AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i251_chemotaxis_pyro_reg_100.orf -o251_pyro_100.ace -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -g0.42 -x5 -e 
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 =  	0.42
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Purged sequences:
RPH00607	300	Pyrococcus_OT3

Input sequences:
#1	RPH00606	300	Pyrococcus_OT3
#2	RPH00604	17	Pyrococcus_OT3

Motif number 1

TTTTTACATATTTTAACGAAGGTCATAATTG	1	86	0	TTTTAAGAAG	    0.995738	-215
TCGTTAAAATATGTAAAAAAGTTTTCGTCTC	1	98	1	ATGTAAAAAG	    0.937916	-203
TCGTCTCTTCTTTTAATGAAGCCTAGTAGTT	1	122	1	TTTTAAGAAG	    0.993726	-179
AAAATATTTTTATTAAGGAAGGTTTATCATT	1	214	1	TATTAAGAAG	    0.986512	-87
AGGTTTATCATTGTATAGAAGCCGAAAATAT	1	233	1	TTGTATGAAG	    0.987476	-68
          ****** ****

Masking position 5
Map Score:   6.07522

Number of sites scoring better than the average of aligned sites = 49
Number in coding regions = 38
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 2

ATGAAGAGTTCATAAGTCTTCCTGGGTCATG	1	43	0	CATAAGCTTC	    0.933894	-258
GATGTAAAACTACTAGGCTTCATTAAAAGAA	1	129	0	TACTAGCTTC	    0.978446	-172
GCCTAGTAGTTTTACATCTCCATTTTTGAAG	1	142	1	TTTACACTCC	    0.912776	-159
TTTGTAGATTTTCTAAACTTCAAAAATGGAG	1	159	0	TTCTAACTTC	    0.966521	-142
TTAGAAAATCTACAAAGCTACCTACACAACT	1	174	1	TACAAACTAC	    0.969989	-127
CAAAGCTACCTACACAACTACGTGCATAAAA	1	186	1	TACACACTAC	    0.969401	-115
TCTATACAATGATAAACCTTCCTTAATAAAA	1	221	0	GATAAACTTC	    0.935119	-80
GATCATGATATTTTCGGCTTCTATACAATGA	1	240	0	TTTTCGCTTC	    0.945906	-61
          ****** ****

Masking position 9
Map Score:   5.80337

Number of sites scoring better than the average of aligned sites = 364
Number in coding regions = 330
Number in noncoding regions = 34
Number of orfs with sites within 600 bp upstream = 37
Fraction of orfs with sites within 600 bp upstream = 0.00594282


Motif number 3

ATGATAATAAGGTTATCCTAAAATAAAAAT	1	16	0	GGTTATCCTA	    0.919617	-285
AGTCTTCCTGGGTCATGATAATAAGGTTAT	1	30	0	GGTCATGATA	    0.985477	-271
AAAATGAAGAGTTCATAAGTCTTCCTGGGT	1	47	0	GTTCATAAGT	    0.906392	-254
TTTTAACGAAGGTCATAATTGGTAGTGAGC	1	77	0	GGTCATAATT	    0.982274	-224
ATTAAGGAAGGTTTATCATTGTATAGAAGC	1	225	1	GTTTATCATT	    0.932723	-76
TATCTAAGACGATCATGATATTTTCGGCTT	1	251	0	GATCATGATA	    0.902349	-50
          **********

Masking position 5
Map Score:   3.56197

Number of sites scoring better than the average of aligned sites = 157
Number in coding regions = 142
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 4

GACTTATGAACTCTTCATTTTGCTCACTAC	1	56	1	CTCTTCATTT	    0.993817	-245
AAGTTTTCGTCTCTTCTTTTAATGAAGCCT	1	116	1	CTCTTCTTTT	    0.989152	-185
GTAGTTTTACATCTCCATTTTTGAAGTTTA	1	147	1	ATCTCCATTT	    0.980195	-154
          **********

Masking position 4
Map Score:   1.90231

Number of sites scoring better than the average of aligned sites = 64
Number in coding regions = 56
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 5

          **********

No masking
Map Score:   -8.2833e-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:   -8.2833e-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 7

          **********

No masking
Map Score:   -8.2833e-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