AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i242_hfl_operon_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	HI0151	109	hflK protein (hflK)

Motif number 1

GATTTTATATAAGGATTTTTTTGA      	1	5	0	AAGGATTTTT	    0.943021	-105
ATATAAAATCAAGGATTTTTTATTGCCTAA	1	25	1	AAGGATTTTT	    0.943021	-85
ATGAAAATACAAGGCTTTTTAGGCAATAAA	1	43	0	AAGGCTTTTT	    0.993431	-67
CTAAACTCTTAACAATTTTTTGACAA    	1	94	1	AACAATTTTT	    0.674463	-16
          **********

Masking position 6
Map Score:   11.3504

Number of sites scoring better than the average of aligned sites = 76
Number in coding regions = 57
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 2

AAAAAAATCCTTATATAAAATCAAGGATTT	1	13	1	TTATATAAAA	     0.78562	-97
GGATTTTTTATTGCCTAAAAAGCCTTGTAT	1	37	1	TTGCCTAAAA	    0.991928	-73
CCCCATTTATTTAGCTAAACTCTTAACAAT	1	80	1	TTAGCTAAAC	    0.984155	-30
          TTGTCAAAAAATTGTTAAGA	1	100	0	TTGTCAAAAA	     0.98065	-10
          **********

Masking position 7
Map Score:   3.60225

Number of sites scoring better than the average of aligned sites = 257
Number in coding regions = 201
Number in noncoding regions = 56
Number of orfs with sites within 600 bp upstream = 44
Fraction of orfs with sites within 600 bp upstream = 0.00706714


Motif number 3

TCCTTATATAAAATCAAGGATTTTTTATTG	1	20	1	AAATCAAGGA	    0.977621	-90
GCTTTTTAGGCAATAAAAAATCCTTGATTT	1	30	0	CAATAAAAAA	    0.928973	-80
ACGTCTATGAAAATACAAGGCTTTTTAGGC	1	49	0	AAATACAAGG	    0.987705	-61
GAGTTTAGCTAAATAAATGGGGCACGTCTA	1	72	0	AAATAAATGG	    0.987152	-38
          **********

Masking position 4
Map Score:   1.23412

Number of sites scoring better than the average of aligned sites = 299
Number in coding regions = 241
Number in noncoding regions = 58
Number of orfs with sites within 600 bp upstream = 52
Fraction of orfs with sites within 600 bp upstream = 0.00835207


Motif number 4

          **********

No masking
Map Score:   1.16119e-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:   1.16119e-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:   1.16119e-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