AlignACE 3.0 10/20/99
AlignACE2 -i TH/TH_operons006_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944244187
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	MTH709	300	GMP synthetase, subunit A
#1	MTH710	102	GMP synthetase, subunit B
#2	MTH736	133	conserved protein
#3	MTH738	24	conserved protein
#4	MTH739	286	conserved protein
#5	MTH846	170	N-acetyl-gamma-glutamyl-phosphate reductase
#6	MTH847	59	unknown
#7	MTH848	103	protein-export membrane protein, SecF 
#8	MTH997	31	carbamoyl-phosphate synthase, large subunit 
#9	MTH1107	107	oxaloacetate decarboxylase, alpha subunit 
#10	MTH1127	90	dihydroorotase
#11	MTH1413	42	aspartate carbamoyltransferase
#12	MTH1415	175	ATP-dependent RNA helicase, eIF-4A family 
#13	MTH1418	107	conserved protein
#14	MTH1445	64	glycinamide ribonucleotide synthetase
#15	MTH1476	127	tryptophan synthase, beta subunit homolog 
#16	MTH1655	78	anthranilate synthase component I
#17	MTH1660	37	tryptophan synthase, subunit alpha 
#18	MTH1917	189	biotin carboxylase

Motif 1
CATCTATTTAATGTTAAGGATGGACGGTGTTCT	1	45	0
TTTATCCTCGGGGACAGCCATGGTGTCTGCGAT	4	121	1
GGCCACGACCGGGTCAGTGATGGACATTATATG	5	69	1
CAGAGTACCCAGGTCAGTGATGGACATTATATA	5	136	1
GGAATATTAGATGAGAGGAATGGGGATAAA   	8	11	1
GAGATAAATAAGGATAGTTCTGGATGGAGTGGA	10	28	1
GAGCCTTCAAAGGATAGTTCTGG          	10	77	1
       CCCATGATAGCTATGGTATAACCATG	13	3	1
GATAGTAGATAGGAGAGAGAAGGAGGTATCTTG	18	39	0
          **** **  ****
MAP Score: 14.0324

Motif 2
GAGTGTTTGATACTCAAGCTGATGCTATCCTGAATAATCATAT	0	76	0
TTATAAGGACCACTAACACGGGTAGCAGCCATACCAGAACATA	0	153	1
CCCTAACACGGGTCAGAACACCGTCCATCCTTAACATTAAATA	1	31	1
AATCTTGACCGGTTCAGGTAAAATTCATCCAGAATTCTCAATA	2	49	0
GAGGCCCCACCATACCCTCGCAGACTATCCAGAGTACCCAGGT	5	107	1
AAATATATATGATGCCATCAAATCTCATCCCTAG         	6	35	1
ATTTTAAAGTCATACAGGCCACTCATAGCCATACCAGCAGCCA	7	61	1
TGACACCGTCCACTCCATCCAGAACTATCCTTATTTATCTCGC	10	26	0
TCTTTTAGACCGGTTGAACACGCATCATCCCCAATAAACCCCC	12	21	1
AAACTAGGAAGGCCAAAGCCTCAGGTAACCTGATTTTCAGCAC	12	95	1
         GCAGCATCTCAGGGCTCATCCATATCCCCCAAGA	18	1	1
ACCCGGTTACCGTAAGTCCCCATGTCATCCACATGGCAGTTAC	18	79	1
          **  *   *      *****  *
MAP Score: 10.3924

Motif 3
TAGCCATACCAGCAGCCATAACTGTAA    	7	86	1
CACCGTCCACTCCATCCAGAACTATCCTTAT	10	35	0
AGGGACCAGTTCCAGCCATGAGGTGAT    	15	110	1
CAAGGACGAGTGCAACCAGAATGTAAATTAT	0	210	1
CCAGCAAACCAGCAACCATGAACACATCAGC	17	12	0
TTATATCCACTGCCTCCATAATATTTAATTA	0	237	1
GCTGATTGAATTCAACCCTAAAAA       	2	3	0
TCAGGTAAAATTCATCCAGAATTCTCAATAC	2	48	0
GGTGGGGCCTCCCACCCATATAATGTCCATC	5	87	0
TAACACGGGTAGCAGCCATACCAGAACATAG	0	166	1
CAGAACACCGTCCATCCTTAACATTAAATAG	1	44	1
ACCTGAAGGTACCCACCCTAACACGGGTCAG	1	16	1
CATCTCAGGGCTCATCCATATCCCCCAAGAT	18	14	1
GTTGAATTCAATCAGCCCTGTATTTTGAGGG	2	18	1
GGGTGGGAGGCCCCACCATACCCTCGCAGAC	5	101	1
GTAGCAGATGCGCAACCTGATTTAAACTCAT	0	38	0
          **** ******
MAP Score: 10.118

Motif 4
ACCAGAATGTAAATTATATCCACTGCCTCCATAATATT	0	224	1
CTGCCTCCATAATATTTAATTATTCGGTAAAATATAAA	0	246	1
ATTATTCGGTAAAATATAAATAGCTTTTCAGAATCAGA	0	264	1
CTTTGGTGGGATCTTATAAAAACTTAATCTTGACCGGT	2	79	0
AAGCTAAAAAAAGGTTTAAATATGACTTTAGAATAATA	4	217	1
CTTTAGAATAATAATATAATAAATTCATATCAAACCAC	4	242	1
TGGCCACCAAAATTTATAAGTATTTCATGGACAACCTT	5	36	0
GATCAATTAGATTCTTTATATACATAGTAGGAACTTCC	9	63	0
CATGATAGCTATGGTATAACCATGAATTATAACTTTAG	13	12	1
ACTTTAGAGAAAAATTTAAATATTGGGTTTTTATACTT	13	43	1
CCTATACATGATAGTATAACTATACGATAAAGTATAAA	13	72	0
ATGTACAGTAAAGTTTTAAATAGTTCTTTAAAGATATC	15	42	1
TTATACAGACAAGATTTAAATAGTACCTCCGTGTATAT	16	12	1
          **  ***** **     *
MAP Score: 10.0021

Motif 5
GAGAAGGAGGTATCTTGGGGGATATGGATGA	18	25	0
TATGCTTTGTTATCCTGAGGGCATTGTTATG	4	59	1
TATCCTTATTTATCTCGCGGGACAGATTAAT	10	13	0
CTGTATCTTTTATCCTCGGGGACAGCCATGG	4	113	1
TGAATAATCATATCTGGAGAGTAGCAGATGC	0	58	0
ATTGATTTATTATCTTGCAGGACATCTATTT	1	69	0
TGATGGACATTATATGGGTGGGAGGCCCCAC	5	86	1
TGATGGACATTATATAGGTGGGTATAG    	5	153	1
ATCAGCCCTGTATTTTGAGGGTATTGAGAAT	2	28	1
  GGGGAAGATATCCCCATGGACAGTTAAAG	5	8	1
TATATATGAAAATCTGGAAGGGGTACTG   	11	24	1
ACAAAGTACATATACACGGAGGTACTATTTA	16	28	0
ATCACCTCTGTATCCACAAAGTACATATACA	16	43	0
AATACTTATAAATTTTGGTGGCCACGACCGG	5	50	1
TTAGATTCTTTATATACATAGTAGGAACTTC	9	64	0
          ***** *****
MAP Score: 9.66164

Motif 6
ATGGCTGCTACCCGTGTTAGTGGTCCTTAT	0	155	0
GGTGTTCTGACCCGTGTTAGGGTGGGTACC	1	23	0
CTTAATCTTGACCGGTTCAGGTAAAATTCA	2	65	0
TCTTTTATCCTCGGGGACAGCCATGGTGTC	4	118	1
GGTGGCCACGACCGGGTCAGTGATGGACAT	5	66	1
ATCCAGAGTACCCAGGTCAGTGATGGACAT	5	133	1
TTATTTATCTCGCGGGACAGATTAATATT 	10	9	0
GATGGAGTGGACGGTGTCAGAATGCTTGAG	10	50	1
          CCCATGATAGCTATGGTATA	13	0	1
ACTTACGGTAACCGGGTTTGCATTGATAGT	18	66	0
ACCGTAAGTCCCCATGTCATCCACATGGCA	18	87	1
          **********
MAP Score: 9.47799

Motif 7
CATCCTTAACATTAAATAGATGTCCTGCAAGA	1	56	1
ACAACAGGTTATTACATGAATAATTAACACGA	4	166	0
ATTTATAAGTATTTCATGGACAACCTTTAACT	5	31	0
AGTGATGGACATTATATGGGTGGGAGGCCCCA	5	84	1
AGTGATGGACATTATATAGGTGGGTATAG   	5	151	1
CAGGACCGTTATTAAATGGGCAGAAATATATA	6	12	1
    GGGAATATTAGATGAGAGGAATGGGGAT	8	6	1
TAAAAGAAGGAATAAATGGGGGTTTATTGGGG	12	49	0
GAAAGTATATATTTTATAGGAAATATGTCATT	14	36	0
TTGCATTGATAGTAGATAGGAGAGAGAAGGAG	18	47	0
TGCCATGTGGATGACATGGGGACTTACGGTAA	18	85	0
          **** ***** *
MAP Score: 6.39606

Motif 8
TTGAGTATCAAACACTCCTTCCCCGCAGGAAGA	0	102	1
TAACACGGGTAGCAGCCATACCAGAACATAGAA	0	166	1
TTCATCCAGAATTCTCAATACCCTCAAAATACA	2	36	0
GGCATAATTGCATAACAATGCCCTCAGGATAAC	4	67	0
GGGTGGGAGGCCCCACCATACCCTCGCAGACTA	5	101	1
ACAGGCCACTCATAGCCATACCAGCAGCCATAA	7	74	1
    TTTATCCCCATTCCTCTCATCTAATATTC	8	12	0
         CAGTACCCCTTCCAGATTTTCATA	11	28	0
CCGGTTGAACACGCATCATCCCCAATAAACCCC	12	30	1
     TGTTTATTAACCATTCCCTTTGATGTAC	15	5	1
CTACTGATGAAATCATCATTTCCATGCAGTAAG	15	79	0
CATCTCAGGGCTCATCCATATCCCCCAAGATAC	18	14	1
GGTTACCGTAAGTCCCCATGTCATCCACATGGC	18	83	1
          * ** **** ***
MAP Score: 6.27108

Motif 9
TGAATTCAATCAGCCCTGTATTTTGAGGGTATT	2	20	1
CTAATTAATATATCACTGTATCTTTTTATGCTT	4	33	1
CCGGTGCCGACATCACTGTATCTTTTATCCTCG	4	98	1
GCCATGGTGTCTGCGATGCATTTAAATAGTCGT	4	137	1
ATTAATACATCTGCTGTGTATTTAAGGAAGTTC	9	38	1
AAGGAAGTTCCTACTATGTATATAAAGAATCTA	9	61	1
CCCCAATAAACCCCCATTTATTCCTTCTTTTAA	12	49	1
TTTATCTGGTCATCAATTTATTTAAGGTTCAGG	12	147	0
TTAAATAGTACCTCCGTGTATATGTACTTTGTG	16	27	1
ACATGCATATCACCTCTGTATCCACAAAGTACA	16	49	0
          *  * ********
MAP Score: 5.88882

Motif 10
CAAACACTCCTTCCCCGCAGGAAGATGTATAT	0	110	1
ATTAAATAGATGTCCTGCAAGATAATAAATCA	1	66	1
TTTTATAAGATCCCACCAAAGAGTAAACCAGT	2	96	1
ACACCATGGCTGTCCCCGAGGATAAAAGATAC	4	115	0
  GGGGAAGATATCCCCATGGACAGTTAAAGG	5	8	1
GGCCCCACCATACCCTCGCAGACTATCCAGAG	5	109	1
AATATTAATCTGTCCCGCGAGATAAATAAGGA	10	10	1
GGCTCATCCATATCCCCCAAGATACCTCCTTC	18	22	1
          * ****** ***
MAP Score: 5.01013

Motif 11
ATAAGGACCACTAACACGGGTAGCAGCCATA	0	155	1
GGTACCCACCCTAACACGGGTCAGAACACCG	1	23	1
AAAACTTAATCTTGACCGGTTCAGGTAAAAT	2	68	0
TTTTGGTGGCCACGACCGGGTCAGTGATGGA	5	62	1
ATGTCCATCACTGACCTGGGTACTCTGGATA	5	132	0
ATATGAAAATCTGGAAGGGGTACTG      	11	27	1
CTTAAATCTTTTAGACCGGTTGAACACGCAT	12	15	1
CACCTCATGGCTGGAACTGGTCCCTACTGAT	15	104	0
ACTATCAATGCAAACCCGGTTACCGTAAGTC	18	66	1
          ** ********
MAP Score: 4.44561