AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -imetR_pyro_opreg_300.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
#2	PH1654	185	427aa long hypothetical serine hydroxymethyltransferase

Motif number 1

AGATCCTGGAGAGGGTTGAGGTGCCCAT        	1	3	0	GAGGTAGTCC	    0.995475	-183
CGAGGGGATTAAGGGTGAAGACATAGTCAGGGAGAT	1	35	0	AAGGTAGCAG	       0.991	-151
TCTTAGCCCATAGGCTTTTGATTAAGGCCGAGCACG	1	75	0	TAGGTTGTAG	      0.8791	-111
GAAATTCCTAGCGGTTCCAGTCTTAGCCCATAGGCT	1	95	0	GCGGTAGCAG	     0.97608	-91
AGCTTTCCTTGAGGGTAGGGATTACGTGATTCCAGA	1	137	0	GAGGTGGTCG	    0.986377	-49
TTACGCTTCAAAGGCTAAAGCTTTCCTTGAGGGTAG	1	155	0	AAGGTAGTCC	    0.992844	-31
CTTTTTAAGGAAGTATTAAGGCAACCAAATTTTGGC	2	18	0	AAGTTAGCCC	    0.918166	-168
AAAACTCACAGAGGATAAAACTCCACAATTTCTTGA	2	82	0	GAGGTAATAC	    0.971092	-104
AAAAATGCACAAGGTTTAAATTTAAGTTAAGCAAAT	2	141	1	AAGGTAATAG	    0.963352	-45
          **** *  ** *  **

Masking position 6
Map Score:   8.59094

Number of sites scoring better than the average of aligned sites = 561
Number in coding regions = 529
Number in noncoding regions = 32
Number of orfs with sites within 600 bp upstream = 32
Fraction of orfs with sites within 600 bp upstream = 0.00513974


Motif number 2

CATAGTCAGGGAGATCCTGGAGAGGGTTGAGGT	1	17	0	GAGATTGGGA	    0.997497	-169
GGCCGAGCACGAGATCGAGGGGATTAAGGGTGA	1	53	0	GAGATAGGGA	    0.989933	-133
TACGTGATTCCAGATGATGTGAAATTCCTAGCG	1	118	0	CAGATTGTAA	    0.915896	-68
TTAAGGCAACCAAATTTTGGCGAGGGAT     	2	6	0	CAAATTGGGA	    0.992509	-180
ACAATTTCTTGAATTATTGTCGAATGTTCAGTT	2	61	0	GAATTTGTGA	    0.954813	-125
AATAATTCAAGAAATTGTGGAGTTTTATCCTCT	2	76	1	GAAATTGGGT	     0.98426	-110
          *****  *** **

Masking position 5
Map Score:   3.84173

Number of sites scoring better than the average of aligned sites = 292
Number in coding regions = 279
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 3

CCATAGGCTTTTGATTAAGGCCGAGCACGA	1	74	0	TTGATTAAGG	    0.871362	-112
GGCTAAAGCTTTCCTTGAGGGTAGGGATTA	1	149	0	TTCCTTGAGG	    0.967175	-37
          TTGCTTTACGCTTCAAAGGC	1	176	0	TTGCTTTACG	    0.973294	-10
CAAAATTTGGTTGCCTTAATACTTCCTTAA	2	20	1	TTGCCTTAAT	    0.868533	-166
GCCTTAATACTTCCTTAAAAAGGTTATGTA	2	32	1	TTCCTTAAAA	      0.8642	-154
AACTCCACAATTTCTTGAATTATTGTCGAA	2	70	0	TTTCTTGAAT	    0.864013	-116
ATGCTAATATTTGCTTAACTTAAATTTAAA	2	155	0	TTGCTTAACT	     0.97077	-31
          **********

Masking position 8
Map Score:   1.45078

Number of sites scoring better than the average of aligned sites = 464
Number in coding regions = 427
Number in noncoding regions = 37
Number of orfs with sites within 600 bp upstream = 50
Fraction of orfs with sites within 600 bp upstream = 0.00803084


Motif number 4

GGAACCGCTAGGAATTTCACATCATCTGGAA	1	113	1	GGAATTCACA	    0.981614	-73
AAAAGGTTATGTAACTGAACATTCGACAATA	2	49	1	GTAATGAACA	    0.914363	-137
CACAGAGGATAAAACTCCACAATTTCTTGAA	2	81	0	AAAATCCACA	     0.97139	-105
TAGACGTTTTGAAAACTCACAGAGGATAAAA	2	98	0	GAAACTCACA	    0.976191	-88
AGGATTGCCCAAAAATGCACAAGGTTTAAAT	2	131	1	AAAATGCACA	    0.984248	-55
          **** ******

Masking position 4
Map Score:   0.757883

Number of sites scoring better than the average of aligned sites = 61
Number in coding regions = 50
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 5

          **********

No masking
Map Score:   -1.25466e-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:   -1.25466e-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:   -1.25466e-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