AlignACE 3.0 10/20/99
AlignACE2 -i TH/TH_operons021_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944245016
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	MTH661	119	ammonium transporter
#1	MTH662	61	nitrogen regulatory protein P-II
#2	MTH663	205	ammonium transporter
#3	MTH1228	117	conserved protein
#4	MTH1229	92	conserved protein
#5	MTH1230	40	unknown
#6	MTH1552	139	formate dehydrogenase, alpha subunit homolog
#7	MTH1553	71	tungsten formylmethanofuran dehydrogenase, subunit H
#8	MTH1560	107	nitrogenase NifH subunit
#9	MTH1570	74	glutamine synthetase
#10	MTH1571	300	molybdopterin biosynthesis protein MoeB homolog

Motif 1
TGGTAGATTTTCGGAAGTAGGTTACCGGCATCCTTA	0	47	1
TCTGCAATCACCAATATAAGGATGCCGGTAACCTAC	0	63	0
GATTTATATATCAGCATCATCTTACTCTCATTGTCG	2	110	1
ACTCTCATTGTCGGAAGTTACCTTCCTATTTCCGAC	2	133	1
TATCCAGACACCAGCAGCATCCCCCCGACACC    	3	6	0
      GCACCCAGGAGTTTCACTCCGGATCTCCAG	4	4	1
CCAGGTTCAGCCTCAAGTTCCCTTCCATCTATTCTA	6	112	0
CTTAACTTCACCGGAAGTAACTTTCCTTCTACTGGT	9	25	0
TCAGAATGGCTCCAGAGGACCGCCCCAGACATCTGC	10	122	1
TTTTCACTGATCTGAAGAATCTTTCCCACAGGATCT	10	158	1
AGGCTGTGGTCCTACAGGATGACCCCCTCATGATTT	10	226	1
          ** * ** * * * **
MAP Score: 19.4105

Motif 2
ATTTATATATCAGCATCATCTTACTCTCATT	2	111	1
CAGACACCAGCAGCATCCCCCCGACACC   	3	7	0
TAAGGTGTTTCAGGATAGGCTACCCGGGTCC	3	80	1
GATAGGCTACCCGGGTCCCCATTCAACAGTT	3	93	1
GAGTTTCACTCCGGATCTCCAGCCGGGGCCT	4	18	1
        TCCAGGTTCAGCCTCAAGTTCCC	6	126	0
ATCTTTCCCACAGGATCTCCAGTGATAGGCT	10	176	1
TATCTGCTTGCAGCATGAGCCTATCACTGGA	10	193	0
TGTGGTCCTACAGGATGACCCCCTCATGATT	10	230	1
          ******* ***
MAP Score: 9.40663

Motif 3
TTTTTATTCTCATGATATTTATAATGTTGGT	0	20	1
        ACACAGATTTAAACATGGTTCAC	1	2	1
TGGTTCACAGAAGTACTTATAAGAAATCCGG	1	25	1
AAATCCGGTTAAGGATATTTAAG        	1	48	1
GAAATTAAACAATTATTTTTATTTAACATAT	2	10	1
ACTATATCCGAAAGATTTATATATCAGCATC	2	97	1
TTTTCTCTCCAACAATTTATATCATAGTCGG	2	164	0
      ATGAAAAGATTTATAGTCACATCAG	5	25	0
TCAAATAGAAAAATATATATATAGGTGTGTG	7	11	0
CCATTTACCAAAAAATTTAAATAG       	8	93	1
       ACAAAAAATATATAAACCAGTAGA	9	3	1
ATGACCCCCTCATGATTTATATCAACACACA	10	244	1
          ** ********
MAP Score: 7.81783

Motif 4
GGATGCCGGTAACCTACTTCCGAAAATCTACC	0	48	0
GGATTTCTTATAAGTACTTCTGTGAACCATGT	1	22	0
ATTTTTATTTAACATATTTCAGTAATTGAGGT	2	24	1
TTACTCAGCATACATTTATCTGAAACTATATC	2	73	1
CATTTATCTGAAACTATATCCGAAAGATTTAT	2	85	1
GGAAGTTACCTTCCTATTTCCGACTATGATAT	2	145	1
CGGATCTTTTAAGGTGTTTCAGGATAGGCTAC	3	71	1
CTCTACTCATAACCTTTATCTGTGCATCATGA	6	25	1
AGTAGAAGGAAAGTTACTTCCGGTGAAGTTAA	9	28	1
AACGTGATTTTTGTTTTTTCAGAAGAATTCAT	10	36	0
TCCTGTGGGAAAGATTCTTCAGATCAGTGAAA	10	159	0
          *** ****** *
MAP Score: 7.65135

Motif 5
TCTCTACTTTTTTTATTCTCATGATATTTATA	0	11	1
ATTGCAGATATGTTAGGCACATCCAAAAGGAG	0	91	1
ATCAGCATCATCTTACTCTCATTGTCGGAAGT	2	119	1
CTGGATTCATTGATACTGTCATCTATGGAGGA	4	68	1
ATGAAAAGATTTATAGTCACATCAGGCATTTA	5	18	0
ATTTTTCCCATTTTCTTCTCATGAAAACTGTT	8	31	1
CTTCCGGTGAAGTTAAGCTCATGCCATGGAGG	9	44	1
GGATCTCCAGTGATAGGCTCATGCTGCAAGCA	10	188	1
          * *** ******
MAP Score: 6.7194

Motif 6
TATCATGAGAATAAAAAAAGTAGAGAG      	0	4	0
AAATCTACCAACATTATAAATATCATGAGAATA	0	24	0
GAAATATGTTAAATAAAAATAATTGTTTAATTT	2	11	0
ATTGTTGGAGAGAAAAAATATAATTAAGAACAA	2	179	1
          AGATAAATTAAATGCCTGATGTG	5	0	1
         ATGAAAAGATTTATAGTCACATCA	5	26	0
AGGACACTGAAGATAACATGAAGGGGACTGTTA	6	75	1
ATCAAATAGAAAAATATATATATAGGTGTGTGG	7	10	0
TGATTTTTGTAGAAAATTATTATATGGACGGCG	7	39	1
GTCCGATCCTAAATAAATTCTATTTTTCCCATT	8	10	1
ACCATTTACCAAAAAATTTAAATAG        	8	92	1
          ACAAAAAATATATAAACCAGTAG	9	0	1
TCCTTAAAACAGAAAAGATGAATTCTTCTGAAA	10	19	1
AATTCTTCTGAAAAAACAAAAATCACGTTTCTT	10	39	1
          * **** ** ***
MAP Score: 5.43938

Motif 7
    ATCACTCTCCTTTTGGATGTGCCTAACATA	0	99	0
ACACACCAGTATCCAGACACCAGCAGCATCCCCC	3	17	0
CTACCCGGGTCCCCATTCAACAGTTGAA      	3	99	1
GATAAAGTTTCACCATAAAAAGGACACTGAAGAT	6	55	1
CCATTTTCTTCTCATGAAAACTGTTCAGTTTTTG	8	38	1
AAAATATATAAACCAGTAGAAGGAAAGTTACTTC	9	14	1
  ACTTTTTTATCCTTAAAACAGAAAAGATGAAT	10	8	1
TTCAGAATGGCTCCAGAGGACCGCCCCAGACATC	10	121	1
CAGAGGACCGCCCCAGACATCTGCTTTTCACTGA	10	134	1
CCCACAGGATCTCCAGTGATAGGCTCATGCTGCA	10	182	1
GTAGGACCACAGCCTTATATCTGCTTGCAGCATG	10	207	0
          * ***** * * **
MAP Score: 4.55753

Motif 8
AGGATATGGCCAGGACCCGGATCTTTTAAGG	3	54	1
GATAGGCTACCCGGGTCCCCATTCAACAGTT	3	93	1
GAGTTTCACTCCGGATCTCCAGCCGGGGCCT	4	18	1
GATCTCCAGCCGGGGCCTCCGTGCATGAATT	4	31	1
GAACTTGAGGCTGAACCTGGA          	6	128	1
ATCTTTCCCACAGGATCTCCAGTGATAGGCT	10	176	1
          * *********
MAP Score: 2.3236

Motif 9
CTATATCCGAAAGATTTATATATCAGCATCATCTTACTCT	2	98	1
ACTGGTGTGTCTGAGGATATGGCCAGGACCCGGATCTTTT	3	41	1
AAGGTGTTTCAGGATAGGCTACCCGGGTCCCCATTCAACA	3	81	1
     GCACCCAGGAGTTTCACTCCGGATCTCCAGCCGGG	4	5	1
GCCTCCGTGCATGAATTCATCCACTGGATTCATTGATACT	4	45	1
CTCTCTACTCATAACCTTTATCTGTGCATCATGATAAAGT	6	23	1
AAGGACACTGAAGATAACATGAAGGGGACTGTTAAATTTA	6	74	1
TTTTCGATTTCAGAATGGCTCCAGAGGACCGCCCCAGACA	10	113	1
ACTGATCTGAAGAATCTTTCCCACAGGATCTCCAGTGATA	10	163	1
ATGCTGCAAGCAGATATAAGGCTGTGGTCCTACAGGATGA	10	208	1
GTGGTCCTACAGGATGACCCCCTCATGATTTATATCAACA	10	231	1
          * **       * * *****
MAP Score: 1.08049