AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i198_enolase_pyro_reg_300.orf -o198_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	RPH01790	122	Pyrococcus_OT3
#2	RPH01791	41	Pyrococcus_OT3

Motif number 1

  CTCCTTCACCTCCTCGCCAGGCCCGGTG	1	9	1	CCTCCTCGCC	    0.998534	-114
GAAAGGGAACCCACCGGGCCTGGCGAGGAG	1	20	0	CCACCGGGCC	      0.9974	-103
CTTTCGGACACCCCCGAGCCGTGCTAAGTG	1	45	1	CCCCCGAGCC	      0.9974	-78
          **********

Masking position 5
Map Score:   5.43295

Number of sites scoring better than the average of aligned sites = 12
Number in coding regions = 12
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 2

CCTGGCGAGGAGGTGAAGGAG         	1	2	0	AGGTGAAGGA	    0.993225	-121
CTATCACCAAAGAAGATAGAATAAAAGCGA	2	19	0	AGAAGATAGA	    0.984606	-23
CTATCTTCTTTGGTGATAGACC        	2	30	1	TGGTGATAGA	    0.994289	-12
          **********

Masking position 6
Map Score:   0.979802

Number of sites scoring better than the average of aligned sites = 118
Number in coding regions = 109
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 3

CGGCTCGGGGGTGTCCGAAAGGGAACCCACC	1	35	0	GGTCCGAAAG	     0.97966	-88
ATGCAATCATGGGTTATAAAGTACCTTTAAA	1	78	1	GGTTATAAAG	    0.988693	-45
CTTAAGTAAAGATTTTTAAAGGTACTTTATA	1	92	0	GTTTTTAAAG	    0.974872	-31
     CACTTGGAATCTTAAGTAAAGATTTT	1	107	0	GAATCTTAAG	    0.927194	-16
TAGAATAAAAGCGATTTAAATA         	2	2	0	GGATTTAAAT	    0.953752	-40
          * *********

Masking position 9
Map Score:   0.154822

Number of sites scoring better than the average of aligned sites = 398
Number in coding regions = 368
Number in noncoding regions = 30
Number of orfs with sites within 600 bp upstream = 35
Fraction of orfs with sites within 600 bp upstream = 0.00562159


Motif number 4

          **********

No masking
Map Score:   5.92755e-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 5

          **********

No masking
Map Score:   5.92755e-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:   5.92755e-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