AlignACE 3.0 10/20/99
AlignACE2 -i TH/TH_operons021_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944244998
 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	MTH1560	107	nitrogenase NifH subunit
#5	MTH1570	74	glutamine synthetase
#6	MTH1571	300	molybdopterin biosynthesis protein MoeB homolog

Motif 1
ACCAGTAGAAGGAAAGTTACTTCCGGTGAAGTTAA	5	25	1
AGATCCTGTGGGAAAGATTCTTCAGATCAGTGAAA	6	159	0
    GGTGTCGGGGGGATGCTGCTGGTGTCTGGAT	3	6	1
GTCGGAAATAGGAAGGTAACTTCCGACAATGAGAG	2	134	0
GATCTCCAGTGATAGGCTCATGCTGCAAGCAGATA	6	189	1
TAAGGATGCCGGTAACCTACTTCCGAAAATCTACC	0	48	0
TATAAATCATGAGGGGGTCATCCTGTAGGACCACA	6	230	0
CGACAATGAGAGTAAGATGATGCTGATATATAAAT	2	111	0
TTCCGGTGAAGTTAAGCTCATGCCATGGAGGCATA	5	45	1
TTGCAGATATGTTAGGCACATCCAAAAGGAGAGTG	0	92	1
          ** *** * ** * *
MAP Score: 10.9963

Motif 2
TTGCAGATATGTTAGGCACATCCAAAAGGAGAGTGAT  	0	92	1
TTCCGACAATGAGAGTAAGATGATGCTGATATATAAATC	2	110	0
       GGTGTCGGGGGGATGCTGCTGGTGTCTGGATA	3	3	1
TGTGTCTGAGGATATGGCCAGGACCCGGATCTTTTAAGG	3	46	1
TTCCGGTGAAGTTAAGCTCATGCCATGGAGGCATAACCC	5	45	1
TCGAAAAACAGTTCGGTTCAGGGAAGGGGTTTTATTATC	6	81	0
TCAGATCAGTGAAAAGCAGATGTCTGGGGCGGTCCTCTG	6	134	0
GATCTCCAGTGATAGGCTCATGCTGCAAGCAGATATAAG	6	189	1
TATAAATCATGAGGGGGTCATCCTGTAGGACCACAGCCT	6	226	0
CATAGTATTATGCAAGAACATGAAAGAGGGTTTGA    	6	275	1
          *  ***  ****     **
MAP Score: 7.10897

Motif 3
     CTCTCTACTTTTTTTATTCTCATGA	0	5	1
GAAATTAAACAATTATTTTTATTTAACATA	2	10	1
TTGTTCTTAATTATATTTTTTCTCTCCAAC	2	182	0
         ATATTGTTCTTAATTATATTT	2	194	0
CCTAAATAAATTCTATTTTTCCCATTTTCT	4	17	1
ATGAAAACTGTTCAGTTTTTGCTTTTTTGT	4	51	1
GTTTTTGCTTTTTTGTTCTTTATTTTAACC	4	65	1
      CTATTTAAATTTTTTGGTAAATGG	4	93	0
CTACTGGTTTATATATTTTTTGT       	5	3	0
AATTCATCTTTTCTGTTTTAAGGATAAAAA	6	13	0
GAAACGTGATTTTTGTTTTTTCAGAAGAAT	6	40	0
CCCTGAACCGAACTGTTTTTCGATTTCAGA	6	97	1
CGCCCCAGACATCTGCTTTTCACTGATCTG	6	142	1
          **********
MAP Score: 7.03027

Motif 4
TCTCTACTTTTTTTATTCTCATGATATTTATAA	0	11	1
ATTGCAGATATGTTAGGCACATCCAAAAGGAGA	0	91	1
TATCTAAACTTGTTTTACTCAGCATACATTTAT	2	59	1
ATCAGCATCATCTTACTCTCATTGTCGGAAGTT	2	119	1
ATTTTTCCCATTTTCTTCTCATGAAAACTGTTC	4	31	1
CTTCCGGTGAAGTTAAGCTCATGCCATGGAGGC	5	44	1
ATCGAAAAACAGTTCGGTTCAGGGAAGGGGTTT	6	88	0
ATCTGAAGAATCTTTCCCACAGGATCTCCAGTG	6	167	1
GGATCTCCAGTGATAGGCTCATGCTGCAAGCAG	6	188	1
TCCTACAGGATGACCCCCTCATGATTTATATCA	6	235	1
          ****   ******
MAP Score: 6.22542

Motif 5
TGCCGGTAACCTACTTCCGAAAATCTACCAA	0	46	0
GATGTGCCTAACATATCTGCAATCACCAATA	0	83	0
TTTATTTAACATATTTCAGTAATTGAGGTTA	2	27	1
CTCAGCATACATTTATCTGAAACTATATCCG	2	76	1
TTATCTGAAACTATATCCGAAAGATTTATAT	2	88	1
CGAAAGATTTATATATCAGCATCATCTTACT	2	105	1
ACCAGTATCCAGACACCAGCAGCATCCCCCC	3	16	0
ATATCCTCAGACACACCAGTATCCAGACACC	3	30	0
ATGAGCTTAACTTCACCGGAAGTAACTTTCC	5	35	0
GAAAAGATGAATTCTTCTGAAAAAACAAAAA	6	30	1
AACTGTTTTTCGATTTCAGAATGGCTCCAGA	6	107	1
GGACCGCCCCAGACATCTGCTTTTCACTGAT	6	138	1
TGTGGGAAAGATTCTTCAGATCAGTGAAAAG	6	157	0
          ******* ***
MAP Score: 6.13678

Motif 6
 CTCTCTACTTTTTTTATTCTCATGATATTTATAATG	0	9	1
CACTCTCCTTTTGGATGTGCCTAACATATCTGCAATC	0	90	0
AATTAAACAATTATTTTTATTTAACATATTTCAGTAA	2	12	1
ATTATCTAAACTTGTTTTACTCAGCATACATTTATCT	2	57	1
TCCGAAAGATTTATATATCAGCATCATCTTACTCTCA	2	103	1
CTTAATTATATTTTTTCTCTCCAACAATTTATATCAT	2	170	0
CTATTTTTCCCATTTTCTTCTCATGAAAACTGTTCAG	4	29	1
TGCTTTTTTGTTCTTTATTTTAACCATTTACCAAAAA	4	70	1
AGAATTCATCTTTTCTGTTTTAAGGATAAAAAAGT  	6	8	0
AACGTGATTTTTGTTTTTTCAGAAGAATTCATCTTTT	6	31	0
          ** * * * *  * ***
MAP Score: 4.77307

Motif 7
  CTCTCTACTTTTTTTATTCTCATGATATTT	0	8	1
TTATCTAAACTTGTTTTACTCAGCATACATTT	2	58	1
TTAATTATATTTTTTCTCTCCAACAATTTATA	2	174	0
TAAATAAATTCTATTTTTCCCATTTTCTTCTC	4	19	1
TCAGTTTTTGCTTTTTTGTTCTTTATTTTAAC	4	62	1
TTTTTGTTCTTTATTTTAACCATTTACCAAAA	4	74	1
         ACTTTTTTATCCTTAAAACAGAA	6	1	1
AAACGTGATTTTTGTTTTTTCAGAAGAATTCA	6	37	0
GGAAGGGGTTTTATTATCTCCAATTTAAAGAA	6	67	0
          ** **** ****
MAP Score: 4.39697

Motif 8
TTTCGGAAGTAGGTTACCGGCATCCTTATATTGGT	0	55	1
GATTGCAGATATGTTAGGCACATCCAAAAGGAGAG	0	90	1
CGGAAATAGGAAGGTAACTTCCGACAATGAGAGTA	2	132	0
GGTGTGTCTGAGGATATGGCCAGGACCCGGATCTT	3	44	1
ACTTCCGGTGAAGTTAAGCTCATGCCATGGAGGCA	5	43	1
AGGATCTCCAGTGATAGGCTCATGCTGCAAGCAGA	6	187	1
AGCAGATATAAGGCTGTGGTCCTACAGGATGACCC	6	216	1
GTGGTCCTACAGGATGACCCCCTCATGATTTATAT	6	231	1
          * * ** ** *** *
MAP Score: 2.66432

Motif 9
ATTGCAGATATGTTAGGCACATCCAAAAGGAGAGTGAT  	0	91	1
        GGTGTCGGGGGGATGCTGCTGGTGTCTGGATA	3	2	1
ATGCTGCTGGTGTCTGGATACTGGTGTGTCTGAGGATATG	3	22	1
 TTCAACTGTTGAATGGGGACCCGGGTAGCCTATCCTGAA	3	88	0
ATCGAAAAACAGTTCGGTTCAGGGAAGGGGTTTTATTATC	6	81	0
TTTCGATTTCAGAATGGCTCCAGAGGACCGCCCCAGACAT	6	114	1
GGATCTCCAGTGATAGGCTCATGCTGCAAGCAGATATAAG	6	188	1
ATATAAATCATGAGGGGGTCATCCTGTAGGACCACAGCCT	6	226	0
          ***  **   * ** *   *
MAP Score: 1.76615

Motif 10
ACATTATAAATATCATGAGAATAAAAAAAGTAGAGA	0	11	0
GGATGCCGGTAACCTACTTCCGAAAATCTACCAACA	0	44	0
TGGTTCACAGAAGTACTTATAAGAAATCCGGTTAAG	1	25	1
CAATTACTGAAATATGTTAAATAAAAATAATTGTTT	2	16	0
TTTACTCAGCATACATTTATCTGAAACTATATCCGA	2	72	1
CCAACAATTTATATCATAGTCGGAAATAGGAAGGTA	2	151	0
ACTGAACAGTTTTCATGAGAAGAAAATGGGAAAAAT	4	31	0
TAAAATAAAGAACAAAAAAGCAAAAACTGAACAGTT	4	56	0
TCTTTATTTTAACCATTTACCAAAAAATTTAAATAG	4	81	1
AAAATATATAAACCAGTAGAAGGAAAGTTACTTCCG	5	14	1
  ACTTTTTTATCCTTAAAACAGAAAAGATGAATTC	6	8	1
CTCTGGAGCCATTCTGAAATCGAAAAACAGTTCGGT	6	103	0
TGATAGGCTCATGCTGCAAGCAGATATAAGGCTGTG	6	198	1
ACATAGTATTATGCAAGAACATGAAAGAGGGTTTGA	6	274	1
          ** *   ** * ****
MAP Score: 1.54864