AlignACE 3.0 10/20/99
AlignACE2 -i TH/TH_profile003_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944246578
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	MTH170	141	phosphoribosylaminoimidazolesuccinocarboxamide synthase
#1	MTH723	149	2-isopropylmalate synthase
#2	MTH725	149	conserved protein
#3	MTH726	92	unknown
#4	MTH829	61	3-isopropylmalate dehydratase, LeuD subunit 
#5	MTH831	25	molybdenum cofactor biosynthesis MoaA homolog
#6	MTH1201	95	conserved protein
#7	MTH1202	236	proteasome, beta subunit
#8	MTH1203	69	cleavage and polyadenylation specificity factor
#9	MTH1204	46	phosphoribosylformylglycinamidine cyclo-ligase
#10	MTH1375	22	isoleucyl-tRNA synthetase
#11	MTH1376	65	conserved protein
#12	MTH1386	300	3-isopropylmalate dehydratase, LeuD subunit
#13	MTH1393	141	phosphoribosylaminoimidazole carboxylase

Motif 1
ATTTAAAACCAAACTCTACATAACTATTTTCC	1	105	1
ACTATTTTCCGAACACCTTAAAGGGGATTAAA	1	127	1
CACCGCGCCTATCCACCACAAACTTACCGTCA	2	19	0
CACCGCGCCTATCCACCGCAAACTTACCGTCA	2	67	0
GATGTTTTTCATGGACCAGATAGAACACCAGT	4	27	1
GGACCAGATAGAACACCAGTAAGGGAGATACA	4	39	1
CATTCCTTTTAATGACCGGATAACCGTTCTTC	7	21	1
GTTTAATAAGGACCTCCTGTTATATATTGGTA	7	94	1
        AGATACACCTCTAATAAAAATAAT	7	222	0
        AAGATCACTTCTAAAAAACAGGGA	8	55	0
        TAAATCACCACTAAAGAATAGTTT	9	32	0
TTATTTATATCATCACCCCAAAACCATAAACC	11	37	1
AAGACTTGGTGAGCTCCTGAAAACTAATAAGT	12	50	1
GTCCCCATATGTTCACTGGATAACTGTCTTTC	12	176	0
TTAACCTTCTGATGTCCCCATATGTTCACTGG	12	189	0
ATACTGTTATGAAGACCTGTAAATGGTCCCTG	13	60	1
          ** **** ****
MAP Score: 12.9954

Motif 2
TTCGCAAGATTATATAACTGAATCGCAATATAACTCA	0	39	1
AATTTACACCTATATAAGTATTGGAGAGTTGATCAGG	0	82	1
TATGTTTTTATATGTAATGGTTGGAGA          	3	0	0
TTCCTCCAAGTATTTAATGGCTTTTACGGAAGACAAA	6	55	1
TTGCGATTTTTTTATAATAGATGGGGCTTCCTGAGGG	7	56	0
TCTGTACCAATATATAACAGGAGGTCCTTATTAAACT	7	93	0
GTTTTTATGGTATATAAAGGGTTTTCATTTAACCCTG	7	159	0
TTTTATTATTTTTATTAGAGGTGTATCT         	7	218	1
TTTTCTCCTATTTTTAATTGCAGTAAACACCTGTTTA	8	11	1
AGTTTAAGGTTATCTAAATAGTTAGCC          	9	0	0
TTCATAACAGTATATAAGGGGATTCTACCAATAGAGA	13	36	0
TCGGAGGTCATATTTAATAGATGGCACCTCCCGCAGG	13	88	0
          *** ***  * **   *
MAP Score: 11.3588

Motif 3
CGATTTCATCGTCTGTGGTACCGGTATCAGATAC	1	28	0
TCCACTGCACATAAATGGGCACTTAACCATATAT	1	68	1
TAAGTTTGTGGTGGATAGGCGCGGTGATGAATCC	2	25	1
GCGGTGATGAATCCATGGGATCTGACGGTAAGTT	2	45	1
TAAGTTTGCGGTGGATAGGCGCGGTGATGAATCC	2	73	1
ACCTCCTGTTATATATTGGTACAGAACTTTTATG	7	105	1
GAACTTTTATGTCCATGGGGACAGCCCTTTGCAG	7	128	1
   AGTAATGGTTTATGGTTTTGGGGTGATGATA	11	44	0
TTATCAAAGTATTTATAGGGCCGGGTGAAAATAT	12	105	1
CCAGCAAGTGGTCCATGGGGCAGTCTGTGAAAAT	12	231	0
ATGAAGACCTGTAAATGGTCCCTGCGGGAGGTGC	13	68	1
          **  *****  ***
MAP Score: 10.8477

Motif 4
TTCTATTATGAGTTATATTGCGATTCAGTTATATAATCTTGCGAA	0	39	0
TCCACTGCACATAAATGGGCACTTAACCATATATACCATTTAAAA	1	68	1
ACAATGAGGATTAATTTGTTGTATATGTTTTTATATGTAATGGTT	3	15	0
AATCCATAAGTGTTCTTTTTTCCTCCAAGTATTTAATGGCTTTTA	6	36	1
AATCGCAAAGTTTAATAAGGACCTCCTGTTATATATTGGTACAGA	7	85	1
CAGTCCTGGATCCCATTGTGTTTTTATGGTATATAAAGGGTTTTC	7	170	0
         AATTTCTCCTGAACTGGATGTATATACTTATTTATA	11	1	1
AGTAATGGTTTATGGTTTTGGGGTGATGATATAAATAAGTATATA	11	30	0
TGAGCTCCTGAAAACTAATAAGTTATTACTATATATTTAAATCTT	12	59	1
TACTATATATTTAAATCTTATTATCAAAGTATTTATAGGGCCGGG	12	85	1
TCTGTAACTCTCTATTGGTAGAATCCCCTTATATACTGTTATGAA	13	28	1
ATTAAATATGACCTCCGATAGATTCTCTATATATAAAGTTAAAG 	13	107	1
          *    *  *    *     ******
MAP Score: 10.3055

Motif 5
AATAGAATTTACACCTATATAAGTATTGGAG	0	77	1
ATGGGCACTTAACCATATATACCATTTAAAA	1	82	1
TTTAAAACCAAACTCTACATAACTATTTTCC	1	106	1
    TCTCCAACCATTACATATAAAAACATA	3	6	1
CCTCAGGAAGCCCCATCTATTATAAAAAAAT	7	57	1
AAAGTTCTGTACCAATATATAACAGGAGGTC	7	104	0
TAAATGAAAACCCTTTATATACCATAAAAAC	7	165	1
TAATATCACGCCCCGTCTATAAAAGACTTGG	12	28	1
TTTCACCCGGCCCTATAAATACTTTGATAAT	12	104	0
TCTGAATTTTACATCTATATTTTCACCCGGC	12	124	0
CTTCTGATGTCCCCATATGTTCACTGGATAA	12	185	0
ACCTTTATGAACCCTTCAATTATTCTGCTAA	12	266	1
GATACTCTGTAACTCTCTATTGGTAGAATCC	13	23	1
TTGGTAGAATCCCCTTATATACTGTTATGAA	13	42	1
      CTTTAACTTTATATATAGAGAATCT	13	126	0
          **** ******
MAP Score: 9.26636

Motif 6
GTGGATAGGCGCGGTGATGAATCCATGGGA	2	35	1
GTGGATAGGCGCGGTGATGAATCCATAATG	2	83	1
CGGTAAGTTTGCGGTGGATAGGCGCGGTGA	2	70	1
TTATGGTTTTGGGGTGATGATATAAATAAG	11	36	0
CGGTAAGTTTGTGGTGGATAGGCGCGGTGA	2	22	1
CCATTTATGTGCAGTGGATACTGGCGATTT	1	56	0
GCTTCCTGAGGGGTTGAAGAACGGTTATCC	7	38	0
CTATTCTTTAGTGGTGATTTA         	9	35	1
ACCTATATAAGTATTGGAGAGTTGATCAGG	0	89	1
          **********
MAP Score: 8.03376

Motif 7
ATAGAATTTACACCTATATAAGTATTGGAGAGTTGATCAGG	0	78	1
     ACTATCACTTTTAAAGAATTTGAGTATGAAATCCTG	0	115	0
    TTTAATCCCCTTTAAGGTGTTCGGAAAATAGTTATGT	1	122	0
GAAGCCCCATCTATTATAAAAAAATCGCAAAGTTTAATAAG	7	63	1
TAATAAGGACCTCCTGTTATATATTGGTACAGAACTTTTAT	7	97	1
     AGATACACCTCTAATAAAAATAATAAAAAACCAGTC	7	210	0
TATCACGCCCCGTCTATAAAAGACTTGGTGAGCTCCTGAAA	12	31	1
ACTTGGTGAGCTCCTGAAAACTAATAAGTTATTACTATATA	12	53	1
TTTTCACCCGGCCCTATAAATACTTTGATAATAAGATTTAA	12	95	0
  CTTCTATCCTCCTTTAGCAGAATAATTGAAGGGTTCATA	12	271	0
TTGGTAGAATCCCCTTATATACTGTTATGAAGACCTGTAAA	13	42	1
          * *** ***     * *   *
MAP Score: 4.88333

Motif 8
        TATTTCACCCTAAGAAGCATGAATCTG	0	2	1
ATAATAGAATTTACACCTATATAAGTATTGGAGAG	0	75	1
         TTTAATCCCCTTTAAGGTGTTCGGAA	1	133	0
ATACAACAAATTAATCCTCATTGTAGTTAACTTCT	3	36	1
        TGTATCTCCCTTACTGGTGTTCTATCT	4	44	0
AGGGTTTTCATTTAACCCTGCAAAGGGCTGTCCCC	7	144	0
        TTTTTCTCCTATTTTTAATTGCAGTAA	8	2	1
       GTGTTTCTCCCTCAGCTGGATA      	10	4	0
        AATTTCTCCTGAACTGGATGTATATAC	11	2	1
ACATCTATATTTTCACCCGGCCCTATAAATACTTT	12	110	0
TTAGAGCCTCTTTAACCTTCTGATGTCCCCATATG	12	197	0
        CTTCTATCCTCCTTTAGCAGAATAATT	12	283	0
          ********  *   *
MAP Score: 4.42208

Motif 9
TGGATAGGCGCGGTGATGAATCCATGGGATCTG	2	36	1
TGGATAGGCGCGGTGATGAATCCATAATGGAGA	2	84	1
GTTCTTCAACCCCTCAGGAAGCCCCATCTATTA	7	46	1
AATAAAAAACCAGTCCTGGATCCCATTGTGTTT	7	192	0
CTTGCTGGAACCTTTATGAACCCTTCAATTATT	12	257	1
CCCTTATATACTGTTATGAAGACCTGTAAATGG	13	53	1
          * ** ***** **
MAP Score: 4.13823

Motif 10
GAATTTGAGTATGAAATCCTGATCAACTCT	0	106	0
AGGCGCGGTGATGAATCCATGGGATCTGAC	2	41	1
AGGCGCGGTGATGAATCCATAATGGAGAGA	2	89	1
ACCATTACATATAAAAACATATACAACAAA	3	16	1
GTTTAAAAAAATAAATCCATAAGTGTTCTT	6	23	1
CCCATCTATTATAAAAAAATCGCAAAGTTT	7	68	1
GCAGGGTTAAATGAAAACCCTTTATATACC	7	158	1
TTTATATACCATAAAAACACAATGGGATCC	7	178	1
ACCCGGCCCTATAAATACTTTGATAATAAG	12	101	0
ATATACTGTTATGAAGACCTGTAAATGGTC	13	58	1
          **********
MAP Score: 2.31482