AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i023_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)

Motif number 1

AGCGGCAGAAAAAGGCATCCAAAAAGGCGA	1	21	1	AAAGGCATCC	    0.964537	-280
CTTTAAGACGTTTTGTAACCACGGCGACCG	1	89	0	TTTTGTAACC	    0.830901	-212
CGTACACCATATAGGTCTTCCAATTCACTG	1	141	1	ATAGGTCTTC	    0.951337	-160
CTTTGCCATTTAATGCCTTCATATTCCAGT	1	167	0	TAATGCCTTC	        0.91	-134
ATTAAATGGCAAAGGTAACCGTGGATTCTC	1	183	1	AAAGGTAACC	    0.941197	-118
AAGATGGTGTTAAGGTATTCGTAGAGAATC	1	206	0	TAAGGTATTC	     0.97787	-95
CATCTTGGGGTGAGGCAATCACGCAAACAC	1	230	1	TGAGGCAATC	    0.923035	-71
ACCAAGAATGTTTTGTATTCTGGTGTTTGC	1	252	0	TTTTGTATTC	    0.879151	-49
         ATTATGCCTCCCCAACTTTTT	1	290	0	TTATGCCTCC	    0.967708	-11
          **********

Masking position 10
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

AAGTAATTTTTACCATATCGCCTTTTTGGATG	1	36	0	TACTATCGCC	    0.985455	-265
ATGGTAAAAATTACTTCTCGTCGTGGCTATAT	1	52	1	TTCTCTCGTC	    0.985362	-249
GTCGCCGTGGTTACAAAACGTCTTAAAGATCT	1	91	1	TTCAAACGTC	    0.977175	-210
CCTATATGGTGTACGACACGCCCATCAATTTC	1	124	0	GTCACACGCC	    0.986458	-177
TCTCTACGAATACCTTAACACCATCTTGGGGT	1	209	1	TACTAACACC	    0.960382	-92
GTTTGCGTGATTGCCTCACCCCAAGATGGTGT	1	226	0	TTCTCACCCC	    0.990617	-75
          ** * *******

Masking position 4
Map Score:   3.52126

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 3

TTAGCGGCAGAAAAAGGCATCCAAAAAGGC	1	19	1	AAAAAGGCAT	    0.981054	-282
AAAGGCATCCAAAAAGGCGATATGGTAAAA	1	31	1	AAAAAGGCGA	      0.9776	-270
TTGGAAGACCTATATGGTGTACGACACGCC	1	134	0	TATATGGTGT	    0.853725	-167
TCACTGGAATATGAAGGCATTAAATGGCAA	1	165	1	ATGAAGGCAT	    0.932338	-136
ATGAAGGCATTAAATGGCAAAGGTAACCGT	1	175	1	TAAATGGCAA	     0.93701	-126
GCCTCACCCCAAGATGGTGTTAAGGTATTC	1	216	0	AAGATGGTGT	    0.967428	-85
          **********

Masking position 4
Map Score:   2.89952

Number of sites scoring better than the average of aligned sites = 980
Number in coding regions = 885
Number in noncoding regions = 95
Number of orfs with sites within 600 bp upstream = 63
Fraction of orfs with sites within 600 bp upstream = 0.0101189


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


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