AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i048_Polysaccharide_Biosynthesis_2_pyro_reg_300.orf -o048_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	RPH01490	246	Pyrococcus_OT3

Motif number 1

AATTTATCAAGTTATAAGGATTCTCACTTGG	1	35	1	GTTAAAGGAT	    0.985781	-212
TTTCAGATGCATTTTATGGCTATCTCCTTTT	1	102	1	ATTTATGGCT	    0.973783	-145
TTACCCTGAAATTAAAAGGAGATAGCCATAA	1	115	0	ATTAAAGGAG	    0.985782	-132
TAGCAAGCATATTACAAGGATTAAGCTGAAA	1	155	1	ATTAAAGGAT	    0.994752	-92
AAAATCTTCCAGTTTATGGATAGGACAAGAA	1	183	1	AGTTATGGAT	    0.973783	-64
CTAACGCTTAATTTTAAGGATTTCTTGTCCT	1	204	0	ATTTAAGGAT	    0.994714	-43
          **** ******

Masking position 6
Map Score:   9.82929

Number of sites scoring better than the average of aligned sites = 35
Number in coding regions = 31
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 2

ACTTGATAAATTACAGTTTAATTGTGGTAGA	1	16	0	TTACAGTTAA	    0.934753	-231
TTTCTCATCCTTTCAGATGCATTTTATGGCT	1	92	1	TTTCAGTGCA	    0.981792	-155
CTCCTTTTAATTTCAGGGTAAATAAGGAATT	1	125	1	TTTCAGGTAA	    0.984598	-122
ACTGGAAGATTTTCAGCTTAATCCTTGTAAT	1	165	0	TTTCAGTTAA	     0.99599	-82
GCTGAAAATCTTCCAGTTTATGGATAGGACA	1	179	1	TTCCAGTTAT	    0.977721	-68
          ****** ****

Masking position 5
Map Score:   5.89004

Number of sites scoring better than the average of aligned sites = 44
Number in coding regions = 36
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 3

GTTATCTACCACAATTAAACTGTAATTTAT	1	12	1	ACAATTAAAC	    0.955647	-235
AGAAATTTATATAAATTAACAAAGAAAGCG	1	67	0	ATAAATTAAC	    0.806773	-180
AGGGTAAATAAGGAATTAGCAAGCATATTA	1	139	1	AGGAATTAGC	    0.965706	-108
GCATATTACAAGGATTAAGCTGAAAATCTT	1	161	1	AGGATTAAGC	    0.989903	-86
AGAAATCCTTAAAATTAAGCGTTAGTCTAA	1	210	1	AAAATTAAGC	    0.975792	-37
CCCACCTGGCAAGATTAGACTAACGCTTAA	1	224	0	AAGATTAGAC	    0.936463	-23
          **********

Masking position 6
Map Score:   3.53371

Number of sites scoring better than the average of aligned sites = 184
Number in coding regions = 160
Number in noncoding regions = 24
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 4

GTTTAATTGTGGTAGATAACA         	1	2	0	GGTAGATAAC	    0.985722	-245
CTTATAACTTGATAAATTACAGTTTAATTG	1	23	0	GATAAATTAC	    0.954758	-224
TTAATTTCAGGGTAAATAAGGAATTAGCAA	1	131	1	GGTAAATAAG	    0.983289	-116
CTCCCACCTGGCAAGATTAGACTAACGCTT	1	226	0	GCAAGATTAG	    0.951781	-21
          **********

Masking position 6
Map Score:   0.440054

Number of sites scoring better than the average of aligned sites = 115
Number in coding regions = 100
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 5

          **********

No masking
Map Score:   2.79544e-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:   2.79544e-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:   2.79544e-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