AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i198_enolase_pyro_reg_100.orf -o198_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	RPH01790	122	Pyrococcus_OT3
#2	RPH01791	41	Pyrococcus_OT3

Motif number 1

CACCGGGCCTGGCGAGGAGGTGAAGGAG  	1	9	0	GGCGAGGAGG	    0.998445	-114
CTCCTCGCCAGGCCCGGTGGGTTCCCTTTC	1	20	1	GGCCCGGTGG	    0.997486	-103
CACTTAGCACGGCTCGGGGGTGTCCGAAAG	1	45	0	GGCTCGGGGG	    0.997486	-78
          **********

Masking position 6
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	     0.99279	-121
CTATCACCAAAGAAGATAGAATAAAAGCGA	2	19	0	AGAAGATAGA	    0.983625	-23
CTATCTTCTTTGGTGATAGACC        	2	30	1	TGGTGATAGA	    0.993922	-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

GGTGGGTTCCCTTTCGGACACCCCCGAGCCG	1	35	1	CTTTCGGACC	     0.97966	-88
TTTAAAGGTACTTTATAACCCATGATTGCAT	1	78	0	CTTTATAACC	    0.988693	-45
TATAAAGTACCTTTAAAAATCTTTACTTAAG	1	92	1	CTTTAAAAAC	    0.974872	-31
AAAATCTTTACTTAAGATTCCAAGTG     	1	107	1	CTTAAGATTC	    0.927194	-16
         TATTTAAATCGCTTTTATTCTA	2	2	1	ATTTAAATCC	    0.953752	-40
          ********* *

Masking position 3
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