AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i024_Formate_Dehydrogenase_hinf_reg_100.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)
#2	HI0009	69	fdhE protein (fdhE)

Motif number 1

TTTTTCTGCCGCTAATTTTTCGC       	1	4	0	GCTAATTTTT	    0.858165	-297
TTTTACCATATCGCCTTTTTGGATGCCTTT	1	31	0	TCGCCTTTTT	    0.946095	-270
ATTATGCCTCCCCAACTTTTTCAATATTTA	1	281	0	CCCAACTTTT	    0.975813	-20
TCAATTTTAACCGCACTTTTTCTTTTTCAG	2	20	0	CCGCACTTTT	    0.996885	-50
TTAAAATTGACCGCACTTTTTATTATAAAA	2	40	1	CCGCACTTTT	    0.996885	-30
      ATTCTCTCACTTTTATAATAAAAA	2	56	0	TCTCACTTTT	    0.984386	-14
          **********

Masking position 7
Map Score:   7.66605

Number of sites scoring better than the average of aligned sites = 1662
Number in coding regions = 1121
Number in noncoding regions = 541
Number of orfs with sites within 600 bp upstream = 346
Fraction of orfs with sites within 600 bp upstream = 0.0555734


Motif number 2

TCGCCTTTTTGGATGCCTTTTTCTGCCGCT	1	21	0	GGATGCCTTT	    0.960381	-280
CGGTCGCCGTGGTTACAAAACGTCTTAAAG	1	89	1	GGTTACAAAA	     0.79495	-212
CAGTGAATTGGAAGACCTATATGGTGTACG	1	141	0	GAAGACCTAT	     0.93914	-160
ACTGGAATATGAAGGCATTAAATGGCAAAG	1	167	1	GAAGGCATTA	    0.910223	-134
GAGAATCCACGGTTACCTTTGCCATTTAAT	1	183	0	GGTTACCTTT	    0.926655	-118
GATTCTCTACGAATACCTTAACACCATCTT	1	206	1	GAATACCTTA	    0.972352	-95
GTGTTTGCGTGATTGCCTCACCCCAAGATG	1	230	0	GATTGCCTCA	    0.908492	-71
GCAAACACCAGAATACAAAACATTCTTGGT	1	252	1	GAATACAAAA	    0.851633	-49
AAAAAGTTGGGGAGGCATAAT         	1	290	1	GGAGGCATAA	    0.960118	-11
          **********

Masking position 6
Map Score:   7.3316

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 3

TTCTGCCGCTAATTTTTCGC          	1	1	0	AATTTTTCGC	     0.97207	-300
GACGAGAAGTAATTTTTACCATATCGCCTT	1	44	0	AATTTTTACC	     0.99375	-257
CAACTTTTTCAATATTTACCAAGAATGTTT	1	269	0	AATATTTACC	    0.984358	-32
AAGTGCGGTCAATTTTAACCGCACTTTTTC	2	28	0	AATTTTAACC	    0.984358	-42
          **********

Masking position 5
Map Score:   4.15511

Number of sites scoring better than the average of aligned sites = 153
Number in coding regions = 90
Number in noncoding regions = 63
Number of orfs with sites within 600 bp upstream = 52
Fraction of orfs with sites within 600 bp upstream = 0.00835207


Motif number 4

AAAATTACTTCTCGTCGTGGCTATATTAAA	1	58	1	CTCGTCGTGG	    0.981248	-243
TATTAAAGCGGTCGCCGTGGTTACAAAACG	1	81	1	GTCGCCGTGG	    0.996351	-220
AATGGCAAAGGTAACCGTGGATTCTCTACG	1	187	1	GTAACCGTGG	    0.950454	-114
TTAACACCATCTTGGGGTGAGGCAATCACG	1	223	1	CTTGGGGTGA	    0.971438	-78
GTATTCTGGTGTTTGCGTGATTGCCTCACC	1	238	0	GTTTGCGTGA	    0.959773	-63
TATTGAAAAAGTTGGGGAGGCATAAT    	1	285	1	GTTGGGGAGG	    0.979384	-16
          **********

Masking position 2
Map Score:   3.68059

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 5

GCTTTAATATAGCCACGACGAGAAGTAATT	1	60	0	AGCCACGACG	     0.98896	-241
GACGTTTTGTAACCACGGCGACCGCTTTAA	1	83	0	AACCACGGCG	    0.965729	-218
TTCGTAGAGAATCCACGGTTACCTTTGCCA	1	189	0	ATCCACGGTT	    0.927481	-112
          **********

Masking position 5
Map Score:   0.405126

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 6

          **********

No masking
Map Score:   1.65857e-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:   1.65857e-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:   1.65857e-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