AlignACE 3.0 10/20/99
AlignACE2 -i TH/TH_operons015_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944244720
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	MTH384	249	unknown
#1	MTH387	24	conserved protein
#2	MTH388	35	unknown
#3	MTH393	41	NADH dehydrogenase (ubiquinone), subunit 1 related protein
#4	MTH394	55	unknown
#5	MTH746	96	endonuclease III related protein (probably non-iron-sulfur homolog)
#6	MTH1246	30	NADH dehydrogenase I, subunit N 
#7	MTH1251	147	conserved protein
#8	MTH1252	143	conserved protein
#9	MTH1253	135	unknown
#10	MTH1826	159	unknown (contains ferredoxin domain)

Motif 1
CTCTACAGAAGATTTAGTAATAAATTTTAAGGATT	0	98	0
GGACCCTTCAGATATCAGTAAAAAAAAGTTTCTGT	0	133	1
GAAACCTCCAGATATTAGTAAAAAAGGCCATAATT	0	171	1
ACCTAAAAAAGACCTCTTAATAAAATTATGGCCTT	0	194	0
     ATATAAATCTTTTTAAAAAAGGTGAGTTAG	0	229	0
   AAGACATGATGTGGAATGAAAATGGAAGGGAT	4	7	1
AAATGGAAGGGATTTAATCAGAAAAGAGGGGATTT	4	29	1
ATACCCCGATGATATATTAATTAAAAGTTACACAG	5	17	0
TAAAATAGGGGATCCGATGATTAAACACTTGAAGG	7	43	0
ATTTTATTACGATTTATATAGAAAACTTTATATTA	7	72	1
TATCTATAGTGCTGTAATAAAAACATGAGCGTATC	9	30	0
CCCCCCTGAAGATCCTCTCAGAACACTTCAAAGAA	10	74	0
TCCTGTAAAAGATATCCTCAGAACAGAATATATAA	10	124	0
          *** *  * * ****
MAP Score: 14.3237

Motif 2
ATCCTTAAAATTTATTACTAAATCTTCTGT	0	99	1
ACAGAAACTTTTTTTTACTGATATCTGAAG	0	138	0
AATTATGGCCTTTTTTACTAATATCTGGAG	0	176	0
AGGCCATAATTTTATTAAGAGGTCTTTTTT	0	195	1
CTAACTCACCTTTTTTAAAAAGATTTATAT	0	229	1
TCATTCAGGATTATTTACGGGG        	2	23	1
CGATGATATATTAATTAAAAGTTACACAGT	5	16	0
GACTCATGGGGTTATTACGGCAGCCTCTTC	7	12	1
GATCCCCTATTTTATTACGATTTATATAGA	7	64	1
CGCTCATGTTTTTATTACAGCACTATAGAT	9	34	1
ATTGACATAATTTTATACAGAGAAG     	10	5	0
TCTGAGGATATCTTTTACAGGAGGAATGTT	10	137	1
          **********
MAP Score: 8.92348

Motif 3
GTGACTCCATAGGAACCTCCAGGACATGATGGGG	0	17	0
CTTCTGTAGAGGGACCCTTCAGATATCAGTAAAA	0	122	1
GTTTCTGTAGAGAAACCTCCAGATATTAGTAAAA	0	160	1
  GAATATATAGATGATTACTGGTGA        	1	8	1
TTATGATAATAGAATCATTCCGGTGTTAATGGTG	3	12	1
GGATTTAATCAGAAAAGAGGGGATTTA       	4	38	1
ATATATCATCGGGGTATTGCTGGTTTACTGATTG	5	35	1
  TAAAATGAGGAATCTAACAGGTGAGGAATT  	6	8	1
 CTTATAAATGGAATCATTCTGATACGCTCATGT	9	9	1
GCCCACTTCCGGAAAAATCCGTATACCTGCGGCA	9	100	0
CTTCAGGGGGGGGGCAGTAGCGGTGATTATATAT	10	98	1
          **** * * * ***
MAP Score: 6.98262

Motif 4
CCCCATCATGTCCTGGAGGTTCCTATGGAG	0	17	1
ACTTACCGGTTTCTGTGAATATAATCACGA	0	55	1
TTACTAAATCTTCTGTAGAGGGACCCTTCA	0	113	1
TTTTACTGATATCTGAAGGGTCCCTCTACA	0	126	0
AAAAAAAAGTTTCTGTAGAGAAACCTCCAG	0	152	1
TTTTACTAATATCTGGAGGTTTCTCTACAG	0	164	0
GAGGTTAAATTTCTGGGATTCCAGGGTTTT	8	74	1
ATACGGATTTTTCCGGAAGTGGGCCAGCAA	9	110	1
CTTTGAAGTGTTCTGAGAGGATCTTCAGGG	10	76	1
TGAGAGGATCTTCAGGGGGGGGGCAGTAGC	10	89	1
ATATATTCTGTTCTGAGGATATCTTTTACA	10	126	1
          **********
MAP Score: 6.84047

Motif 5
CCACTTACCGGTTTCTGTGAATATAATCACGAAA	0	53	1
TATTACTAAATCTTCTGTAGAGGGACCCTTCAGA	0	111	1
GTAAAAAAAAGTTTCTGTAGAGAAACCTCCAGAT	0	150	1
ACACCGGAATGATTCTATTATCATAAAC      	3	4	0
AAATCCCCTCTTTTCTGATTAAATCCCTTCCATT	4	30	0
CTGCTTTTTATGTTCTGTGATCATGAGGATGGCG	5	71	1
TAATATAAAGTTTTCTATATAAATCGTAATAAAA	7	73	0
TTTGATGCTGTATTCTGACTTGAGGTTAATTGAT	8	101	1
         CTTCTCTGTATAAAATTATGTCAAT	10	1	1
TTCTTTGAAGTGTTCTGAGAGGATCTTCAGGGGG	10	74	1
GGTGATTATATATTCTGTTCTGAGGATATCTTTT	10	119	1
          * ******  * **
MAP Score: 5.8306

Motif 6
GAAACTTTTTTTTACTGATATCTGAAGGGT	0	135	0
AAATCCCCTCTTTTCTGATTAAATCCCTTC	4	34	0
       GGATTTACTGTGTAACTTTTAAT	5	3	1
GTATTGCTGGTTTACTGATTGTGCTGCTTT	5	48	1
CTGCTTTTTATGTTCTGTGATCATGAGGAT	5	71	1
  GGTTAAATTTCTCTGAGTCGCTGCAGCG	8	8	1
TTTGATGCTGTATTCTGACTTGAGGTTAAT	8	101	1
TAAATGGAATCATTCTGATACGCTCATGTT	9	14	1
CTGCCGCAGGTATACGGATTTTTCCGGAAG	9	99	1
GACATAATTTTATACAGAGAAG        	10	2	0
CTTTGCACTGTATACTGTCTCTCTTTCTTT	10	50	1
TTCTTTGAAGTGTTCTGAGAGGATCTTCAG	10	74	1
TTATATATTCTGTTCTGAGGATATCTTTTA	10	124	1
          **********
MAP Score: 5.46166

Motif 7
CGTTTTCGTGATTATATTCACAGAAACCGGTAAG	0	56	0
TTATTACTAAATCTTCTGTAGAGGGACCCTTCAG	0	110	1
AGTAAAAAAAAGTTTCTGTAGAGAAACCTCCAGA	0	149	1
AAAGGCCATAATTTTATTAAGAGGTCTTTTTTAG	0	193	1
TTGATGCTGTATTCTGACTTGAGGTTAATTGATG	8	102	1
CATTGACATAATTTTATACAGAGAAG        	10	2	0
CTTTCTTTGAAGTGTTCTGAGAGGATCTTCAGGG	10	72	1
GTGATTATATATTCTGTTCTGAGGATATCTTTTA	10	120	1
          *** * *  *****
MAP Score: 5.18288

Motif 8
ATCATGTCCTGGAGGTTCCTATGGAGTCACA	0	21	1
ACCGGTAAGTGGATGTGACTCCATAGGAACC	0	34	0
TAAATTTTAAGGATTTTCATAGTCGTTTTCG	0	82	0
ACTAATATCTGGAGGTTTCTCTACAGAAACT	0	159	0
AGAATCATTCCGGTGTTAATGGTGATGAG  	3	22	1
GAAAATGGAAGGGATTTAATCAGAAAAGAGG	4	27	1
TATATCATCGGGGTATTGCTGGTTTACTGAT	5	36	1
GTCGCTGCAGCGATGTTGCTCACCAGTAAGG	8	26	1
TGGGATTCCAGGGTTTTGATGCTGTATTCTG	8	87	1
TGATGCCTGCGGAGGTTTATAA         	8	131	1
GCAGGTATACGGATTTTTCCGGAAGTGGGCC	9	104	1
          ******* ***
MAP Score: 4.33001

Motif 9
TATTACTAAATCTTCTGTAGAGGGACCCTTCAGAT	0	111	1
GGAAGGGATTTAATCAGAAAAGAGGGGATTTA   	4	33	1
TTTGATGCTGTATTCTGACTTGAGGTTAATTGATG	8	101	1
GTATACGGATTTTTCCGGAAGTGGGCCAGCAATTC	9	108	1
TCTGAGAGGATCTTCAGGGGGGGGGCAGTAGCGGT	10	87	1
GGTGATTATATATTCTGTTCTGAGGATATCTTTTA	10	119	1
          ***** *    ****
MAP Score: 3.6704

Motif 10
ACTTACCGGTTTCTGTGAATATAATCACGAAAACGAC	0	55	1
TCACGAAAACGACTATGAAAATCCTTAAAATTTATTA	0	79	1
ATAGAATCATTCCGGTGTTAATGGTGATGAG      	3	20	1
     GGATTTACTGTGTAACTTTTAATTAATATATC	5	5	1
CTGGTTTACTGATTGTGCTGCTTTTTATGTTCTGTGA	5	54	1
GCTTTTTATGTTCTGTGATCATGAGGATGGCGG    	5	73	1
CTTTGAAGTGTTCTGAGAGGATCTTCAGGGGGGGGGC	10	76	1
ATATATTCTGTTCTGAGGATATCTTTTACAGGAGGAA	10	126	1
          * *****   **  * *
MAP Score: 1.75247