AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i329_not_clear4_pyro_reg_100.orf -o329_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	RPH00798	50	Pyrococcus_OT3
#2	RPH00797	116	Pyrococcus_OT3

Motif number 1

TTAACTTCCTTCATTGGATAATTTCTCCAG	1	22	1	TCATTGGATA	     0.99648	-29
    TTTTCATCACTGGAGAAATTATCCAA	1	35	0	TCACTGGAGA	    0.992396	-16
CTTAACAAATTCATTGGAACTGGGAGTGGG	2	20	0	TCATTGGAAC	    0.980666	-97
GTTAAGTTCCTTACGGGATAAAATATCCAT	2	44	1	TTACGGGATA	    0.971792	-73
AAATATTGTTTCATAGAATAGAATCCCAGG	2	87	1	TCATAGAATA	      0.9557	-30
          **********

Masking position 3
Map Score:   5.82137

Number of sites scoring better than the average of aligned sites = 141
Number in coding regions = 131
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 2

TATCCAATGAAGGAAGTTAAAAAGATAAGGG  	1	9	0	AGAATAAAAA	    0.980764	-42
TCATCACTGGAGAAATTATCCAATGAAGGAAGT	1	25	0	AGAATTCCAA	    0.996085	-26
TTATCCCGTAAGGAACTTAACAAATTCATTGGA	2	32	0	AGAATAACAA	    0.991368	-85
TCCTTACGGGATAAAATATCCATACTAGCAACT	2	51	1	ATAATTCCAT	    0.935807	-66
TATCCATACTAGCAACTCTTAAATATTGTTTCA	2	67	1	AGAATTTAAA	    0.976374	-50
          ** ** * *****

Masking position 7
Map Score:   2.24529

Number of sites scoring better than the average of aligned sites = 166
Number in coding regions = 143
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 31
Fraction of orfs with sites within 600 bp upstream = 0.00497912


Motif number 3

TCATTGGATAATTTCTCCAGTGATGAAAA 	1	32	1	ATTTCTCCAG	    0.987496	-19
AGTATGGATATTTTATCCCGTAAGGAACTT	2	47	0	TTTTATCCCG	    0.992866	-70
          TTTTCTCACCCCTGGGATTC	2	107	0	TTTTCTCACC	    0.986958	-10
          **********

Masking position 6
Map Score:   0.435699

Number of sites scoring better than the average of aligned sites = 96
Number in coding regions = 90
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 4

          **********

No masking
Map Score:   -2.10731e-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:   -2.10731e-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:   -2.10731e-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