTTTAAGAGGGAAAAA	7	13	1
CAGTTTATAAGGTAAACTTTATTTACAATGAAAG	8	75	1
AATTCGTGATAGAAAAGCTTATATAGAAATACCA	10	30	1
          GTAAAACGTTATTTACCCCTCGCA	12	0	1
TACCGTTTAAGGAAAAGGATATATATCAGAGTTC	13	52	1
          GCAAAAAGTTATATTTCAAGTTTC	14	0	1
GGCGTAAGAAGGCAAAGGTTTTAAGAGTTATCTC	15	14	1
CAGGCCAAACGCCAAATTTTTTAATCCCATTTAT	16	22	1
          *  ***  ******
MAP Score: 14.9194

Motif 4
         GGAGGGAAAAGGTTGCGAGGG	12	26	0
GAGGGAGAGTGAGGGAAGGTATTAAACTTT	3	11	1
AGCACAGGAAGAGGGCGGAGCGAACAAAGA	0	58	1
TTTTTTCCGAGAGGTAAGAGTGGAGAGCGA	4	48	0
TATTTCCGTCAAGGGAAGAGATTTT     	2	65	1
CAAAAATTAGGAGGGATAGTAGGCTGAAAA	3	62	0
         GGAGGGAGAGTGAGGGAAGGT	3	1	1
CCCTACATCGGAGGACAGATGGAGGACTGG	1	261	0
AAGTTTTTAAGAGGGAAAAATCCAATTACT	7	27	1
TAAGAGTGGAGAGCGATAGGGGAATAAATA	4	34	0
AGGACAGATGGAGGACTGGTGTCTCCATCT	1	250	0
TCTACCGTTTAAGGAAAAGGATATATATCA	13	50	1
CTGTGCTTCTGATGGAAGAGAAATTCTTAT	0	35	0
ATACCAGCTGAAGGACAAAGTCGGACAGAT	1	224	1
CAAATGTCCGGAGGTAAGGATGATCGATGC	1	52	0
TGTGGCGTAAGAAGGCAAAGGTTTTAAGAG	15	11	1
GGTTGTGAAGGAGCAAGAAGAAGAGTAAAA	1	10	0
AGGAGGGTTAGAGCTATGGGAAACGTCAAA	17	33	0
AATAGTTGAGGAGCTCAAATGTCCGGAGGT	1	67	0
          **********
MAP Score: 14.1547

Motif 5
AAATTCTTATAATTTTTTTCGATGTTGGTGAA	0	13	0
TGATTTTCTGCAGTTTTTATTAGTCCTTGCCA	1	106	1
TATTATGATAAAGTGTTTAAGAAAATATTCCG	1	153	0
TATAATATTTAAGTTTTTCGGATTCTATTATG	1	178	0
AACCATACTTATTTTTTTCCGAGAGGTAAGAG	4	58	0
         TGAGTTTTTTTGAATTGAACCAT	4	84	0
GTACTGGTGAAAGTTTTTAAGAGGGAAAAATC	7	17	1
TTGCTGGCGGCAGTTTTTTGGAATGGATTGCA	11	46	1
GTTATATTTCAAGTTTCTGTGAGGTGGACAC 	14	17	1
TAAGAAGGCAAAGGTTTTAAGAGTTATCTCAG	15	18	1
ACCAATATATGTGTGTTTTGGAAGAATGGTAG	17	61	0
          ********  **
MAP Score: 13.1371

Motif 6
TTCTGCAGTTTTTATTAGTCCTTGCCAAGTA	1	111	1
AGCTGATAACTTTTTTAATCCACCGGCTGTT	3	144	1
ACCAAGTGTTTTATTTATTCCCCTATCGCTC	4	23	1
        CTGTTTTTAATCCCTCCACACTT	5	2	1
AATACGCTTTTTATTTAAACCTTTTTCCCAA	6	64	0
  GTAAAACGTTATTTACCCCTCGCAACCTT	12	8	1
AAACGCCAAATTTTTTAATCCCATTTATTAG	16	28	1
          ******* ***
MAP Score: 7.90095

Motif 7
TCCTTACCTCCGGACATTTGAGCTCCTCAA	1	62	1
ATTATAATGTCGGACAATTGATACCAGCTG	1	204	1
AGGACAAAGTCGGACAGATGGAGACACCAG	1	235	1
CCTACATCGGAGGACAGATGGAGGACTGGT	1	260	0
TCTGAATAATCGGCCAAATGCTTTTATTTA	11	78	1
TTGGTCAATCAGGCCAAACGCCAAATTTTT	16	13	1
          **********
MAP Score: 5.57638

Motif 8
CACCAACATCGAAAAAAATTATAAGAATTTCTCT	0	15	1
ATAACTACTTGGCAAGGACTAATAAAAACTGCAG	1	113	0
AATAGAATCCGAAAAACTTAAATATTATAATGTC	1	181	1
TCTTTCAAACCAAAAAGCTTATTATTTCCGTCAA	2	43	1
TTACCTCTCGGAAAAAAATAAGTATGGTTCAATT	4	61	1
TCTCGATAAAGGCAAGTTTAAAAACAGCAACGCC	6	22	0
GCAAAGTTGGGAAAAAGGTTTAAATAAAAAGCGT	6	58	1
AAGGTTTAAATAAAAAGCGTATTAAATCTTAGCG	6	72	1
TTTTAAGAGGGAAAAATCCAATTACTTCGAAGGT	7	31	1
TTATTTACAATGAAAGTGTTACAATCCAACC   	8	93	1
       CCTTAAAAACCTAATTAAAAAAGATTA	9	16	0
ATTCGTGATAGAAAAGCTTATATAGAAATACCAA	10	31	1
         GTAAAACGTTATTTACCCCTCGCAA	12	1	1
ACCGTTTAAGGAAAAGGATATATATCAGAGTTCG	13	53	1
GGCGTAAGAAGGCAAAGGTTTTAAGAGTTATCTC	15	14	1
TAGAGCTATGGGAAACGTCAAATAGCAGATTGCT	17	21	0
          *****   *** **
MAP Score: 3.84718

Motif 9
CACCAACATCGAAAAAAATTATAAGAATTT	0	15	1
GGGCGGAGCGAACAAAGAATTTATATACTA	0	70	1
ATTGATAATTGAAAAAGAAATGGGGG    	0	106	1
ATAACTACTTGGCAAGGACTAATAAAAACT	1	117	0
AAAGTGTTTAAGAAAATATTCCGCGAATGA	1	146	0
TTCCGTCAAGGGAAGAGATTTT        	2	68	1
TAGGCTGAAAAATAAGGGTTTACATGACAA	3	43	0
ATGGTGGGGCAGCAAAAATTAGGAGGGATA	3	74	0
CTTACCTCTCGGAAAAAAATAAGTATGGTT	4	60	1
GCAAAGTTGGGAAAAAGGTTTAAATAAAAA	6	58	1
TCAATTACAAAGAAAAGACTGTCATTA   	8	7	0
AAACCTAATTAAAAAAGATTACGATTT   	9	7	0
AGGTAACCAAAACAAAAATTAAAAA     	11	5	0
      GGAGGGAAAAGGTTGCGAGGGGTA	12	23	0
TACCGTTTAAGGAAAAGGATATATATCAGA	13	52	1
GGCGTAAGAAGGCAAAGGTTTTAAGAGTTA	15	14	1
          **********
MAP Score: 3.50514

Motif 10
        CCTTTCACCAACATCGAAAAAAATTATAA	0	2	1
TTCTTAAACACTTTATCATAATAGAATCCGAAAAACT	1	162	1
       TGACTTCAGTTAAACCAAGTGTTTTATTTA	4	3	1
TTAAACTTGCCTTTATCGAGATTGCAAAGTTGGGAAA	6	35	1
TGGGAAAAAGGTTTAAATAAAAAGCGTATTAAATCTT	6	65	1
AAGACAGCTACTTCAATTACAAAGAAAAGACTGTCAT	8	12	0
AAGTAGCTGTCTTTATCCATACTGCATGCTCTCCAAC	8	36	1
ATAAGGTAAACTTTATTTACAATGAAAGTGTTACAAT	8	81	1
GGCCAAATGCTTTTATTTACAAAGATAGGCAATAGCC	11	89	1
ATATTCTACCGTTTAAGGAAAAGGATATATATCAGAG	13	46	1
          *****   * *  ** *
MAP Score: 2.45688

Motif 11
ATAAGCTTTTTGGTTTGAAAGAGGAGGAGT	2	35	0
TGAAAAATAAGGGTTTACATGACAATTAAA	3	38	0
GAACAGCCGGTGGATTAAAAAAGTTATCAG	3	146	0
AAAGTGTGGAGGGATTAAAAACAG      	5	4	0
TGCCTTTATCGAGATTGCAAAGTTGGGAAA	6	42	1
       GGTTGGATTGTAACACTTTCATT	8	101	0
ATCACGAATTTAAATTGCAAGCATTTGTTA	10	10	0
CAGAAATTGGTGGATTGGTATTTCTATATA	10	49	0
TTTTTTGGAATGGATTGCATCTGAATAATC	11	59	1
GCTAATAAATGGGATTAAAAAATTTGGCGT	16	30	0
          **********
MAP Score: 1.49447