AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i058_Cystheine_Biosynthesis_pyro_reg_300.orf -o058_pyro_300.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

Input sequences:
#1	RPH00066	300	Pyrococcus_OT3

Motif number 1

TTTAGTAATTGAAAGTTATTAAATAACGAATTG	1	35	0	GAAATTATAA	    0.951726	-266
ATTCCCTCAGAAAAGTTATGGCATATTTAGTAA	1	60	0	AAAATTATCA	     0.97599	-241
TTTCTGAGGGAATATTTTTGGAATTCATCCGAA	1	80	1	AATATTTTAA	    0.950939	-221
AAAAATTTTCAATATATATGCAAATCAGAATAT	1	133	0	AATAATATAA	    0.931162	-168
ATATATATTGAAAATTTTTAGAAATCACACCTA	1	147	1	AAAATTTTAA	    0.977172	-154
TTACAAAGTTAAAATGTAAACAATAATTTAGGT	1	175	0	AAAAGTAAAA	    0.874684	-126
TTATCAAAGTAAAATTTTACAAAGTTAAAATGT	1	191	0	AAAATTTAAA	    0.922476	-110
TATCAGGAATAAAACTTATCAAAGTAAAATTTT	1	206	0	AAAATTATAA	    0.989533	-95
AATTCTAGATAATAATTATATCTATCAGGAATA	1	228	0	AATATTATCT	    0.836484	-73
ATTATGTCGAAAAAGATATAAATAGATTCGAGA	1	258	1	AAAAATATAT	    0.892522	-43
          **** ****  **

Masking position 7
Map Score:   10.9628

Number of sites scoring better than the average of aligned sites = 482
Number in coding regions = 336
Number in noncoding regions = 146
Number of orfs with sites within 600 bp upstream = 151
Fraction of orfs with sites within 600 bp upstream = 0.0242531


Motif number 2

CTATTTTGGCTTCTGTTTTCGGATGAATTC	1	100	0	TTCTGTTTTC	    0.952085	-201
TCAGAATATATGCTATTTTGGCTTCTGTTT	1	112	0	TGCTATTTTG	    0.966883	-189
ATAGCATATATTCTGATTTGCATATATATT	1	126	1	TTCTGATTTG	    0.975416	-175
TTGTTTACATTTTAACTTTGTAAAATTTTA	1	185	1	TTTAACTTTG	    0.931147	-116
CTTTGTAAAATTTTACTTTGATAAGTTTTA	1	200	1	TTTTACTTTG	    0.978019	-101
          **********

Masking position 7
Map Score:   1.36271

Number of sites scoring better than the average of aligned sites = 154
Number in coding regions = 140
Number in noncoding regions = 14
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 3

ATAAAGATAGATATGTTCCAATTCGTTATT	1	17	1	ATATGTTCCA	    0.970805	-284
TTCAATTACTAAATATGCCATAACTTTTCT	1	55	1	AAATATGCCA	    0.982691	-246
TGAATTCCAAAAATATTCCCTCAGAAAAGT	1	77	0	AAATATTCCC	    0.935341	-224
CTGTTTTCGGATGAATTCCAAAAATATTCC	1	88	0	ATGAATTCCA	    0.891177	-213
GCAAATCAGAATATATGCTATTTTGGCTTC	1	117	0	ATATATGCTA	    0.961549	-184
AATTTTCAATATATATGCAAATCAGAATAT	1	133	0	ATATATGCAA	    0.961548	-168
AAAGATATAAATAGATTCGAGAACCTTTGA	1	269	1	ATAGATTCGA	    0.918185	-32
          **********

Masking position 1
Map Score:   5.30759

Number of sites scoring better than the average of aligned sites = 265
Number in coding regions = 239
Number in noncoding regions = 26
Number of orfs with sites within 600 bp upstream = 28
Fraction of orfs with sites within 600 bp upstream = 0.00449727


Motif number 4

          **********

No masking
Map Score:   7.91135e-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 5

          **********

No masking
Map Score:   7.91135e-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:   7.91135e-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