AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i340_weak11_pyro_reg_300.orf -o340_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	RPH01548	300	Pyrococcus_OT3

Motif number 1

TTTACAATGAATTAACGATGAGGGCTGAGAT	1	76	1	ATAACGATGA	    0.922093	-225
GAGGGCTGAGATCAGGAATGGGAGAGACCTA	1	95	1	ATAGGAATGG	    0.967588	-206
TGGGAGAGACCTAAGGAAGTAAGAGTGAAGG	1	113	1	CTAGGAAGTA	    0.828208	-188
GGAAGTAAGAGTGAAGGATTGAACCATTCTC	1	127	1	GTAAGGATTG	    0.981846	-174
AGGTGATTACATGGAGAATGGTTCAATCCTT	1	140	0	ATGAGAATGG	    0.815636	-161
ATGTAATCACCTAAAGGATTTAATAAAGGAG	1	159	1	CTAAGGATTT	    0.925207	-142
AAAGGATTTAATAAAGGAGAGTCAAAAATAC	1	171	1	ATAAGGAGAG	    0.910845	-130
GTCAAAAATACTTAGGAATGATGACCGGTTT	1	191	1	CTAGGAATGA	    0.952847	-110
GGTTTCGGGACTGAACGATGATGACACCAGC	1	217	1	CTAACGATGA	    0.949427	-84
TTTAGACAAGGTCAGCGATAGCTGGTGTCAT	1	237	0	GTAGCGATAG	    0.920983	-64
CCTTGCAGGTGTTAAGGATTGATAAAGATTT	1	265	0	GTAAGGATTG	    0.981846	-36
GCAAGGAGTGGTGAGGGAGGT          	1	290	1	GTAGGGAGGT	    0.949423	-11
          ** ********

Masking position 8
Map Score:   13.0849

Number of sites scoring better than the average of aligned sites = 1941
Number in coding regions = 1820
Number in noncoding regions = 121
Number of orfs with sites within 600 bp upstream = 127
Fraction of orfs with sites within 600 bp upstream = 0.0203983


Motif number 2

CTATAAACTTCTTCCCCTCTTTTCATTTTAC	1	50	1	CTTCCCTCTT	    0.944644	-251
CCATTCCTGATCTCAGCCCTCATCGTTAATT	1	85	0	TCTCACCCTC	    0.916832	-216
ACTCTTACTTCCTTAGGTCTCTCCCATTCCT	1	108	0	CCTTAGTCTC	    0.985057	-193
ATGGTTCAATCCTTCACTCTTACTTCCTTAG	1	123	0	CCTTCCTCTT	    0.989171	-178
GTGTCATCATCGTTCAGTCCCGAAACCGGTC	1	213	0	CGTTCGTCCC	    0.924714	-88
CTTTATCAATCCTTAACACCTGCAAGGAGTG	1	269	1	CCTTACACCT	     0.96464	-32
     ACCTCCCTCACCACTCCTTGCAGGTG	1	285	0	CCTCACACTC	    0.990207	-16
          ***** *****

Masking position 3
Map Score:   3.43117

Number of sites scoring better than the average of aligned sites = 1208
Number in coding regions = 1110
Number in noncoding regions = 98
Number of orfs with sites within 600 bp upstream = 93
Fraction of orfs with sites within 600 bp upstream = 0.0149374


Motif number 3

CTATATAGCCGATAAAACTAATGAGAAACC	1	14	1	GATAAAACTA	    0.975928	-287
TAAAACTAATGAGAAACCCAGTAACTATAA	1	26	1	GAGAAACCCA	    0.990692	-275
TCAGGAATGGGAGAGACCTAAGGAAGTAAG	1	106	1	GAGAGACCTA	    0.980558	-195
AAGAGTGAAGGATTGAACCATTCTCCATGT	1	133	1	GATTGAACCA	    0.975014	-168
ACTGAACGATGATGACACCAGCTATCGCTG	1	226	1	GATGACACCA	    0.960215	-75
          **********

Masking position 2
Map Score:   2.67449

Number of sites scoring better than the average of aligned sites = 124
Number in coding regions = 114
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


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