AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i344_weak5_pyro_reg_100.orf -o344_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

Input sequences:
#1	RPH00650	110	Pyrococcus_OT3
#2	RPH00649	27	Pyrococcus_OT3
#3	RPH01152	38	Pyrococcus_OT3
#4	RPH01153	136	Pyrococcus_OT3

Motif number 1

ATGGAAATCCGGAATTTATCTAAGTTAAGCA	1	16	1	GGAATTATCT	    0.944174	-95
GCTTAATGAAGGTATCAATCCTAACACCTAA	1	59	1	GGTATAATCC	    0.979448	-52
    GTTATCTTTATTATTCTTTTTTTTAAT	3	7	1	TTTATATTCT	     0.78223	-32
TTAAAACCTAGGTATTAACTTTTACCGATGG	4	18	0	GGTATAACTT	     0.90209	-119
AGGTTTTAAAGGTATGGATCTAATATCGTTG	4	40	1	GGTATGATCT	    0.985696	-97
CGTTGAACGTTGTATCAATGTTCGTTAATCA	4	69	0	TGTATAATGT	    0.973673	-68
CAACGAGAAGTTTATAAATCCTTAGGGGAAT	4	95	1	TTTATAATCC	    0.919006	-42
AATCCTTAGGGGAATAAATGTATAAGGTGAC	4	111	1	GGAATAATGT	    0.971601	-26
          ***** *****

Masking position 4
Map Score:   5.80061

Number of sites scoring better than the average of aligned sites = 266
Number in coding regions = 238
Number in noncoding regions = 28
Number of orfs with sites within 600 bp upstream = 31
Fraction of orfs with sites within 600 bp upstream = 0.00497912


Motif number 2

CGTATTTCTGCTTAACTTAGATAAATTCCG	1	25	0	CTTAACTTAG	    0.960417	-86
GGATTGATACCTTCATTAAGCTCACCGTAT	1	50	0	CTTCATTAAG	    0.591887	-61
CCTAATTTTTCTTCAAATTGCCTTGGGAGA	1	85	1	CTTCAAATTG	    0.960359	-26
CCCCCTTGCTCTTCACTTTG          	2	1	0	CTTCACTTTG	    0.995583	-27
GATTTATAAACTTCTCGTTGAACGTTGTAT	4	85	0	CTTCTCGTTG	    0.975823	-52
          **********

Masking position 3
Map Score:   3.48062

Number of sites scoring better than the average of aligned sites = 184
Number in coding regions = 168
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


Motif number 3

GCAGAAATACGGTGAGCTTAATGAAGGTAT	1	44	1	GGTGAGCTTA	    0.994743	-67
AATTGCCTTGGGAGAGCATAC         	1	100	1	GGAGAGCATA	    0.994743	-11
AAATGTATAAGGTGACAATAC         	4	126	1	GGTGACAATA	    0.985307	-11
          **********

Masking position 5
Map Score:   1.37563

Number of sites scoring better than the average of aligned sites = 26
Number in coding regions = 24
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 4

AGTTAAGCAGAAATACGGTGAGCTTAATGA	1	38	1	AAATACGGTG	    0.991086	-73
ATTTGAAGAAAAATTAGGTGTTAGGATTGA	1	73	0	AAATTAGGTG	    0.986828	-38
GGGAATAAATGTATAAGGTGACAATAC   	4	120	1	GTATAAGGTG	    0.984389	-17
          **********

Masking position 3
Map Score:   0.588679

Number of sites scoring better than the average of aligned sites = 13
Number in coding regions = 11
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 5

TGAAGAAAAATTAGGTGTTAGGATTGATAC	1	70	0	TTAGGTGTTA	    0.982966	-41
AAGTGAAGAGCAAGGGGGTAGTAGG     	2	13	1	CAAGGGGGTA	    0.968545	-15
AAGTTAATACCTAGGTTTTAAAGGTATGGA	4	28	1	CTAGGTTTTA	    0.965179	-109
TTTATTCCCCTAAGGATTTATAAACTTCTC	4	99	0	TAAGGATTTA	    0.935164	-38
AATAAATGTATAAGGTGACAATAC      	4	123	1	TAAGGTGACA	    0.936629	-14
          **********

Masking position 3
Map Score:   0.737956

Number of sites scoring better than the average of aligned sites = 218
Number in coding regions = 197
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


Motif number 6

          **********

No masking
Map Score:   -2.53363e-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:   -2.53363e-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:   -2.53363e-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