AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -irhaS_aquae_opreg_300.orf -g0.435 -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 =  	0.435
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	ymxG	243	processing protease

Motif number 1

TTAAATTATAGCGAAAGGTAGAGACAGTTAT	1	84	0	GCAAAGGTAG	    0.989714	-160
CTAAGGAAACTCAAAAGGATAATAATCCTCA	1	118	0	TCAAAGGATA	    0.949468	-126
CGACCATAAAGGCACAGGATGATAGAATGAC	1	150	0	GGACAGGATG	    0.993149	-94
GTTATTACTTGGGAAAGGAAGGTTATAAAGT	1	205	1	GGAAAGGAAG	    0.997836	-39
AAGTTAAGGTGGAAAAGGAAAA         	1	232	1	GGAAAGGAAA	    0.995138	-12
          ** ********

Masking position 6
Map Score:   6.24681

Number of sites scoring better than the average of aligned sites = 464
Number in coding regions = 428
Number in noncoding regions = 36
Number of orfs with sites within 600 bp upstream = 34
Fraction of orfs with sites within 600 bp upstream = 0.00546097


Motif number 2

         CTTCAAACCTCCGTTTATCGTA	1	2	1	TTCAACCTCC	    0.985636	-242
AGCTTAATTATTTTAACATTAAAAATTACAA	1	41	1	TTTAACATTA	    0.975627	-203
AAATTACAAGTTTGCAAATTCATAACTGTCT	1	63	1	TTTCAAATTC	    0.878288	-181
TTCGCTATAATTTAAACATGAGGATTATTAT	1	100	1	TTTAACATGA	    0.947458	-144
CTTAGTGTCATTCTATCATCCTGTGCCTTTA	1	144	1	TTCATCATCC	    0.921856	-100
CACCTTAACTTTATAACCTTCCTTTCCCAAG	1	212	0	TTAAACCTTC	    0.968097	-32
   TTTTCCTTTTCCACCTTAACTTTATAAC	1	226	0	TTTCACCTTA	    0.970174	-18
          *** *******

Masking position 9
Map Score:   3.65803

Number of sites scoring better than the average of aligned sites = 621
Number in coding regions = 542
Number in noncoding regions = 79
Number of orfs with sites within 600 bp upstream = 98
Fraction of orfs with sites within 600 bp upstream = 0.0157404


Motif number 3

CCTTTATGGTCGGTGCGGCCGCTGGCGGAG	1	169	1	CGGTGCGGCC	    0.996503	-75
CGGCCGCTGGCGGAGCTGCCGGTTATTACT	1	184	1	CGGAGCTGCC	    0.954467	-60
          **********

Masking position 5
Map Score:   1.09117

Number of sites scoring better than the average of aligned sites = 2
Number in coding regions = 1
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 4

CTAAACTCTTTACGATAAACGGAGGTTTGA	1	13	0	TACGATAAAC	    0.965339	-231
TTAAAATAATTAAGCTAAACTCTTTACGAT	1	27	0	TAAGCTAAAC	    0.985989	-217
TTTAGCTTAATTATTTTAACATTAAAAATT	1	38	1	TTATTTTAAC	    0.894496	-206
CCTTTCGCTATAATTTAAACATGAGGATTA	1	97	1	TAATTTAAAC	    0.981859	-147
          **********

Masking position 6
Map Score:   0.446936

Number of sites scoring better than the average of aligned sites = 70
Number in coding regions = 55
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 19
Fraction of orfs with sites within 600 bp upstream = 0.00305172


Motif number 5

          **********

No masking
Map Score:   2.72438e-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:   2.72438e-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 7

          **********

No masking
Map Score:   2.72438e-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