AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -imetJ_pyro_opreg_100.orf -g0.419 -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 =  	0.419
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	PH0386	185	129aa long hypothetical protein

Motif number 1

AGATCCTGGAGAGGGTTGAGGTGCCCAT  	1	9	0	GAGGGTTGAG	    0.987382	-177
CGAGGGGATTAAGGGTGAAGACATAGTCAG	1	41	0	AAGGGTGAAG	    0.992342	-145
CCTTAATCAAAAGCCTATGGGCTAAGACTG	1	84	1	AAGCCTATGG	    0.962666	-102
AGCTTTCCTTGAGGGTAGGGATTACGTGAT	1	143	0	GAGGGTAGGG	    0.995337	-43
TTACGCTTCAAAGGCTAAAGCTTTCCTTGA	1	161	0	AAGGCTAAAG	    0.993393	-25
TTAGCCTTTGAAGCGTAAAGCAA       	1	173	1	AAGCGTAAAG	    0.993393	-13
          **********

Masking position 6
Map Score:   10.1841

Number of sites scoring better than the average of aligned sites = 427
Number in coding regions = 401
Number in noncoding regions = 26
Number of orfs with sites within 600 bp upstream = 25
Fraction of orfs with sites within 600 bp upstream = 0.00401542


Motif number 2

ATCCTGGAGAGGGTTGAGGTGCCCAT    	1	7	0	GGGTTGAGGT	    0.950645	-179
AGGATCTCCCTGACTATGTCTTCACCCTTA	1	32	1	TGACTATGTC	    0.901988	-154
GAGATCGAGGGGATTAAGGGTGAAGACATA	1	46	0	GGATTAAGGG	    0.992946	-140
CATAGGCTTTTGATTAAGGCCGAGCACGAG	1	73	0	TGATTAAGGC	    0.989148	-113
AAAAGCCTATGGGCTAAGACTGGAACCGCT	1	92	1	GGGCTAAGAC	    0.986904	-94
TTGAGGGTAGGGATTACGTGATTCCAGATG	1	135	0	GGATTACGTG	    0.945859	-51
TACGCTTCAAAGGCTAAAGCTTTCCTTGAG	1	160	0	AGGCTAAAGC	    0.907455	-26
          **********

Masking position 5
Map Score:   4.71046

Number of sites scoring better than the average of aligned sites = 730
Number in coding regions = 682
Number in noncoding regions = 48
Number of orfs with sites within 600 bp upstream = 51
Fraction of orfs with sites within 600 bp upstream = 0.00819146


Motif number 3

CACCTCAACCCTCTCCAGGATCTCCCTGACT	1	16	1	CTCCCAGGAT	    0.993717	-170
TTCACCCTTAATCCCCTCGATCTCGTGCTCG	1	52	1	ATCCCTCGAT	    0.932193	-134
TAAGACTGGAACCGCTAGGAATTTCACATCA	1	106	1	ACCCTAGGAA	    0.984685	-80
GGAATTTCACATCATCTGGAATCACGTAATC	1	123	1	ATCTCTGGAA	    0.969819	-63
GTAATCCCTACCCTCAAGGAAAGCTTTAGCC	1	148	1	CCCCAAGGAA	    0.986923	-38
          *** *******

Masking position 10
Map Score:   2.66092

Number of sites scoring better than the average of aligned sites = 567
Number in coding regions = 523
Number in noncoding regions = 44
Number of orfs with sites within 600 bp upstream = 41
Fraction of orfs with sites within 600 bp upstream = 0.00658529


Motif number 4

          **********

No masking
Map Score:   2.37484e-14

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:   2.37484e-14

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:   2.37484e-14

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