AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -irpoE_mthe_opreg_300.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

ATCCTCTCTTACTTTAATAATCATACCTTC	1	15	1	ACTTTAATAA	     0.95538	-167
CCCCGGGAAAACCTTTATATATAAGGACTT	1	71	1	ACCTTTATAT	    0.965401	-111
ATATATAAGGACTTTTAATAACTTAATTTA	1	87	1	ACTTTTAATA	    0.953099	-95
AACTTAATTTAACTAAAAATTCAGTAACCT	1	106	1	AACTAAAAAT	     0.76925	-76
AAATTCAGTAACCTGAAAAAAGTTCCAGAA	1	122	1	ACCTGAAAAA	    0.974266	-60
AAGTTCCAGAACATTTAAAATAAACTTAAA	1	141	1	ACATTTAAAA	    0.959171	-41
ATTTAAAATAAACTTAAAAACCAATTAAAA	1	153	1	AACTTAAAAA	    0.964958	-29
   TTTTCTAACTTTTAATTGGTTTTTAAG	1	165	0	ACTTTTAATT	    0.863075	-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

  TATTATCCTCTCTTACTTTAATAATCAT	1	9	1	TCTCTTACTT	    0.986934	-173
TCATACCTTCTTTCTTACCCTATTTAAACC	1	35	1	TTTCTTACCC	     0.93574	-147
ATAAGGACTTTTAATAACTTAATTTAACTA	1	91	1	TTAATAACTT	     0.92361	-91
AACTAAAAATTCAGTAACCTGAAAAAAGTT	1	116	1	TCAGTAACCT	    0.977268	-66
TTTTAAATGTTCTGGAACTTTTTTCAGGTT	1	131	0	TCTGGAACTT	    0.972511	-51
         TTTTCTAACTTTTAATTGGTT	1	171	0	TTTCTAACTT	    0.988966	-11
          **********

Masking position 7
Map Score:   5.46498

Number of sites scoring better than the average of aligned sites = 110
Number in coding regions = 92
Number in noncoding regions = 18
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 3

          **********

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 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