AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i227_rna_methyltransferase_pyro_reg_300.orf -o227_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	RPH00468	128	Pyrococcus_OT3

Motif number 1

 TCTTCATCACCAAAAAGAATTTACCTTCT	1	10	1	CCAAAAAGAA	    0.989644	-119
GCTTTAAATACCTAAAGAAGGTAAATTCTT	1	25	0	CCTAAAGAAG	    0.982155	-104
AAACCTCAAGCCAAAAGCAAGCTTTAAATA	1	45	0	CCAAAAGCAA	    0.996337	-84
TTCATAGTTGCCAAAACCGACATCCTAATA	1	73	1	CCAAAACCGA	    0.985204	-56
AAACCGACATCCTAATAAAATTCCTGGATG	1	86	1	CCTAATAAAA	    0.960138	-43
          **********

Masking position 5
Map Score:   5.42561

Number of sites scoring better than the average of aligned sites = 128
Number in coding regions = 105
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 26
Fraction of orfs with sites within 600 bp upstream = 0.00417604


Motif number 2

AATTCTTTTTGGTGATGAAGA         	1	2	0	GGTGATGAAG	    0.991304	-127
AATACCTAAAGAAGGTAAATTCTTTTTGGT	1	19	0	GAAGGTAAAT	    0.979464	-110
AAAATTCCTGGATGGAGATTAAGGAGGTGA	1	102	1	GATGGAGATT	    0.967401	-27
TGGAGATTAAGGAGGTGAAGGGTGA     	1	114	1	GGAGGTGAAG	    0.997799	-15
          **********

Masking position 8
Map Score:   2.77301

Number of sites scoring better than the average of aligned sites = 522
Number in coding regions = 458
Number in noncoding regions = 64
Number of orfs with sites within 600 bp upstream = 76
Fraction of orfs with sites within 600 bp upstream = 0.0122069


Motif number 3

CCTAAAGAAGGTAAATTCTTTTTGGTGATG	1	15	0	GTAAATTCTT	    0.933307	-114
AAAGCAAGCTTTAAATACCTAAAGAAGGTA	1	32	0	TTAAATACCT	    0.989583	-97
TTTTGGCAACTATGAAACCTCAAGCCAAAA	1	59	0	TATGAAACCT	    0.897225	-70
GACATCCTAATAAAATTCCTGGATGGAGAT	1	91	1	TAAAATTCCT	    0.989494	-38
          **********

Masking position 5
Map Score:   0.441311

Number of sites scoring better than the average of aligned sites = 356
Number in coding regions = 301
Number in noncoding regions = 55
Number of orfs with sites within 600 bp upstream = 72
Fraction of orfs with sites within 600 bp upstream = 0.0115644


Motif number 4

          **********

No masking
Map Score:   -1.89414e-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:   -1.89414e-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:   -1.89414e-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