AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i024_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)
#2	HI0009	69	fdhE protein (fdhE)

Motif number 1

       GCGAAAAATTAGCGGCAGAAAAAG	1	4	1	AAAAATTAGG	    0.962605	-297
AAAGGCATCCAAAAAGGCGATATGGTAAAAA	1	31	1	AAAAAGGCGT	     0.95516	-270
GCGATATGGTAAAAATTACTTCTCGTCGTGG	1	47	1	AAAAATTACT	    0.803841	-254
TAAATATTGAAAAAGTTGGGGAGGCATAAT 	1	281	1	AAAAGTTGGG	    0.968931	-20
CTGAAAAAGAAAAAGTGCGGTTAAAATTGAC	2	20	1	AAAAGTGCGT	    0.993055	-50
TTTTATAATAAAAAGTGCGGTCAATTTTAAC	2	39	0	AAAAGTGCGT	    0.993055	-31
TTTTTATTATAAAAGTGAGAGAAT       	2	56	1	AAAAGTGAGG	    0.990975	-14
          ********* *

Masking position 4
Map Score:   7.73223

Number of sites scoring better than the average of aligned sites = 918
Number in coding regions = 592
Number in noncoding regions = 326
Number of orfs with sites within 600 bp upstream = 248
Fraction of orfs with sites within 600 bp upstream = 0.039833


Motif number 2

AGCGGCAGAAAAAGGCATCCAAAAAGGCGA	1	21	1	AAAGGCATCC	    0.960729	-280
CTTTAAGACGTTTTGTAACCACGGCGACCG	1	89	0	TTTTGTAACC	    0.797581	-212
CGTACACCATATAGGTCTTCCAATTCACTG	1	141	1	ATAGGTCTTC	    0.940059	-160
CTTTGCCATTTAATGCCTTCATATTCCAGT	1	167	0	TAATGCCTTC	     0.91034	-134
ATTAAATGGCAAAGGTAACCGTGGATTCTC	1	183	1	AAAGGTAACC	    0.927748	-118
AAGATGGTGTTAAGGTATTCGTAGAGAATC	1	206	0	TAAGGTATTC	    0.972772	-95
CATCTTGGGGTGAGGCAATCACGCAAACAC	1	230	1	TGAGGCAATC	     0.90961	-71
ACCAAGAATGTTTTGTATTCTGGTGTTTGC	1	252	0	TTTTGTATTC	     0.85367	-49
         ATTATGCCTCCCCAACTTTTT	1	290	0	TTATGCCTCC	    0.960697	-11
          **********

Masking position 10
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

CATCCAAAAAGGCGATATGGTAAAAATTACTT	1	36	1	GGCGATAGTA	    0.980594	-265
ATATAGCCACGACGAGAAGTAATTTTTACCAT	1	52	0	GACGAGAGAA	    0.980451	-249
AGATCTTTAAGACGTTTTGTAACCACGGCGAC	1	91	0	GACGTTTGAA	    0.969601	-210
GAAATTGATGGGCGTGTCGTACACCATATAGG	1	124	1	GGCGTGTGAC	    0.981908	-177
ACCCCAAGATGGTGTTAAGGTATTCGTAGAGA	1	209	0	GGTGTTAGTA	    0.947569	-92
ACACCATCTTGGGGTGAGGCAATCACGCAAAC	1	226	1	GGGGTGAGAA	    0.987446	-75
          ******* * **

Masking position 4
Map Score:   2.39282

Number of sites scoring better than the average of aligned sites = 192
Number in coding regions = 179
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 4

TTACCATATCGCCTTTTTGGATGCCTTTTT	1	29	0	GCCTTTTTGG	    0.978425	-272
CGTGTCGTACACCATATAGGTCTTCCAATT	1	136	1	ACCATATAGG	    0.966639	-165
ATACCTTAACACCATCTTGGGGTGAGGCAA	1	218	1	ACCATCTTGG	    0.994735	-83
AGAATACAAAACATTCTTGGTAAATATTGA	1	261	1	ACATTCTTGG	    0.981121	-40
          **********

Masking position 5
Map Score:   2.1694

Number of sites scoring better than the average of aligned sites = 48
Number in coding regions = 46
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 5

  GCGAAAAATTAGCGGCAGAAAAAGGCAT	1	9	1	TTAGCGGCAG	    0.983417	-292
GCGGTCAATTTTAACCGCACTTTTTCTTTT	2	24	0	TTAACCGCAC	    0.995915	-46
GCGGTTAAAATTGACCGCACTTTTTATTAT	2	36	1	TTGACCGCAC	    0.994743	-34
          **********

Masking position 9
Map Score:   0.623185

Number of sites scoring better than the average of aligned sites = 413
Number in coding regions = 260
Number in noncoding regions = 153
Number of orfs with sites within 600 bp upstream = 129
Fraction of orfs with sites within 600 bp upstream = 0.0207196


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