AlignACE 3.0 10/20/99
AlignACE2 -i MJ/MJ_operons007_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944240201
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	MJ0081	300	methyl coenzyme M reductase II, subunit beta (mrtB)
#1	MJ0085	134	iron transport periplasmic binding protein, putative (ceuE)
#2	MJ0086	36	unspecified methyltransferase
#3	MJ0087	23	hemin permease (hemU)
#4	MJ0090	80	collagenase (prtC)
#5	MJ0091	95	Na+/Ca+ exchanger protein, putative
#6	MJ0118	231	methyl coenzyme M reductase II, operon protein D (mtrD)
#7	MJ0841_MJ0842	219	MJ0841: conserved hypothetical protein, MJ0842: methyl coenzyme M reductase I, subunit beta (mcrB)
#8	MJ0846	131	methyl coenzyme M reductase I, subunit alpha (mcrA)
#9	MJ0847	219	N5-methyl-tetrahydromethanopterin:coenzyme M methyltransferase, subunit E (mtrE)
#10	MJ0849	29	N5-methyl-tetrahydromethanopterin:coenzyme M methyltransferase, subunit C (mrtC)

Motif 1
AAATTTAAATTTTTAATTTTCTTAAAGTAATAT	6	162	1
AATATTATTATTTTAACATTTTTTAGTAATTTT	0	191	1
 TTTTTAATTTTTTATAATTTTTATTTTGGTGA	2	9	1
AATTTTATCATTTTAATATTATTATTTTAACAT	0	177	1
GATTTTTATTTTTTATTTTTCTAAGTTATATTT	8	83	0
ATTCTAAATTTTTTAATTTTTTATTATGTTGAT	9	10	1
ACTATCACATTTTTTGAATTATT          	3	0	0
        CTTTTTTCTATTTTTTATATAATTT	1	2	1
AAATTAAAAATTTAAATTTTATTATCTAAATTC	6	148	0
TTAATTTTTATTTAACTTTTTTTTAGTTATAGG	9	116	0
TTTATATAATTTTTATGAATATTGATGTATTTT	1	23	1
TTTGCTTAAGTTTAAATATTATTGCAGAATATA	5	34	1
TTTTAAAGATTTTAAAGATTTTTTTAATTTTAT	0	152	1
TTGATGTATTTTTAACGATTATTTTTGATAAAC	1	44	1
 TTAGAAATTTTTTTAAATTTTAAATTATATTT	4	58	0
AGAATTTAAGTTTTTGTATTTTACGTTTTAATA	9	54	0
GCTTTGCCCATTTAACCTTTATAACTTTCTCCC	8	17	1
AATTATTGGATTTTATGTTATTTTAATTTTAAA	7	122	0
ATTTTTGAGATTTATAATTTATTTTTGTAGTTT	8	54	0
AATTCAATCTTTTTATATTACTACATTATAATT	6	42	0
TGAACAAAAATTTTTAATATCTAATATATATTT	1	84	0
GTGAATTTGCTTTTTCATTATTTGAGTTTAAGA	6	76	1
ATTCTGTTCCTTTAAAATTAATTATAATGTAGT	6	23	1
TTTCGATAAATTTAATATTACTTTAAGAAAATT	6	176	0
TAAAGTTTGTTTTTGAATATATTCTGCAATAAT	5	51	0
AAAAACAAACTTTAATTAATTTAGTAGGGATAA	5	70	1
TGATGATACTTTTAGGCTTTCTTTATGATTCAA	0	64	1
ATATATCCAGTTTTTCATTTGAACAAAATCGTA	7	48	1
        TCTTTTTTATATAATGAGGTCATAT	4	2	1
CTGTGAGGAATTTTGATTTTTATTTTTTATTTT	8	97	0
ACACCAACCTTTTTGTTAATATATTACTACAGC	0	272	0
ACTTACGCATTTTTTTGAATCATAAAGAAAGCC	0	78	0
CTTTAAAATCTTTAAAAAAATTTTGAATTCCTC	0	136	0
TTTTAGTAATTTTTAGGATAAAATAGAAAATTT	0	211	1
ATCTGAAATTTTTTATTAAAAATAACAGTTATA	7	186	1
          *****  *** **
MAP Score: 43.9255