AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -irpoE_mthe_opreg_100.orf -g0.495 -x5 
Parameter values:
 expect =  	5
 ncols =   	10
 npass =   	1000
 maxnpass =	100
 nruns =   	1000
 maxnruns =	100
 repeat =  	15
 maxreps = 	3
 nread =   	500
 ncycles = 	1
 fragment =	1
 psfact =  	0.1
 gcback =  	0.495
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	MTH1813	181	serine protease HtrA

Motif number 1

GAAGGTATGATTATTAAAGTAAGAGAGGAT	1	15	0	TTATTAAAGT	    0.956357	-167
AAGTCCTTATATATAAAGGTTTTCCCGGGG	1	71	0	ATATAAAGGT	    0.966185	-111
TAAATTAAGTTATTAAAAGTCCTTATATAT	1	87	0	TATTAAAAGT	    0.954018	-95
AGGTTACTGAATTTTTAGTTAAATTAAGTT	1	106	0	ATTTTTAGTT	    0.772845	-76
TTCTGGAACTTTTTTCAGGTTACTGAATTT	1	122	0	TTTTTCAGGT	    0.974862	-60
TTTAAGTTTATTTTAAATGTTCTGGAACTT	1	141	0	TTTTAAATGT	    0.960095	-41
TTTTAATTGGTTTTTAAGTTTATTTTAAAT	1	153	0	TTTTTAAGTT	    0.965727	-29
CTTAAAAACCAATTAAAAGTTAGAAAA   	1	165	1	AATTAAAAGT	    0.863064	-17
          **********

Masking position 7
Map Score:   8.66918

Number of sites scoring better than the average of aligned sites = 401
Number in coding regions = 275
Number in noncoding regions = 126
Number of orfs with sites within 600 bp upstream = 112
Fraction of orfs with sites within 600 bp upstream = 0.0179891


Motif number 2

TGATTATTAAAGTAAGAGAGGATAATA   	1	8	0	AGTAAGAGAG	    0.979315	-174
GTTTAAATAGGGTAAGAAAGAAGGTATGAT	1	34	0	GGTAAGAAAG	    0.961459	-148
AGTTAAATTAAGTTATTAAAAGTCCTTATA	1	90	0	AGTTATTAAA	    0.901332	-92
ACTTTTTTCAGGTTACTGAATTTTTAGTTA	1	115	0	GGTTACTGAA	    0.970154	-67
ACCTGAAAAAAGTTCCAGAACATTTAAAAT	1	132	1	AGTTCCAGAA	    0.963961	-50
ACCAATTAAAAGTTAGAAAA          	1	172	1	AGTTAGAAAA	     0.98541	-10
          **********

Masking position 3
Map Score:   4.66754

Number of sites scoring better than the average of aligned sites = 91
Number in coding regions = 67
Number in noncoding regions = 24
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


Motif number 3

ATTATCCTCTCTTACTTTAATAATCATACC	1	12	1	CTTACTTTAA	    0.984349	-170
TCTTTCTTACCCTATTTAAACCCACCACCC	1	43	1	CCTATTTAAA	    0.966248	-139
ATTAAAAGTCCTTATATATAAAGGTTTTCC	1	76	0	CTTATATATA	    0.867396	-106
CTTTTAATAACTTAATTTAACTAAAAATTC	1	98	1	CTTAATTTAA	    0.959062	-84
GGTTTTTAAGTTTATTTTAAATGTTCTGGA	1	145	0	TTTATTTTAA	    0.870862	-37
          **********

Masking position 4
Map Score:   3.97585

Number of sites scoring better than the average of aligned sites = 47
Number in coding regions = 22
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 4

          **********

No masking
Map Score:   -1.60993e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 5

          **********

No masking
Map Score:   -1.60993e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 6

          **********

No masking
Map Score:   -1.60993e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0