AlignACE 3.0 10/20/99
AlignACE2 -i TH/TH_operons011_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944244433
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	MTH174	169	sensory transduction histidine kinase
#1	MTH175	128	conserved protein
#2	MTH176	168	tRNA-guanine transglycosylase
#3	MTH179	117	unknown
#4	MTH181	49	unknown
#5	MTH182	36	glutamate N-acetyltransferase
#6	MTH225	300	histidinol dehydrogenase
#7	MTH226	93	aspartyl-tRNA synthetase
#8	MTH242	231	shikimate 5-dehydrogenase
#9	MTH545	194	conserved protein
#10	MTH546	93	cationic amino acid transporter related protein
#11	MTH747	96	conserved protein
#12	MTH766	29	5-enolpyruvylshikimate 3-phosphate synthase
#13	MTH767	83	valyl-tRNA synthetase
#14	MTH800	52	dihydrodipicolinate reductase
#15	MTH802	49	aspartokinase II alpha subunit
#16	MTH804	40	chorismate mutase, subunit A
#17	MTH805	240	conserved protein (homoserine kinase related)
#18	MTH846	170	N-acetyl-gamma-glutamyl-phosphate reductase
#19	MTH1337	81	N-acetylornithine aminotransferase

Motif 1
CCTATGGCAACAATATTTATCGCTGATGGT	8	38	1
TATCTAAGTGCAATATTTATATAGTGGTAG	17	114	0
ATGGTACTTACAATATTTATTTACCATCAG	8	60	0
TCATTTTTTCCAACATTTAAAAGGTTGTGA	15	23	1
CTACCATTTGCAATTTTTATATTAATCTGT	6	105	0
      TACCCAATCTTTATAAAGATGTTT	13	69	0
TCGTGGCCACCAAAATTTATAAGTATTTCA	18	47	0
AACTGATAATAAATATTTATGTTGAGGTGG	19	14	0
GGGGTAATGGCAAAATTTAAGTTGTAATTA	1	93	1
CCAGTAATATAAACATTTATTTATATGCTT	6	181	0
ATTTCATGGACAACCTTTAACTGTCCATGG	18	23	0
AACCATCAACCAATGTTTAAGTGAAAGCAT	6	157	1
 GATATCACCAAAAATTTATATGGGGACCT	19	62	0
GTACCATCCTAAATTTTTAACCATTTTTAT	17	72	1
TAATGGACCAAAATTTTTAAATAATAAGTT	6	44	0
AGTTTAAAGTGAATATTTAAGGTCTCTGAT	7	57	0
AGTTTAGGTTCAACATTAATACAGGTCCCC	19	40	1
          **********
MAP Score: 17.4511

Motif 2
CAGACATGCTGCGTCAGGTTCCTCCACAGAGGGGCATG	0	104	1
AAAACCCCCACCTACATCACCCCCCGATTTACATCATG	0	138	0
CACAGGAATACCCTCAAATCACAGATCA          	1	0	0
ATTTTCAGACCCTCCAAGACCCACAGGAATACCCTCAA	1	21	0
CATAATCCATGCCTCAGAAACACTGGAAGCAGGGCTGG	2	18	0
    TTACCAGCCTCAGTCTCCTTATAAGTGTGTATTA	6	6	1
ACTGACCGGTGCAGCATCTAAACCCGAAGAGATTCTTT	8	112	1
GTTGGAGTCAGCTCCATACTCCTTGCCACAGTTTGGAC	9	21	1
ACCGTTCCAGGCCTCATACCCTTTTTCTCAGCGAGTCT	9	91	1
          CCGCCATCCTCATGATCACAGAACATAA	11	0	1
AATCAGTAAACCAGCAATACCCCGATGATATATTAATT	11	48	1
   AAAAACACCTGCAGATACCTCCAGATGGA      	12	4	0
AGTGCCAGTTCCTCCAGGACCATCATGAGCCTC     	14	5	0
          GCATCACACCCCCTAGATCAGTGCCAGT	14	34	0
       TAACCTTCACAACCTTTTAAATGTTGGAAAA	15	28	0
AGATTATTAGGCTGCAAAGCACTCCAGAGAGCACCTCA	17	184	0
CATATAATGTCCATCACTGACCCGGTCGTGGCCACCAA	18	64	0
GTGGGAGGCCCCACCATACCCTCGCAGACTATCCAGAG	18	103	1
TATATAATGTCCATCACTGACCTGGGTACTCTGGATAG	18	131	0
          **  **   *****   *
MAP Score: 15.8538

Motif 3
   TTTCCAGTATTCTGTTCAATCAGTTTCCATCCAGAATT	0	7	1
TCAGTTTCCATCCAGAATTTCATCAATTCCATCAATTTATA	0	29	1
ATAGTGGGGCAGACATGCTGCGTCAGGTTCCTCCACAGAGG	0	95	1
CTACATCACCCCCCGATTTACATCATGCCCCTCTGTGGAGG	0	124	0
   GGGAAAACCCCCACCTACATCACCCCCCGATTTACATC	0	141	0
AAATTTTGCCATTACCCCTGAATCAGAGTCGGTGCCTGCTC	1	70	0
ATCCTCCCACATAATCCATGCCTCAGAAACACTGGAAGCAG	2	24	0
GATGATACTGATTAATATGTAATCAGCACCCTAAAAATCCT	2	60	0
TAGGGTGCTGATTACATATTAATCAGTATCATCGTGGATAT	2	68	1
GCCACTGCAGAGTACCTGTTAATCAGTATCATTCTGC    	2	141	1
ATTCCATGAGAATAGTTCTCAATCAGGTGCAGGGAGAGAGC	3	85	1
ATTATTTAAAAATTTTGGTCCATTAGATGCCCCCTAATCCA	6	49	1
ACTCTGATAATGCATGGTTTCATCAGAGACCTTAAATATTC	7	36	1
GGAAAAACACATGTAACCGGAATCATGGGCCATCCCCTGGG	8	182	1
     GCATCACACCCCCTAGATCAGTGCCAGTTCCTCCAG	14	26	0
CCTCCCACCCATATAATGTCCATCACTGACCCGGTCGTGGC	18	70	0
ATACCCACCTATATAATGTCCATCACTGACCTGGGTACTCT	18	137	0
          *       * ******   **
MAP Score: 14.487

Motif 4
GGGGCATGATGTAAATCGGGGGGTGATGTAGG	0	134	1
AATCGGGGGGTGATGTAGGTGGGGGTTTTCCC	0	147	1
    TGATCTGTGATTTGAGGGTATTCCTGTG	1	6	1
GTATTCCTGTGGGTCTTGGAGGGTCTGAAAAT	1	27	1
GCACCGACTCTGATTCAGGGGTAATGGCAAAA	1	76	1
GAGGCATGGATTATGTGGGAGGATTTTTAGGG	2	41	1
TGAGCATGTAGTATCTGGTGGTAGCCACTGCA	2	118	1
CCCCTTAATATTATCTTGAAGTATCCTTAAAT	4	20	0
TTCCTTAATTTGGATTAGGGGGCATCTAATGG	6	68	0
TCCCTTTTAAGAATTTAGGGGGCACACCGGAT	6	232	0
TCTTTGCCTGTAATGCCGGGGTGATAAACTGA	8	145	1
AGGCTCATGATGGTCCTGGAGGAACTGGCACT	14	11	1
GAACTGGCACTGATCTAGGGGGTGTGATGC  	14	32	1
AGTGCAATATTTATATAGTGGTAGAACATTCT	17	106	0
GTGATGGACATTATATGGGTGGGAGGCCCCAC	18	85	1
TAGTCTGCGAGGGTATGGTGGGGCCTCCCACC	18	102	0
GTGATGGACATTATATAGGTGGGTATAG    	18	152	1
TAATAAATATTTATGTTGAGGTGGTTAA    	19	6	0
          **** * *****
MAP Score: 13.5222

Motif 5
AATTAATAACATAGTGGGGCAGACATGCTGC	0	85	1
AGGTTCCTCCACAGAGGGGCATGATGTAAAT	0	119	1
ACCGACTCTGATTCAGGGGTAATGGCAAAAT	1	78	1
CATCCCTCAAACTGAGGGGTAAAGATATTAA	3	25	1
AATAGTTCTCAATCAGGTGCAGGGAGAGAGC	3	95	1
TCAAGATAATATTAAGGGGAATTGAA     	4	33	1
CTTAATTTGGATTAGGGGGCATCTAATGGAC	6	66	0
CTTTTAAGAATTTAGGGGGCACACCGGATCA	6	230	0
TCACATCTAAATTGAGGGAAAGATTAAATCC	10	50	1
TTGTAGGAGAAATAAGGGGAAGCAAGTTCTC	13	25	0
CTTGAATGGAAGAAAGGGGAATGTAATTT  	16	21	1
CGACCGGGTCAGTGATGGACATTATATGGGT	18	74	1
TACCCAGGTCAGTGATGGACATTATATAGGT	18	141	1
TGGACATTATATAGGTGGGTATAG       	18	156	1
          * *********
MAP Score: 11.4061

Motif 6
         TTTCCAGTATTCTGTTCAATCAGTTTCC	0	1	1
TTCAATCAGTTTCCATCCAGAATTTCATCAATTCCAT	0	24	1
TTTTCAGACCCTCCAAGACCCACAGGAATACCCTCAA	1	21	0
GTGGTAGCCACTGCAGAGTACCTGTTAATCAGTATCA	2	135	1
ATGGGATGAATTCCAACCATCAACCAATGTTTAAGTG	6	143	1
ATTTGAAGAATTCCAGTAATATAAACATTTATTTATA	6	186	0
AAGGGAATGGCTCCATAAAACTAACCATTCGCCCTAA	6	258	1
         CCTCCAGTGAAAAAGTTAGGGCGAATGG	6	282	0
ACATGTGTTTTTCCAGTTATCAGTTTATCACCCCGGC	8	159	0
TTGGAGTCAGCTCCATACTCCTTGCCACAGTTTGGAC	9	22	1
  AAAAACACCTGCAGATACCTCCAGATGGA      	12	4	0
GTGCCAGTTCCTCCAGGACCATCATGAGCCTC     	14	5	0
          CTCCAGTGACCCTTGAATGGAAGAAAG	16	0	1
ACCTTTTTACCTCCAGTCATGTTTTCAGGAGTTTTTG	17	18	1
TATATCAGACATCCATGTACCATCCTAAATTTTTAAC	17	56	1
CTGCAAAGCACTCCAGAGAGCACCTCAAGCTCTCAAA	17	174	0
          ******  * **    *
MAP Score: 11.086

Motif 7
GATAGTCTGCGAGGGTATGGTGGGGCCTCC	18	106	0
AGGCTGTGCCCAGGGGATGGCCCATGATTC	8	201	0
AATATATCATCGGGGTATTGCTGGTTTACT	11	52	0
ATGTAAATCGGGGGGTGATGTAGGTGGGGG	0	142	1
AAATTCTTAAAAGGGAATGGCTCCATAAAA	6	248	1
ACTCTGATTCAGGGGTAATGGCAAAATTTA	1	82	1
CACTGATCTAGGGGGTGTGATGC       	14	39	1
CGCTGAGAAAAAGGGTATGAGGCCTGGAAC	9	94	0
GAATGGAAGAAAGGGGAATGTAATTT    	16	24	1
CATCTAAATTGAGGGAAAGATTAAATCCAA	10	53	1
GTGGGTCTTGGAGGGTCTGAAAATCATAAC	1	35	1
TCTGTGATTTGAGGGTATTCCTGTGGGTCT	1	13	1
GATAATATTAAGGGGAATTGAA        	4	37	1
TTCCTCCACAGAGGGGCATGATGTAAATCG	0	122	1
TAGGAGAAATAAGGGGAAGCAAGTTCTCAT	13	23	0
CCTGTAATGCCGGGGTGATAAACTGATAAC	8	151	1
CAATCAGGTGCAGGGAGAGAGCA       	3	104	1
AATTTGGATTAGGGGGCATCTAATGGACCA	6	64	0
CCTCAAACTGAGGGGTAAAGATATTAACTC	3	29	1
          **********
MAP Score: 10.6602

Motif 8
CCATTAGATGCCCCCTAATCCAAATTAAGGA	6	68	1
  GCATCACACCCCCTAGATCAGTGCCAGTT	14	33	0
GAACTTGCTTCCCCTTATTTCTCCTACAAGG	13	27	1
CCTACATCACCCCCCGATTTACATCATGCCC	0	135	0
GGGAAAACCCCCACCTACATCACCCCCCGAT	0	148	0
TAATACAGGTCCCCATATAAATTTTTGGTGA	19	56	1
TTTGCCATTACCCCTGAATCAGAGTCGGTGC	1	76	0
TTGGAGTCAGCTCCATACTCCTTGCCACAGT	9	22	1
AAAAATCCTCCCACATAATCCATGCCTCAGA	2	38	0
GGGAAGATATCCCCATGGACAGTTAAAGGTT	18	11	1
    TGCTCTCTCCCTGCACCTGATTGAGAA	3	100	0
    CTATACCCACCTATATAATGTCCATCA	18	153	0
ATCCGGTGTGCCCCCTAAATTCTTAAAAGGG	6	232	1
AAGGGAATGGCTCCATAAAACTAACCATTCG	6	258	1
GTCACACTCTCCCCTGGATTATAGGTAACCT	8	10	1
ATAACAAAAACTCCTGAAAACATGACTGGAG	17	28	0
TAAGGAATGACCACAGATTAATATAAAAATT	6	93	1
   TTCAATTCCCCTTAATATTATCTTGAAG	4	31	0
CCTCCAAGACCCACAGGAATACCCTCAAATC	1	18	0
          ******* ***
MAP Score: 8.64436

Motif 9
GTATTCTGTTCAATCAGTTTCCATCCAGAA	0	16	1
GATTACATATTAATCAGTATCATCGTGGAT	2	77	1
GAGTACCTGTTAATCAGTATCATTCTGC  	2	150	1
CTCAGTCTCCTTATAAGTGTGTATTAAACT	6	18	1
AATTTTTAAATAATAAGTTTAATACACACT	6	33	0
GTTTTTCCAGTTATCAGTTTATCACCCCGG	8	160	0
CAGCTTGTTATAATAAGGTTACC       	9	181	1
     GGATTTAATAAGTTAGTTGGTTGGA	10	78	0
AAAAGCAGCACAATCAGTAAACCAGCAATA	11	37	1
CCACCAAAATTTATAAGTATTTCATGGACA	18	41	0
TAAATATTTATTATCAGTTTAGGTTCAACA	19	25	1
          **********
MAP Score: 7.65765

Motif 10
AATTTTGCCATTACCCCTGAATCAGAGTCG	1	80	0
GTTAATATCTTTACCCCTCAGTTTGAGGGA	3	27	0
     TTCAATTCCCCTTAATATTATCTTG	4	34	0
GTCCATTAGATGCCCCCTAATCCAAATTAA	6	66	1
TGATCCGGTGTGCCCCCTAAATTCTTAAAA	6	230	1
AAACTAACCATTCGCCCTAACTTTTTCACT	6	275	1
GAGAACTTGCTTCCCCTTATTTCTCCTACA	13	25	1
    CTCCAGTGACCCTTGAATGGAAGAAA	16	6	1
          **********
MAP Score: 7.32823

Motif 11
GCTGCGTCAGGTTCCTCCACAGAGGGGCATGATGT	0	111	1
TGATGAGCAGGCACCGACTCTGATTCAGGGGTAAT	1	66	1
     TATGTGATCCAGCCCTGCTTCCAGTGTTTC	2	5	1
GTATCATCGTGGATATACACTGATCTGAGCATGTA	2	93	1
         TGCTCTCTCCCTGCACCTGATTGAGA	3	101	0
CCAAATTAAGGAATGACCACAGATTAATATAAAAA	6	87	1
ATAATGCATGGTTTCATCAGAGACCTTAAATATTC	7	42	1
AAAAAAATCAGATTCTATACTGACCGGTGCAGCAT	8	94	1
TTCTCAGCTTTCTCGGGCTCAGATCTCACCGTTCC	9	64	1
 CCGCCATCCTCATGATCACAGAACATAAAAAGCA	11	9	1
GGTCCTGGAGGAACTGGCACTGATCTAGGGGGTGT	14	22	1
AGGATTCTATGATCGTTCACTGAATAGATTATTAG	17	212	0
ACCCATATAATGTCCATCACTGACCCGGTCGTGGC	18	70	0
ACCTATATAATGTCCATCACTGACCTGGGTACTCT	18	137	0
          * **   ****** *
MAP Score: 6.52776

Motif 12
ATGCTGCGTCAGGTTCCTCCACAGAGGGGCATGATGTAAAT	0	109	1
CAAGACCCACAGGAATACCCTCAAATCACAGATCA      	1	4	0
CTTGATGAGCAGGCACCGACTCTGATTCAGGGGTAATGGCA	1	64	1
       TATGTGATCCAGCCCTGCTTCCAGTGTTTCTGAG	2	3	1
CAGTATCATCGTGGATATACACTGATCTGAGCATGTAGTAT	2	91	1
ATCCAAATTAAGGAATGACCACAGATTAATATAAAAATTGC	6	85	1
CTGTAATGCCGGGGTGATAAACTGATAACTGGAAAAACACA	8	152	1
GCTGTGCCCAGGGGATGGCCCATGATTCCGGTTACATGTGT	8	188	0
ATGGTCCTGGAGGAACTGGCACTGATCTAGGGGGTGTGATG	14	20	1
TTAAAAATTTAGGATGGTACATGGATGTCTGATATAACAAA	17	51	0
          *** *    * * ***    *
MAP Score: 2.2749