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

Motif number 1

AGTCTTAGCCCATAGGCTTTTGATTAAGGCCGAGCAC	1	76	0	CAATTTATTA	    0.982973	-110
CTAGGAATTTCACATCATCTGGAATCACGTAATCCCT	1	120	1	CAATCTAATA	     0.99413	-66
TGTTCAGTTACATAACCTTTTTAAGGAAGTATTAAGG	2	33	0	CAATTTAAGA	    0.988925	-153
GATAAAACTCCACAATTTCTTGAATTATTGTCGAATG	2	68	0	CAATCTAATA	     0.99413	-118
TGTGAGTTTTCAAAACGTCTAAAAGGATTGCCCAAAA	2	108	1	CAATCTAAGA	    0.992928	-78
CCCAAAAATGCACAAGGTTTAAATTTAAGTTAAGCAA	2	138	1	CAATTTATTA	    0.982972	-48
          ** *   ***  *** *

Masking position 8
Map Score:   7.37708

Number of sites scoring better than the average of aligned sites = 18
Number in coding regions = 13
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 2

GGGAGATCCTGGAGAGGGTTGAGGTGCCCA	1	12	0	GGAGAGGGTT	     0.95817	-174
AAAGCCTATGGGCTAAGACTGGAACCGCTA	1	93	1	GGCTAAGACT	    0.989454	-93
AGACTGGAACCGCTAGGAATTTCACATCAT	1	108	1	CGCTAGGAAT	    0.959504	-78
CTTTCCTTGAGGGTAGGGATTACGTGATTC	1	141	0	GGGTAGGGAT	    0.986356	-45
ACGCTTCAAAGGCTAAAGCTTTCCTTGAGG	1	159	0	GGCTAAAGCT	    0.981168	-27
ACCAAATTTTGGCGAGGGAT          	2	1	0	GGCGAGGGAT	    0.994196	-185
AACTCACAGAGGATAAAACTCCACAATTTC	2	86	0	GGATAAAACT	    0.896364	-100
          **********

Masking position 5
Map Score:   7.31746

Number of sites scoring better than the average of aligned sites = 496
Number in coding regions = 463
Number in noncoding regions = 33
Number of orfs with sites within 600 bp upstream = 35
Fraction of orfs with sites within 600 bp upstream = 0.00562159


Motif number 3

GAGATCGAGGGGATTAAGGGTGAAGACATA	1	46	0	GGATTAAGGG	    0.996419	-140
CATAGGCTTTTGATTAAGGCCGAGCACGAG	1	73	0	TGATTAAGGC	    0.986417	-113
TTGAGGGTAGGGATTACGTGATTCCAGATG	1	135	0	GGATTACGTG	    0.977538	-51
TTTTAAGGAAGTATTAAGGCAACCAAATTT	2	22	0	GTATTAAGGC	    0.983365	-164
          **********

Masking position 5
Map Score:   3.6544

Number of sites scoring better than the average of aligned sites = 65
Number in coding regions = 63
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 4

ATTCCAGATGATGTGAAATTCCTAGCGGTT	1	115	0	ATGTGAAATT	    0.888868	-71
ATTTCACATCATCTGGAATCACGTAATCCC	1	126	1	ATCTGGAATC	    0.935396	-60
TTATTGTCGAATGTTCAGTTACATAACCTT	2	51	0	ATGTTCAGTT	    0.911258	-135
ACTCCACAATTTCTTGAATTATTGTCGAAT	2	69	0	TTCTTGAATT	    0.852384	-117
ATTCAAGAAATTGTGGAGTTTTATCCTCTG	2	80	1	TTGTGGAGTT	     0.97192	-106
TTGTGCATTTTTGGGCAATCCTTTTAGACG	2	123	0	TTGGGCAATC	    0.946364	-63
AATTTAAACCTTGTGCATTTTTGGGCAATC	2	133	0	TTGTGCATTT	    0.944555	-53
AAATATTAGCATGGTGATTCTTA       	2	173	1	ATGGTGATTC	    0.829213	-13
          **********

Masking position 7
Map Score:   3.88045

Number of sites scoring better than the average of aligned sites = 380
Number in coding regions = 337
Number in noncoding regions = 43
Number of orfs with sites within 600 bp upstream = 47
Fraction of orfs with sites within 600 bp upstream = 0.00754899


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