AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i169_Reductases_bsub_reg_100.orf -aORF_bsub.txt -zbsub.fna -g0.435 -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 =  	0.435
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	cysH	300	phosphoadenosine phosphosulfate

Motif number 1

ATAGGTCCAGTCCCTCAGCCGCTCTTGATAAG	1	46	0	TCCTCGCCGC	    0.989832	-255
TACAAACTATGCAGGTTGCCGGGCTTCATAGG	1	73	0	GCGGTGCCGG	    0.993293	-228
AAAATGGAATTCATTTTGCTGGAAGTAGCACC	1	106	0	TCTTTGCTGG	    0.975522	-195
GACAGGAACAGCATGCAGCCCTTATCTTTCAA	1	136	0	GCTGCGCCCT	    0.977612	-165
TTCCTGTCTTTCTTTCCGCCGGATTGAAAGTT	1	160	1	TCTTCGCCGG	     0.99869	-141
ACAAACAGTAGCTTTCTGCCGGTTGTCTTTTC	1	253	0	GCTTCGCCGG	    0.999166	-48
          ** *** *****

Masking position 8
Map Score:   7.15165

Number of sites scoring better than the average of aligned sites = 718
Number in coding regions = 692
Number in noncoding regions = 26
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 2

CAACCTGCATAGTTTGTAAGGTGCTACTTC	1	87	1	AGTTTGTAAG	    0.918291	-214
AATGAATTCCATTTTGAAAGATAAGGGCTG	1	123	1	ATTTTGAAAG	    0.874481	-178
TCAATCCGGCGGAAAGAAAGACAGGAACAG	1	157	0	GGAAAGAAAG	    0.960096	-144
TCTTTCCGCCGGATTGAAAGTTTTTTATTT	1	170	1	GGATTGAAAG	    0.978208	-131
TTATTTTAAGAGGTAAAAAGGCTATCTGTA	1	194	1	AGGTAAAAAG	    0.940561	-107
AAAAGACAACCGGCAGAAAGCTACTGTTTG	1	254	1	CGGCAGAAAG	    0.961178	-47
TGTCTCCGAAAGGAGGAAAGAAGAA     	1	286	1	AGGAGGAAAG	    0.974591	-15
          **********

Masking position 8
Map Score:   3.16249

Number of sites scoring better than the average of aligned sites = 1111
Number in coding regions = 904
Number in noncoding regions = 207
Number of orfs with sites within 600 bp upstream = 196
Fraction of orfs with sites within 600 bp upstream = 0.0314809


Motif number 3

          **********

No masking
Map Score:   7.91135e-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 4

          **********

No masking
Map Score:   7.91135e-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:   7.91135e-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