AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i287_hypothetical_nitrate_reductase_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	HI0345	300	ferredoxin-type protein (napG)

Motif number 1

GCCATGACGTAAACCACGTGCTTGTGCATCT	1	19	0	AAACACGTGC	    0.990896	-282
GGTAAATACTAAGCCACGAGGTGGTTTATTA	1	112	0	AAGCACGAGG	    0.963344	-189
GACCTGCATCAAAGAAAGTGGTAAATACTAA	1	131	0	AAAAAAGTGG	    0.991845	-170
AACCGACTTCAAAAAATGTGCGGTAAAAGTG	1	211	1	AAAAATGTGC	    0.979648	-90
TGATGGGAGAAAATAAAGTGCGGTTGATTTT	1	267	0	AAAAAAGTGC	    0.991845	-34
TTCTCCCATCAATAAAAGAGGAAG       	1	287	1	AATAAAGAGG	    0.951954	-14
          *** *******

Masking position 6
Map Score:   6.45539

Number of sites scoring better than the average of aligned sites = 221
Number in coding regions = 182
Number in noncoding regions = 39
Number of orfs with sites within 600 bp upstream = 33
Fraction of orfs with sites within 600 bp upstream = 0.00530035


Motif number 2

TTTACGTCATGGCGATAAAATTAAGATTTC	1	37	1	GGCGATAAAA	    0.985758	-264
ATTTCGCCTCGACGAGATGAAATCTTAATT	1	55	0	GACGAGATGA	    0.937861	-246
ATCTCGTCGAGGCGAAATGATTTCTTATTT	1	67	1	GGCGAAATGA	    0.980862	-234
GATACTCGCGGACGTAATAAACCACCTCGT	1	98	1	GACGTAATAA	      0.9176	-203
TCAAAAAATGTGCGGTAAAAGTGGAAAAGG	1	219	1	TGCGGTAAAA	    0.937874	-82
TGGAAAAGGCTGCGTAAAAACCATGTAAAA	1	240	1	TGCGTAAAAA	    0.962598	-61
CTTTTATTGATGGGAGAAAATAAAGTGCGG	1	275	0	TGGGAGAAAA	    0.908804	-26
          **********

Masking position 7
Map Score:   5.11933

Number of sites scoring better than the average of aligned sites = 766
Number in coding regions = 693
Number in noncoding regions = 73
Number of orfs with sites within 600 bp upstream = 47
Fraction of orfs with sites within 600 bp upstream = 0.00754899


Motif number 3

    CACCCATTAGATGCACAAGCACGTGGT	1	7	1	TTAGATGCCA	    0.949417	-294
GATTTCTTATTTAGATACTCGCGGACGTAAT	1	85	1	TTAGATACCG	    0.977646	-216
TACCACTTTCTTTGATGCAGGTCAGCTTGCA	1	139	1	TTTGATGCGG	    0.995145	-162
GTCGGTTTCTTTTGAAATTGGGTCTGTCGCA	1	187	0	TTTGAAATGG	    0.965858	-114
CCGCACATTTTTTGAAGTCGGTTTCTTTTGA	1	203	0	TTTGAAGTGG	    0.984554	-98
          ******** **

Masking position 5
Map Score:   2.3473

Number of sites scoring better than the average of aligned sites = 104
Number in coding regions = 92
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 4

ACGTGGTTTACGTCATGGCGATAAAATTAA	1	31	1	CGTCATGGCG	    0.591718	-270
GATTTCATCTCGTCGAGGCGAAATGATTTC	1	61	1	CGTCGAGGCG	    0.937314	-240
TAATAAACCACCTCGTGGCTTAGTATTTAC	1	112	1	CCTCGTGGCT	    0.994305	-189
          **********

Masking position 3
Map Score:   3.25361

Number of sites scoring better than the average of aligned sites = 12
Number in coding regions = 9
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


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