AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i121_Acriflavin_Resistance_pump_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	HI0893	241	transcriptional repressor (Bm3R1)
#2	HI0894	79	lipoprotein, putative

Motif number 1

TTAACCGCACTTTTCATCATTAAATAAACGC	1	27	0	TTTTCTCATT	    0.972748	-215
CTGCATTTTATATTCCTATTTTTTATATCCT	1	64	1	TATTCTATTT	    0.934778	-178
TATCCTACTTTGTTCATCATTCATCTTGTGG	1	89	1	TGTTCTCATT	     0.96003	-153
TTGTTACGTTTTTTGTTTTTTAACTTGCCAA	1	146	1	TTTTGTTTTT	    0.981529	-96
TTTATTTATTTTTTGTTTTTTGGCAAGTTAA	1	165	0	TTTTGTTTTT	    0.981529	-77
TGAGCGTTCATTTTATTTATTTTTTGTTTTT	1	176	0	TTTTATTATT	    0.811754	-66
AATGAACGCTCATTCATTTTTGAGCAATTAT	1	195	1	CATTCTTTTT	    0.847953	-47
TTTGAGCAATTATTGCTCCTTATTTTACTCA	1	213	1	TATTGTCCTT	    0.941746	-29
         TTGTTGTTATTTTTATAACGGA	2	2	1	TGTTGTATTT	    0.950408	-78
TATGTGAGCGTTTTGGTCTTTGATGTTGAGT	2	51	0	TTTTGTCTTT	    0.988275	-29
          ***** *****

Masking position 7
Map Score:   13.5253

Number of sites scoring better than the average of aligned sites = 785
Number in coding regions = 611
Number in noncoding regions = 174
Number of orfs with sites within 600 bp upstream = 148
Fraction of orfs with sites within 600 bp upstream = 0.0237713


Motif number 2

AATGATGAAAAGTGCGGTTAATTTTGACTG	1	37	1	AGTGCGGTTA	    0.966171	-205
TCATTCATCTTGTGGGTTTACGGCTTACCT	1	105	1	TGTGGGTTTA	    0.978603	-137
CAAAAATGAATGAGCGTTCATTTTATTTAT	1	187	0	TGAGCGTTCA	    0.784604	-55
CATTCATTTTTGAGCAATTATTGCTCCTTA	1	205	1	TGAGCAATTA	    0.945468	-37
AGAAAATATGTGAGCGTTTTGGTCTTTGAT	2	58	0	TGAGCGTTTT	    0.982079	-22
          **********

Masking position 8
Map Score:   3.18656

Number of sites scoring better than the average of aligned sites = 215
Number in coding regions = 188
Number in noncoding regions = 27
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


Motif number 3

     GTGGGCTTCAGTCCACGCGTTTATT	1	6	1	CTTCAGTCCA	    0.983671	-236
CCGCACTTTTCATCATTAAATAAACGCGTG	1	24	0	CATCATTAAA	    0.949518	-218
GGAATATAAAATGCAGTCAAAATTAACCGC	1	50	0	ATGCAGTCAA	    0.903078	-192
CTACTTTGTTCATCATTCATCTTGTGGGTT	1	93	1	CATCATTCAT	    0.932123	-149
    AAGATCCTTGAGTAAAATAAGGAGCA	1	226	0	CTTGAGTAAA	     0.96677	-16
GAGCTTTAAACATGAGTCAAACTCAACATC	2	31	1	CATGAGTCAA	     0.98852	-49
          **********

Masking position 5
Map Score:   3.99697

Number of sites scoring better than the average of aligned sites = 278
Number in coding regions = 256
Number in noncoding regions = 22
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 4

TTTGACTGCATTTTATATTCCTATTTTTTA	1	59	1	TTTTATATTC	     0.95013	-183
TATTCCTATTTTTTATATCCTACTTTGTTC	1	74	1	TTTTATATCC	    0.986855	-168
ACGTTTTTTGTTTTTTAACTTGCCAAAAAA	1	151	1	TTTTTTAACT	    0.916641	-91
TTGTTGTTATTTTTATAACGGAGCTTTAAA	2	11	1	TTTTATAACG	    0.974359	-69
          **********

Masking position 6
Map Score:   1.30822

Number of sites scoring better than the average of aligned sites = 145
Number in coding regions = 104
Number in noncoding regions = 41
Number of orfs with sites within 600 bp upstream = 30
Fraction of orfs with sites within 600 bp upstream = 0.0048185


Motif number 5

          **********

No masking
Map Score:   -7.93376e-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:   -7.93376e-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:   -7.93376e-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