AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i169_Reductases_bsub_reg_300.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

AATTCCATTTTGAAAGATAAGGGCTGCATG	1	127	1	TGAAAGATAA	     0.93466	-174
TCAATCCGGCGGAAAGAAAGACAGGAACAG	1	157	0	GGAAAGAAAG	    0.991553	-144
TCTTTCCGCCGGATTGAAAGTTTTTTATTT	1	170	1	GGATTGAAAG	    0.913809	-131
TTTTACCTCTTAAAATAAAAAACTTTCAAT	1	182	0	TAAAATAAAA	    0.777903	-119
TCGCGGCTGCTGATATACAGATAGCCTTTT	1	209	0	TGATATACAG	    0.848292	-92
CATTACATGGGAAAAGACAACCGGCAGAAA	1	243	1	GAAAAGACAA	    0.956493	-58
TCCGAAAGGAGGAAAGAAGAA         	1	290	1	GGAAAGAAGA	     0.96765	-11
          **********

Masking position 7
Map Score:   2.95392

Number of sites scoring better than the average of aligned sites = 2527
Number in coding regions = 2171
Number in noncoding regions = 356
Number of orfs with sites within 600 bp upstream = 359
Fraction of orfs with sites within 600 bp upstream = 0.0576614


Motif number 3

        TAGAATTGTGCTAAAATTTACT	1	3	1	GAATTGTGCT	    0.980894	-298
TGCATAGTTTGTAAGGTGCTACTTCCAGCA	1	92	1	GTAAGGTGCT	    0.995038	-209
CTTTTCCCATGTAATGTGATTCGCGGCTGC	1	229	0	GTAATGTGAT	    0.970279	-72
ACAACCGGCAGAAAGCTACTGTTTGTTTGT	1	259	1	GAAAGCTACT	    0.949589	-42
          **********

Masking position 7
Map Score:   1.10761

Number of sites scoring better than the average of aligned sites = 206
Number in coding regions = 186
Number in noncoding regions = 20
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 4

GGGCTGCATGCTGTTCCTGTCTTTCTTTCCGC	1	147	1	CTGTTCTTCT	    0.937793	-154
TCCTGTCTTTCTTTCCGCCGGATTGAAAGTTT	1	161	1	CTTTCCCGGA	    0.963646	-140
TACAGATAGCCTTTTTACCTCTTAAAATAAAA	1	192	0	CTTTTTCTCT	    0.975468	-109
TGCCGGTTGTCTTTTCCCATGTAATGTGATTC	1	237	0	CTTTTCCTGT	    0.993676	-64
CAAACAGTAGCTTTCTGCCGGTTGTCTTTTCC	1	252	0	CTTTCTCGGT	    0.984081	-49
CAGAAAGCTACTGTTTGTTTGTCTCCGAAAGG	1	267	1	CTGTTTTTGT	    0.933178	-34
     TTCTTCTTTCCTCCTTTCGGAGACAAA	1	284	0	CTTTCCCTTT	    0.973233	-17
          ****** * ***

Masking position 4
Map Score:   5.21665

Number of sites scoring better than the average of aligned sites = 830
Number in coding regions = 709
Number in noncoding regions = 121
Number of orfs with sites within 600 bp upstream = 122
Fraction of orfs with sites within 600 bp upstream = 0.0195952


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


Motif number 6

          **********

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 7

          **********

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