AlignACE 3.0 10/20/99
AlignACE2 -i TH/TH_operons009_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944244298
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	MTH184	125	isocitrate dehydrogenase
#1	MTH474	300	conserved protein
#2	MTH475	87	unknown
#3	MTH723	149	2-isopropylmalate synthase
#4	MTH829	61	3-isopropylmalate dehydratase, LeuD subunit 
#5	MTH831	25	molybdenum cofactor biosynthesis MoaA homolog
#6	MTH1386	300	3-isopropylmalate dehydratase, LeuD subunit
#7	MTH1442	75	ketol-acid reductoisomerase
#8	MTH1444	64	acetolactate synthase, large subunit 
#9	MTH1449	135	dihydroxy-acid dehydratase
#10	MTH1481	142	isopropylmalate synthase
#11	MTH1602	63	acetolactate synthase, large subunit homolog
#12	MTH1630	191	2-isopropylmalate synthase

Motif 1
GATCATTCAGCTTCATGAGAACACTTCAAG	0	95	1
CATGAGAACACTTCAAGAGGAATTTAA   	0	108	1
ACATAATATTCTACAGGTGATATCATGGCC	1	35	1
GGGTGAGGGGCTCAAGGAGATCGCCGAGGC	1	201	1
GTACAAGGGCCTCGAAGTGGTTCCTGTCCT	1	242	0
CGGCGGTGAACTTCCAGGGGAC        	1	288	1
CATCAGGTCACTTCATGAGGCGCGGTGAGA	2	15	1
AGACATCATCCTTCGTGAGGAAGTTCCTGG	2	42	1
        TACGTCAGGTGGAGGCTGGTAT	3	2	1
TTCCGAACACCTTAAAGGGGATTAAA    	3	133	1
ACATCAGAAGGTTAAAGAGGCTCTAATTTT	6	206	1
CCAGCAAGTGGTCCATGGGGCAGTCTGTGA	6	235	0
AATTATTCTGCTAAAGGAGGATAGAAG   	6	283	1
GGCCGCAGGCCCTCAGGAGGGATCG     	9	5	0
CTGCAAGTTCCCTCAGGTGGATGTGGCCGG	9	98	0
CCTGAGGGAACTTGCAGAGGCTGTTAAGGA	9	111	1
TGCAGAGGCTGTTAAGGAGGGT        	9	123	1
GTGCATCCATATTCCGGTGGCTGAAATATG	12	89	0
TTAATAAAGCATTAAGGTGGTAATCCC   	12	174	1
          **********
MAP Score: 17.021

Motif 2
GATCATTCAGCTTCATGAGAACACTTCAAG	0	95	1
CATGAGAACACTTCAAGAGGAATTTAA   	0	108	1
CATCAGGTCACTTCATGAGGCGCGGTGAGA	2	15	1
AGACATCATCCTTCGTGAGGAAGTTCCTGG	2	42	1
ATACCAGCCTCCACCTGACGTA        	3	2	0
         ACCCCAAGATGACTGATGATG	4	1	1
CTATAAAAGACTTGGTGAGCTCCTGAAAAC	6	44	1
GCCTCTTTAACCTTCTGATGTCCCCATATG	6	197	0
     CGATCCCTCCTGAGGGCCTGCGGCC	9	5	1
CCGGCCACATCCACCTGAGGGAACTTGCAG	9	98	1
CCTGAGGGAACTTGCAGAGGCTGTTAAGGA	9	111	1
          **********
MAP Score: 8.2157

Motif 3
GGACTCGAGGGTGAGGGGCTCAAGGAGATC	1	193	1
ATGAAGTGACCTGATGGTCCC         	2	1	0
ATTTCATCGTCTGTGGTACCGGTATCAGAT	3	30	0
TATTAATCAAGTGAGGGACC          	6	0	0
CTTTAACCTTCTGATGTCCCCATATGTTCA	6	193	0
 CGATCCCTCCTGAGGGCCTGCGGCCTGAC	9	9	1
CCACATCCACCTGAGGGAACTTGCAGAGGC	9	102	1
        GGCTGATGGTCCTCAGATATTT	12	2	1
          **********
MAP Score: 7.8498

Motif 4
TTGTTAAGAACGCGGCTGCTGAACTCACAAC	1	126	1
TCAAGGAGATCGCCGAGGCTGCAAGGATAGA	1	212	1
GGAACTTCCTCACGAAGGATGATGTCTCACC	2	38	0
   TACGTCAGGTGGAGGCTGGTATCTGATA	3	7	1
ATACCGGTACCACAGACGATGAAATCGCCAG	3	35	1
ACCCCAAGATGACTGATGATGTTTTTCATGG	4	10	1
CCTGCGGCCTGACAGATGATGACTTCGAGAA	9	26	1
TGAGGGAACTTGCAGAGGCTGTTAAGGAGGG	9	113	1
TTTTCAAATTCACTGATGCAGTCTCTGATCA	12	29	1
          *** *******
MAP Score: 6.94673

Motif 5
TGGGGGTTTTTATGATGTCTTCATATTCCCT	0	15	0
ATATTCTACAGGTGATATCATGGCCAGGGTT	1	40	1
TATAGATCTGGATGAACTTGTGGAACTGCTT	1	97	1
GAACGCGGCTGCTGAACTCACAACCTTCTAT	1	133	1
TTGCAGCCTCGGCGATCTCCTTGAGCCCCTC	1	205	0
TGAACTCGGCGGTGAACTTCCAGGGGAC   	1	282	1
CCTCACGAAGGATGATGTCTCACCGCGCCTC	2	31	0
TACCACAGACGATGAAATCGCCAGTATCCAC	3	42	1
CAAGATGACTGATGATGTTTTTCATGGACCA	4	14	1
TAAAAGACTTGGTGAGCTCCTGAAAACTAAT	6	47	1
TCTTTAACCTTCTGATGTCCCCATATGTTCA	6	193	0
CGGCCTGACAGATGATGACTTCGAGAAACCA	9	30	1
CAAATTCACTGATGCAGTCTCTGATCATTAT	12	33	1
CCGGAATATGGATGCACTCTCAAACCTTTTA	12	102	1
          ********* *
MAP Score: 6.83234

Motif 6
AAAGGGAATATGAAGACATCATAAAAACCCCCAGCTTCCAAAC	0	13	1
TTTTTATCATTACAGCCTTAAAATATTATCCCATGCAGATCAT	0	58	1
GCGATCTCCTTGAGCCCCTCACCCTCGAGTCCAATCAGATTGG	1	182	0
CCACAGACGATGAAATCGCCAGTATCCACTGCACATAAATGGG	3	44	1
TGCACATAAATGGGCACTTAACCATATATACCATTTAAAACCA	3	73	1
AAAACTCGTCTGAATTTTACATCTATATTTTCACCCGGCCCTA	6	120	0
TTTTTCAGTATGAAGGCGAAAGACAGTTATCCAGTGAACATAT	6	159	1
TTAAAGAGGCTCTAATTTTCACAGACTGCCCCATGGACCACTT	6	217	1
GAAGGGTTCATAAAGGTTCCAGCAAGTGGTCCATGGGGCAGTC	6	240	0
GGAACCTTTATGAACCCTTCAATTATTCTGCTAAAGGAGGATA	6	263	1
CATTCATAGGTATAGCCAACAGTTACACTGACATAGTTCCCGG	9	59	1
AGCTTTTAATTGTAGCCCACAGAAATTTAAGCAGATAAAATGC	10	90	1
          ** *  *  **   *     ***
MAP Score: 5.64175

Motif 7
TATGTGAATCATATCTAATAAAATGGGACA 	1	9	0
TTAACCATATATACCATTTAAAACCAAACTC	3	90	1
CAAACTCTACATAACTATTTTCCGAACACCT	3	114	1
TGAGCTCCTGAAAACTAATAAGTTATTACTA	6	59	1
CTATATATTTAAATCTTATTATCAAAGTATT	6	87	1
CGGGACTCCCATAAATTTTATTTTAAATGAG	7	40	1
ATTTGAAAGTATATATTTTATAGGAAATATG	8	12	1
AACCCGGGTTATAACTTATAAGATATAACTT	10	40	1
CTTATAAGATATAACTTATAACATACTGTGT	10	54	1
ACTGTGTGTAAAAGCTTTTAATTGTAGCCCA	10	78	1
CATGAATTAAAAAAATATTAACAGAAGGGGG	11	10	0
ATGCACTCTCAAACCTTTTATACTAATATAT	12	113	1
TTATACTAATATATCTAATTTTAAATAAATG	12	130	1
          *** *******
MAP Score: 4.08343

Motif 8
TCTTGAAGTGTTCTCATGAAGCTGAATGATC	0	95	0
TTAAGAACGCGGCTGCTGAACTCACAACCTT	1	129	1
GAGGGTGAGGGGCTCAAGGAGATCGCCGAGG	1	199	1
TCATGAAGTGACCTGATGGTCCC        	2	2	0
GTCTCACCGCGCCTCATGAAGTGACCTGATG	2	15	0
       TACGTCAGGTGGAGGCTGGTATCT	3	3	1
ACCCCAAGATGACTGATGATGTTTTTCATGG	4	10	1
TTCACAGACTGCCCCATGGACCACTTGCTGG	6	234	1
CCTGCGGCCTGACAGATGATGACTTCGAGAA	9	26	1
          GGCTGATGGTCCTCAGATATT	12	0	1
          * *********
MAP Score: 3.01547

Motif 9
TGATATCATGGCCAGGGTTACCCGTGAGATGGTTGAAAATTC	1	52	1
GGACTCGAGGGTGAGGGGCTCAAGGAGATCGCCGAGGCTGCA	1	193	1
CAAGGAGATCGCCGAGGCTGCAAGGATAGAGGACAGGAACCA	1	213	1
CCACTTCGAGGCCCTTGTACCCAGGATATATGAACTCGGCGG	1	252	1
GTGGAGGCTGGTATCTGATACCGGTACCACAGACGATGAAAT	3	18	1
AAAGGTTCCAGCAAGTGGTCCATGGGGCAGTCTGTGAAAATT	6	230	0
GTTCCCTCAGGTGGATGTGGCCGGGAACTATGTCAGTGTAAC	9	80	0
TTTCTGTAAATTACCTGGCACCCGGGAACCCGGGTTATAACT	10	14	1
          **   **   ** ***     *
MAP Score: 2.48974

Motif 10
CTGAACTCACAACCTTCTATTTTACACCCTA	1	144	1
ATGGGCACTTAACCATATATACCATTTAAAA	3	82	1
TTTAAAACCAAACTCTACATAACTATTTTCC	3	106	1
CTTATTATCAAAGTATTTATAGGGCCGGGTG	6	101	1
AACCTTTATGAACCCTTCAATTATTCTGCTA	6	265	1
  TTATTTGAAAGTATATATTTTATAGGAAA	8	8	1
GACTTCGAGAAACCATTCATAGGTATAGCCA	9	46	1
CTGTGTGTAAAAGCTTTTAATTGTAGCCCAC	10	79	1
ATATTCTGCCAACTATTTAAATCATGAATTA	11	32	0
TGCACTCTCAAACCTTTTATACTAATATATC	12	114	1
AATAAATGCCAAGTATTCATTTTAATAAAGC	12	153	1
          **** ******
MAP Score: 2.40659

Motif 11
CTTCATGAGAACACTTCAAGAGGAATTTAA        	0	105	1
      TGTCCCATTTTATTAGATATGATTCACATAAT	1	4	1
TATTTTCCGAACACCTTAAAGGGGATTAAA        	3	129	1
GGTCCATGAAAAACATCATCAGTCATCTTGGGGT    	4	6	0
TGAGCTCCTGAAAACTAATAAGTTATTACTATATATTT	6	59	1
GGACTCCCATAAATTTTATTTTAAATGAGCTGTTAATT	7	42	1
TTGAAAGTATATATTTTATAGGAAATATGTCATTAATA	8	14	1
GTTATAAGTTATATCTTATAAGTTATAACCCGGGTTCC	10	38	0
CCGGTGGCTGAAATATGGTGGGTCATTACGTGTTATGG	12	68	0
TTATACTAATATATCTAATTTTAAATAAATGCCAAGTA	12	130	1
          * ** * **  *  ** *
MAP Score: 0.704256