AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00472_pyro_reg_100.orf -o00472_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	PH1830	100	334aa long hypothetical glyceraldehyde-3-phosphate dehydrogenase

Motif number 1

AGGTAAGGGCGGTGGGGGGAAG         	1	2	0	GGTGGGGGAA	    0.997257	-99
TCTTAACTATTTTGTCGGGATAATTTTTAAA	1	46	0	TTTGTGGGAT	    0.996238	-55
TTCTATCTTTTTTGGAGGTATCTCTTAACTA	1	68	0	TTTGGGGTAT	    0.996254	-33
AAAGATAGAATTCGGTGGGAAC         	1	89	1	TTCGGGGGAA	    0.994975	-12
          ***** *****

Masking position 10
Map Score:   5.79137

Number of sites scoring better than the average of aligned sites = 87
Number in coding regions = 74
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 2

CCGCCCTTACCTATCTTCCTGGGCTTTTAAAAA	1	21	1	CTATCTTGGG	    0.999508	-80
TATCTCTTAACTATTTTGTCGGGATAATTTTTA	1	48	0	CTATTTTGGG	    0.998709	-53
CCACCGAATTCTATCTTTTTTGGAGGTATCTCT	1	74	0	CTATCTTTGG	    0.998424	-27
          *******   ***

Masking position 3
Map Score:   3.91276

Number of sites scoring better than the average of aligned sites = 14
Number in coding regions = 11
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 3

AGATAGGTAAGGGCGGTGGGGGGAAG    	1	7	0	GGGCGGTGGG	    0.993996	-94
CTCTTAACTATTTTGTCGGGATAATTTTTA	1	48	0	TTTTGTCGGG	     0.98739	-53
ATTCTATCTTTTTTGGAGGTATCTCTTAAC	1	70	0	TTTTGGAGGT	    0.981422	-31
AAAAGATAGAATTCGGTGGGAAC       	1	88	1	ATTCGGTGGG	    0.996929	-13
          **********

Masking position 5
Map Score:   1.94829

Number of sites scoring better than the average of aligned sites = 169
Number in coding regions = 146
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 25
Fraction of orfs with sites within 600 bp upstream = 0.00401542


Motif number 4

          **********

No masking
Map Score:   -1.04149e-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:   -1.04149e-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:   -1.04149e-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