AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00472_pyro_reg_300.orf -o00472_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	PH1830	100	334aa long hypothetical glyceraldehyde-3-phosphate dehydrogenase

Motif number 1

         CTTCCCCCCACCGCCCTTACCT	1	2	1	TTCCCCCACC	    0.997319	-99
TTTAAAAATTATCCCGACAAAATAGTTAAGA	1	46	1	ATCCCACAAA	    0.996322	-55
TAGTTAAGAGATACCTCCAAAAAAGATAGAA	1	68	1	ATACCCCAAA	    0.996338	-33
         GTTCCCACCGAATTCTATCTTT	1	89	0	TTCCCCCGAA	    0.994932	-12
          ***** *****

Masking position 2
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

TTTTTAAAAGCCCAGGAAGATAGGTAAGGGCGG	1	21	0	CCCAAGATAG	    0.999465	-80
TAAAAATTATCCCGACAAAATAGTTAAGAGATA	1	48	1	CCCAAAATAG	    0.998588	-53
AGAGATACCTCCAAAAAAGATAGAATTCGGTGG	1	74	1	CCAAAGATAG	    0.998328	-27
          ***   *******

Masking position 7
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

CCCCCCACCGCCCTTACCTATCTTCCTGGG	1	14	1	CCCTTACCTA	    0.984607	-87
TCTTCCTGGGCTTTTAAAAATTATCCCGAC	1	34	1	CTTTTAAAAA	    0.888444	-67
TTGGAGGTATCTCTTAACTATTTTGTCGGG	1	58	0	CTCTTAACTA	    0.994359	-43
TAAGAGATACCTCCAAAAAAGATAGAATTC	1	72	1	CTCCAAAAAA	     0.96532	-29
          **********

Masking position 6
Map Score:   2.00366

Number of sites scoring better than the average of aligned sites = 284
Number in coding regions = 251
Number in noncoding regions = 33
Number of orfs with sites within 600 bp upstream = 35
Fraction of orfs with sites within 600 bp upstream = 0.00562159


Motif number 4

AGATAGGTAAGGGCGGTGGGGGGAAG    	1	7	0	GGGCGGTGGG	     0.99767	-94
TCTCTTAACTATTTTGTCGGGATAATTTTT	1	49	0	ATTTTGTCGG	    0.981371	-52
AAAAGATAGAATTCGGTGGGAAC       	1	88	1	ATTCGGTGGG	    0.998616	-13
          **********

Masking position 7
Map Score:   1.26747

Number of sites scoring better than the average of aligned sites = 48
Number in coding regions = 43
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


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


Motif number 7

          **********

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