AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -ioxyR_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	PH1477	239	142aa long hypothetical protein

Motif number 1

     AATTATGGCATATCTTCATGGGATCAACTGG	1	6	1	TGGATACTGG	    0.995129	-234
TGGGATCAACTGGAAGAAAATAAGGGATACATTGAA	1	29	1	TGGAGAAGGG	    0.995919	-211
AAGGGATACATTGAAGATAGTTGGGGCTCCAACGAC	1	50	1	TTGAGAAGGG	    0.985199	-190
CTTACGAACTAGGTATAGATCCCGAGATTATAATAG	1	88	1	AGGATAAGAG	    0.987076	-152
CCTAATTGTATGGGCTATCGTTAGAGCTTCTATTAT	1	117	0	TGGCTACGAG	    0.991117	-123
TTACCCAGGATTGTATATCTCTCTGGCCTAATTGTA	1	143	0	TTGATACTGG	    0.982368	-97
TGGGTAAGGAAGGCATAACTAGAGAGGCCGCTGAAA	1	172	1	AGGATACGAG	    0.993701	-68
          *** *** *    ***

Masking position 7
Map Score:   8.30325

Number of sites scoring better than the average of aligned sites = 259
Number in coding regions = 245
Number in noncoding regions = 14
Number of orfs with sites within 600 bp upstream = 19
Fraction of orfs with sites within 600 bp upstream = 0.00305172


Motif number 2

TCTTCCAGTTGATCCCATGAAGATATGCCA	1	16	0	GATCCCATGA	     0.99475	-224
GAAAATAAGGGATACATTGAAGATAGTTGG	1	44	1	GATACATTGA	    0.930122	-196
GATAGTTGGGGCTCCAACGACAGCTTACGA	1	65	1	GCTCCAACGA	    0.996593	-175
ACTAGGTATAGATCCCGAGATTATAATAGA	1	95	1	GATCCCGAGA	    0.984361	-145
TATAATAGAAGCTCTAACGATAGCCCATAC	1	116	1	GCTCTAACGA	    0.982438	-124
          **********

Masking position 3
Map Score:   4.54467

Number of sites scoring better than the average of aligned sites = 225
Number in coding regions = 210
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 3

TCCAGTTGATCCCATGAAGATATGCCATAATT	1	11	0	CCCAGAAGTA	    0.988469	-229
AGGTATAGATCCCGAGATTATAATAGAAGCTC	1	98	1	CCCGGATTTA	    0.998252	-142
GCCTTCCTTACCCAGGATTGTATATCTCTCTG	1	154	0	CCCAGATTTA	    0.997293	-86
TCAAATTACACCCGTTATTTTAGCAGCCTTTT	1	205	0	CCCGTATTTA	    0.993091	-35
          **** **** **

Masking position 7
Map Score:   4.51898

Number of sites scoring better than the average of aligned sites = 18
Number in coding regions = 17
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 4

ACATTGAAGATAGTTGGGGCTCCAACGACA	1	57	1	TAGTTGGGGC	    0.970537	-183
TCTGGCCTAATTGTATGGGCTATCGTTAGA	1	128	0	TTGTATGGGC	    0.985576	-112
TTAGCAGCCTTTTCAGCGGCCTCTCTAGTT	1	188	0	TTTCAGCGGC	    0.984551	-52
ACACCCGTTATTTTAGCAGCCTTTTCAGCG	1	200	0	TTTTAGCAGC	    0.979683	-40
CGGGTGTAATTTGAAGGAGGTGTTATT   	1	223	1	TTGAAGGAGG	    0.946775	-17
          **********

Masking position 1
Map Score:   1.24733

Number of sites scoring better than the average of aligned sites = 364
Number in coding regions = 339
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 27
Fraction of orfs with sites within 600 bp upstream = 0.00433665


Motif number 5

CCATACAATTAGGCCAGAGAGATATACAAT	1	140	1	AGGCCAGAGA	    0.986592	-100
ATAACTAGAGAGGCCGCTGAAAAGGCTGCT	1	186	1	AGGCCGCTGA	    0.998465	-54
GCCGCTGAAAAGGCTGCTAAAATAACGGGT	1	198	1	AGGCTGCTAA	    0.988743	-42
          **********

Masking position 1
Map Score:   0.708773

Number of sites scoring better than the average of aligned sites = 53
Number in coding regions = 50
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 6

          **********

No masking
Map Score:   -2.7468e-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:   -2.7468e-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 8

          **********

No masking
Map Score:   -2.7468e-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