AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i136_Transmembrane_Transport_10_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	HI1051	77	ABC transporter, ATP-binding protein
#2	HI1052	111	transcriptional regulator, araC family, putative

Motif number 1

     ATTGATTTGTTTTTGTGCTATAATA	1	6	1	TTTGTTTTTG	    0.923356	-72
CCTTTTAGAAGTGCATATTATTATAGCACA	1	24	0	GTGCATATTA	     0.94391	-54
GCAACGCAGGTTGCCTTTTAGAAGTGCATA	1	37	0	TTGCCTTTTA	    0.985552	-41
CTGCGTTGCCTTTCTTTTTAAGGAAAAGAT	1	58	1	TTTCTTTTTA	     0.98083	-20
GCCACACCAGTTGGTTATTAATTCAATATA	2	25	0	TTGGTTATTA	    0.987523	-87
ATTATGATACTTGCTTATTTATCTCAATTT	2	73	1	TTGCTTATTT	    0.978734	-39
          **********

Masking position 6
Map Score:   6.16687

Number of sites scoring better than the average of aligned sites = 406
Number in coding regions = 329
Number in noncoding regions = 77
Number of orfs with sites within 600 bp upstream = 67
Fraction of orfs with sites within 600 bp upstream = 0.0107613


Motif number 2

TAGCACAAAAACAAATCAAT          	1	1	0	ACAAATCAAT	    0.972565	-77
CAGTTGGTTATTAATTCAATATATTTAGGA	2	18	0	TTAATTCAAT	    0.958285	-94
ACTTGCTTATTTATCTCAATTTTTATCGCT	2	81	1	TTATCTCAAT	    0.984289	-31
TTTATCGCTAACATCTCATT          	2	102	1	ACATCTCATT	    0.974595	-10
          **********

Masking position 6
Map Score:   1.04123

Number of sites scoring better than the average of aligned sites = 196
Number in coding regions = 172
Number in noncoding regions = 24
Number of orfs with sites within 600 bp upstream = 25
Fraction of orfs with sites within 600 bp upstream = 0.00401542


Motif number 3

TGCATATTATTATAGCACAAAAACAAATCA	1	13	0	TATAGCACAA	    0.964797	-65
GCCTTTCTTTTTAAGGAAAAGAT       	1	65	1	TTAAGGAAAA	    0.951665	-13
ATTCAATATATTTAGGAGAACATT      	2	5	0	TTTAGGAGAA	    0.992349	-107
TGTGGCAAATTATAGGCGGATTAGATTATG	2	49	1	TATAGGCGGA	    0.979609	-63
          **********

Masking position 4
Map Score:   0.243743

Number of sites scoring better than the average of aligned sites = 101
Number in coding regions = 69
Number in noncoding regions = 32
Number of orfs with sites within 600 bp upstream = 37
Fraction of orfs with sites within 600 bp upstream = 0.00594282


Motif number 4

          **********

No masking
Map Score:   3.64809e-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:   3.64809e-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:   3.64809e-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