AlignACE 3.0 10/20/99
AlignACE2 -i TH/TH_operons019_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944244877
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	MTH235	93	riboflavin-specific deaminase
#1	MTH409	258	unknown
#2	MTH410	62	unknown
#3	MTH481	91	H+-transporting ATPase
#4	MTH753	292	conserved protein
#5	MTH1001	285	cation-transporting P-ATPase PacL
#6	MTH1386	300	3-isopropylmalate dehydratase, LeuD subunit
#7	MTH1390	98	riboflavin synthase beta subunit
#8	MTH1493	78	cation transporting P-type ATPase related protein
#9	MTH1494	266	conserved protein
#10	MTH1499	84	GTP cyclohydrolase II
#11	MTH1500	22	conserved protein
#12	MTH1501	189	phenylalanyl-tRNA synthetase alpha subunit
#13	MTH1516	152	cation-transporting P-ATPase PacL
#14	MTH1534	40	aryldialkylphosphatase related protein
#15	MTH1535	43	heavy-metal transporting CPx-type ATPase

Motif 1
      GTTATCACCATTCCATATATCTCTCTCCC	3	4	1
    TGTGGATCACCCGATCATCTATACACATGAA	4	6	1
TAAGGTACAGTCAACCCCTCAATTAATAAAGCGCC	4	237	1
      TGGTTCCCCCTCACCATTATTTATGTTGA	4	273	0
TTTCAGGAGCTCACCAAGTCTTTTATAGACGGGGC	6	37	0
ATCTATATTTTCACCCGGCCCTATAAATACTTTGA	6	108	0
GGAACCTTTATGAACCCTTCAATTATTCTGCTAAA	6	263	1
    CTGGAGGCACCCTGCCGCCGATAATCATCAC	9	6	1
AGCATGTACCCCACCAGGACGTATATGAATGAACT	9	96	1
TCACAAGGATGGACCATGTCTTCGAGAGGATGAGG	9	133	1
AAGAGATAGACCACCACCTCTCAGAGATAATGAGG	9	208	1
TGATGAACCATCACCCGGTCCTCTACGGACGTTCT	12	81	1
TTGAAACACACCACCCTCATTATTAAATTAATGTA	13	119	0
   TTACATTCCACCAGATCCATGATTCAACCTGA	15	21	0
          ******  **   **
MAP Score: 14.3749

Motif 2
TGACATCTATAAATAGGTCGGAGGAGGAAGGCC    	0	70	1
CATCAAAATTAGAGAGATTAGGGGAATACCTGAAAAT	1	22	1
GGGGAGCTGTTGAAAGATACCTGGAGGTTTCCATAGA	1	115	1
CAGAGAGGTAATAGAGATACTCGGGGAAATAGGAGTT	1	216	1
ATTATTGGGGAGAGAGATATATGGAATGGTGATAAC 	3	9	0
GGACAAACTGATAAAGATATCCGGAAG          	3	74	1
AAATTCATGTGTATAGATGATCGGGTGATCCACA   	4	7	0
ATCAACATAAATAATGGTGAGGGGGAACCA       	4	272	1
TGAAGGGTTCATAAAGGTTCCAGCAAGTGGTCCATGG	6	247	0
CCGATAATCATCACAGATGACTGGAAGGATCCTTATA	9	27	1
GATTTATTCGATAATGATCACTGGGGGTTCTGT    	12	166	1
CTATATACCTATATAGATTTAGGGGCTGATCTAC   	14	7	0
          * * ****    *** *
MAP Score: 12.6858

Motif 3
CTTAAAATTCCACATTAATTTATAGGATGACA	0	43	1
TTCAACAGCTCCCCTTAAAGTGACGTCATTTT	1	97	0
TCACAGTATTCCCCTGTAATGATGATTCAATA	2	38	1
TATCTCTCTCCCCAATAATGTATTTTTTCACT	3	27	1
CACTGAACATCAGATTCATGGACAAACTGATA	3	55	1
ATCATCTATACACATGAATTTGATGGGACAGT	4	23	1
TTAGCATGGACCCCTTAATGAAAAACTGGCAT	4	92	1
CATGCATCATCAGATGAATGAAGTGAAGAGAT	4	121	1
GTACAGTCAACCCCTCAATTAATAAAGCGCCA	4	241	1
GGTTCCCCCTCACCATTATTTATGTTGATGGC	4	269	0
CGTTGAAGAACAGCTGGACTTATGATGGATAT	5	128	1
CTTTAATTAGCACATTTAATAAGTTCATTCTG	5	254	0
CCTCCTTTAGCAGAATAATTGAAGGGTTCATA	6	271	0
AGTACAAGTGCACCTGCAATGGTACTCAGGAC	7	59	0
GATACAGTGGCACCTGTAAGCGAGACCCATAA	8	15	0
GCATGTACCCCACCAGGACGTATATGAATGAA	9	97	1
ATGAACTCCTCACAAGGATGGACCATGTCTTC	9	124	1
CATAGGATATCACATTAATTTAATAACATGAG	13	13	1
AAGTGTAAGTCCCCTTGATGAAGCTGGTGGCT	13	56	1
          ****** *** *
MAP Score: 10.734

Motif 4
CTAATCTCTCTAATTTTGATGAGATCTCATT	1	12	0
AGTTTGTCCATGAATCTGATGTTCAGTGAAA	3	52	0
TCTATACACATGAATTTGATGGGACAGTTAA	4	27	1
TCACCATTATTTATGTTGATGGCGCTTTATT	4	261	0
TCAACATAAATAATGGTGAGGGGGAACCA  	4	273	1
GATATGGAAATAACGTTGAAGAACAGCTGGA	5	115	1
TATGAAAGAATAACGTTGAAGAACAGCTGGT	5	211	1
       TGATAATCCTGATGTATATTTTAT	10	70	0
CAGTCAATAGTTAAGGTGATGAACCATAACC	12	29	1
CGTTCTAATCTGAGGGTGATGTATGGATTTA	12	110	1
GTCCCCTTGATGAAGCTGGTGGCTGTGCAAC	13	64	1
AATTTAATAATGAGGGTGGTGTGTTTCAAGT	13	125	1
          *** *******
MAP Score: 10.7021

Motif 5
AGGTATCTTTCAACAGCTCCCCTTAAAGTG	1	107	0
TTTCACTGAACATCAGATTCATGGACAAAC	3	52	1
      TGTGGATCACCCGATCATCTATAC	4	4	1
TGGCATGCATCATCAGATGAATGAAGTGAA	4	118	1
TGGATGTGCACATCAGTTTATATTATATTT	5	74	1
TAACGTTGAAGAACAGCTGGACTTATGATG	5	125	1
TAACGTTGAAGAACAGCTGGTTGACAGAAT	5	221	1
CTGCCCCATGGACCACTTGCTGGAACCTTT	6	242	1
GGGTACATGCTATCAGCTCCATATCAATTT	9	77	0
GGTTATGGTTCATCACCTTAACTATTGACT	12	30	0
GGTGATGGTTCATCACCTGAGCTTGACTTT	12	66	0
GGTGATGAACCATCACCCGGTCCTCTACGG	12	79	1
TAAATCCATACATCACCCTCAGATTAGAAC	12	111	0
CTTCAATCAGGATCAGTCGCCTGATTTATT	12	144	1
GTTGCACAGCCACCAGCTTCATCAAGGGGA	13	65	0
ACTTGAAACACACCACCCTCATTATTAAAT	13	126	0
       GTAGATCAGCCCCTAAATCTATA	14	3	1
  TTACATTCCACCAGATCCATGATTCAAC	15	25	0
          **********
MAP Score: 10.6642

Motif 6
TATAGATGTCATCCTATAAATTAATGTGGA	0	51	0
TGGGATTGATAACCCCTCAATATTTTCAGG	1	50	0
GAAAAATGACGTCACTTTAAGGGGAGCTGT	1	95	1
TTAATTAACTGTCCCATCAAATTCATGTGT	4	32	0
TATTAGCATGGACCCCTTAATGAAAAACTG	4	90	1
AGGTACAGTCAACCCCTCAATTAATAAAGC	4	239	1
AACCTTTATGAACCCTTCAATTATTCTGCT	6	265	1
CTGTAAGCGAGACCCATAAACATC      	8	4	0
GTGCCACTGTATCCTCTCAAAATCTTAATA	8	34	1
AACTATCCTCATCCTCTCGAAGACATGGTC	9	144	0
GCCGGACAAGGTCCCTTAAAAGAGAAGAGA	9	175	1
GTTATGGTTCATCACCTTAACTATTGACTG	12	29	0
TTCATAGGATATCACATTAATTTAATAACA	13	11	1
TCAAGTGTAAGTCCCCTTGATGAAGCTGGT	13	54	1
   GTAGATCAGCCCCTAAATCTATATAGG	14	7	1
          **********
MAP Score: 10.6281

Motif 7
GTATGGGATTGATAACCCCTCAATATTTTC	1	53	0
GGAAAGCAGCCATGGCCCCTGTT       	2	3	0
CCCCTATTAGCATGGACCCCTTAATGAAAA	4	86	1
CAGACTGCCCCATGGACCACTTGCTGGAAC	6	238	1
CTGGAACCTTTATGAACCCTTCAATTATTC	6	261	1
GAGCTGATAGCATGTACCCCACCAGGACGT	9	88	1
TCCTCACAAGGATGGACCATGTCTTCGAGA	9	130	1
AGATCGAAGAGATAGACCACCACCTCTCAG	9	202	1
TAGTTAAGGTGATGAACCATAACCGAGAAT	12	36	1
AAGCTCAGGTGATGAACCATCACCCGGTCC	12	72	1
          **********
MAP Score: 10.3629

Motif 8
GTATTTTTTCACTGAACATCAGATTCATGGACA	3	46	1
ATTCATGTGTATAGATGATCGGGTGATCCACA 	4	9	0
TGGACCCCTTAATGAAAAACTGGCATGCATCAT	4	98	1
ACCGAATCCAGATGAAGTACCGCACAGAGGAAG	4	184	1
TGGAAATAACGTTGAAGAACAGCTGGACTTATG	5	119	1
TGAGAACAACATTGAATAACTGGACTGAGAGAA	5	159	1
AACTGGACTGAGAGAAAATCCGCAGACGGAACT	5	176	1
AAAGAATAACGTTGAAGAACAGCTGGTTGACAG	5	215	1
TCGCCTTCATACTGAAAAACTCGTCTGAATTTT	6	145	0
ACAGTTATCCAGTGAACATATGGGGACATCAGA	6	181	1
AGTCATCTGTGATGATTATCGGCGGCAGGGTGC	9	16	0
       TTGGCTGAAGTTCAGGTTGAATCATG	15	3	1
          * **** *** **
MAP Score: 9.02153

Motif 9
AAGGGGAGCTGTTGAAAGATACCTGGAGGTTTCCATA	1	113	1
TTAACTGTCCCATCAAATTCATGTGTATAGATGATCG	4	21	0
TTCATCTGATGATGCATGCCAGTTTTTCATTAAGGGG	4	102	0
CTTCCTCTGTGCGGTACTTCATCTGGATTCGGTAGTA	4	180	0
TGGAAATAACGTTGAAGAACAGCTGGACTTATGATGG	5	119	1
AAAGAATAACGTTGAAGAACAGCTGGTTGACAGAATC	5	215	1
TGCAGGTGCACTTGTACTCTAAATGGAGGTATTGA  	7	73	1
GAGCTGATAGCATGTACCCCACCAGGACGTATATGAA	9	88	1
TAACATGAGTGGTGCATTTCAAGTGTAAGTCCCCTTG	13	36	1
TAATGAGGGTGGTGTGTTTCAAGTGTAAAT       	13	132	1
       TTGGCTGAAGTTCAGGTTGAATCATGGATC	15	3	1
          * ** *   **  ****
MAP Score: 6.19309

Motif 10
GGTGACTGAAGATAATAAGGTACAGTCAAC	4	222	1
TAAATACTTTGATAATAAGATTTAAATATA	6	90	0
TACTGATAGTGATAATAATGGTCCTGAGTA	7	39	1
CCCTGCCGCCGATAATCATCACAGATGACT	9	19	1
ACCTCTCAGAGATAATGAGGATACTGAACA	9	223	1
         TGATAATCCTGATGTATATTT	10	73	0
 CTTTCCTCTGATAATCAGAGGT       	11	3	0
TGCCAAACCTTATAATAATGA         	12	1	0
TGATTTATTCGATAATGATCACTGGGGGTT	12	165	1
ACATTAATTTAATAATGAGGGTGGTGTGTT	13	120	1
          **********
MAP Score: 5.77821

Motif 11
ATCCCATACCCTGGAAGATTTGAAAAATGACGT	1	74	1
TGAAAGATACCTGGAGGTTTCCATAGAATCCTG	1	125	1
GTACCGAGCACTGGATGTGCACATCAGTTTATA	5	63	1
TGTACTCTAAATGGAGGTATTGA          	7	85	1
          CTGGAGGCACCCTGCCGCCGATA	9	0	1
TCACAGATGACTGGAAGGATCCTTATACTATGA	9	37	1
CATATACGTCCTGGTGGGGTACATGCTATCAGC	9	90	0
ATAATGATCACTGGGGGTTCTGT          	12	176	1
AATCATGGATCTGGTGGAATGTAA         	15	29	1
          *******  * **
MAP Score: 4.339

Motif 12
CACATTAATTTATAGGATGACATCTATAAATAG	0	53	1
CCTGCCTTGATATTGGAGAAATGATCATATCAC	1	154	1
GAAATGATCATATCACAGGAAAGGGCCAGAAAA	1	171	1
ATAGGAGTTTTACCAGAGGATTTT         	1	244	1
TCCATGCTAATAGGGGAGGCGATCATAAAATTC	4	69	0
ATTATTCTGCTAAAGGAGGATAGAAG       	6	284	1
CAAGGTCCCTTAAAAGAGAAGAGATCGAAGAGA	9	181	1
 ACCTCTGATTATCAGAGGAAAG          	11	9	1
ACCCCAAGGGTATGGGATGAGAGTATTACATTA	13	93	1
          **  ****** **
MAP Score: 3.26602