AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i023_Formate_Dehydrogenase_hinf_reg_300.orf -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -g0.38 -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 =  	0.38
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	HI0007	300	formate dehydrogenase, beta subunit (fdxH)

Motif number 1

TCGCCTTTTTGGATGCCTTTTTCTGCCGCT	1	21	0	GGATGCCTTT	    0.964724	-280
CGGTCGCCGTGGTTACAAAACGTCTTAAAG	1	89	1	GGTTACAAAA	    0.832867	-212
CAGTGAATTGGAAGACCTATATGGTGTACG	1	141	0	GAAGACCTAT	    0.951982	-160
ACTGGAATATGAAGGCATTAAATGGCAAAG	1	167	1	GAAGGCATTA	    0.909858	-134
GAGAATCCACGGTTACCTTTGCCATTTAAT	1	183	0	GGTTACCTTT	    0.941968	-118
GATTCTCTACGAATACCTTAACACCATCTT	1	206	1	GAATACCTTA	    0.978159	-95
GTGTTTGCGTGATTGCCTCACCCCAAGATG	1	230	0	GATTGCCTCA	     0.92378	-71
GCAAACACCAGAATACAAAACATTCTTGGT	1	252	1	GAATACAAAA	    0.880636	-49
AAAAAGTTGGGGAGGCATAAT         	1	290	1	GGAGGCATAA	    0.968103	-11
          **********

Masking position 6
Map Score:   9.06774

Number of sites scoring better than the average of aligned sites = 289
Number in coding regions = 247
Number in noncoding regions = 42
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 2

AAAATTACTTCTCGTCGTGGCTATATTAAA	1	58	1	CTCGTCGTGG	    0.984389	-243
TATTAAAGCGGTCGCCGTGGTTACAAAACG	1	81	1	GTCGCCGTGG	     0.99697	-220
AATGGCAAAGGTAACCGTGGATTCTCTACG	1	187	1	GTAACCGTGG	    0.958535	-114
TTAACACCATCTTGGGGTGAGGCAATCACG	1	223	1	CTTGGGGTGA	    0.976182	-78
GTATTCTGGTGTTTGCGTGATTGCCTCACC	1	238	0	GTTTGCGTGA	    0.966389	-63
TATTGAAAAAGTTGGGGAGGCATAAT    	1	285	1	GTTGGGGAGG	    0.982831	-16
          **********

Masking position 2
Map Score:   4.83689

Number of sites scoring better than the average of aligned sites = 254
Number in coding regions = 237
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 3

          GCGAAAAATTAGCGGCAGAA	1	1	1	GCGAAAAATT	     0.98055	-300
AAGGCGATATGGTAAAAATTACTTCTCGTC	1	44	1	GGTAAAAATT	     0.99102	-257
AAACATTCTTGGTAAATATTGAAAAAGTTG	1	269	1	GGTAAATATT	    0.984252	-32
          **********

Masking position 5
Map Score:   1.15638

Number of sites scoring better than the average of aligned sites = 113
Number in coding regions = 73
Number in noncoding regions = 40
Number of orfs with sites within 600 bp upstream = 30
Fraction of orfs with sites within 600 bp upstream = 0.0048185


Motif number 4

GCTTTAATATAGCCACGACGAGAAGTAATT	1	60	0	AGCCACGACG	    0.988629	-241
GACGTTTTGTAACCACGGCGACCGCTTTAA	1	83	0	AACCACGGCG	    0.957042	-218
TTCGTAGAGAATCCACGGTTACCTTTGCCA	1	189	0	ATCCACGGTT	    0.918388	-112
          **********

Masking position 5
Map Score:   0.98272

Number of sites scoring better than the average of aligned sites = 13
Number in coding regions = 11
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 5

TAAAGATCTCGAAATTGATGGGCGTGTCGT	1	114	1	GAAATTGATG	    0.982345	-187
ATATTCCAGTGAATTGGAAGACCTATATGG	1	147	0	GAATTGGAAG	    0.979077	-154
CAATTCACTGGAATATGAAGGCATTAAATG	1	161	1	GAATATGAAG	    0.982354	-140
GGTAAATATTGAAAAAGTTGGGGAGGCATA	1	279	1	GAAAAAGTTG	    0.925648	-22
          **********

Masking position 3
Map Score:   0.582182

Number of sites scoring better than the average of aligned sites = 273
Number in coding regions = 252
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


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


Motif number 8

          **********

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