AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -isoxS_pyro_opreg_300.orf -g0.419 -x5 
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 =  	0.419
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	PH0623	58	153aa long hypothetical protein
#2	PH0686	30	263aa long hypothetical ORFZ protein
#3	PH1905	90	281aa long hypothetical protein

Motif number 1

ATTAGCTTGAAAATGTTGACTATCGT        	1	3	0	AAAGTTTATC	    0.976735	-56
TCCAATTTATAAATATTAGCTTGAAAATGTTGAC	1	17	0	AAAATTTTGA	     0.86731	-42
    ACGATAAATAGTTTAATTTCCAATTTATAA	1	39	0	AATGTTTTTC	    0.989962	-20
   GGTTTTTAATCTTTCTCCTTCTTTTCTCCT 	2	8	1	AATTTTCTTC	    0.967222	-23
       CGAAAACTCTATTTTTCTTGGCTATTT	3	4	1	AAATCTTTTC	    0.961831	-87
CCTCTAAAGCAATTTTTAAATAGCCAAGAAAAAT	3	21	0	AATTTTTAGC	    0.971709	-70
AGGTTGCTCTAAAATTTAACGTTAATCCTCTAAA	3	47	0	AAATTTGTTA	    0.781089	-44
ACTTCCCTCGAATAGTTAGGTTGCTCTAAAATTT	3	64	0	AATGTTTTGC	    0.991245	-27
          *** ***   ****

Masking position 2
Map Score:   6.22228

Number of sites scoring better than the average of aligned sites = 442
Number in coding regions = 373
Number in noncoding regions = 69
Number of orfs with sites within 600 bp upstream = 92
Fraction of orfs with sites within 600 bp upstream = 0.0147767


Motif number 2

          ACGATAAATAGTTTAATTTC	1	49	0	ACGATAAATA	    0.946729	-10
GGAGAAAAGAAGGAGAAAGATTAAAAACC 	2	10	0	AGGAGAAAGA	    0.990927	-21
          AGGAGAAAAGAAGGAGAAAG	2	21	0	AGGAGAAAAG	    0.991303	-10
ATTGCTTTAGAGGATTAACGTTAAATTTTA	3	42	1	AGGATTAACG	    0.977387	-49
          **********

Masking position 4
Map Score:   1.49757

Number of sites scoring better than the average of aligned sites = 313
Number in coding regions = 296
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 3

          **********

No masking
Map Score:   -3.30951e-14

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 4

          **********

No masking
Map Score:   -3.30951e-14

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:   -3.30951e-14

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