AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i270_hypothetical15_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	HI0090	300	conserved hypothetical protein

Motif number 1

TTATAAAAAAACCCGCTATTCAGTTGAATC	1	20	1	ACCCGCTATT	    0.987601	-281
GATACAGAAAACCCGCGATTCAACTGAATA	1	36	0	ACCCGCGATT	     0.98991	-265
TGCTGCACTAACCCGCACCATTAATCATAA	1	73	1	ACCCGCACCA	    0.939225	-228
TTAGCACGATTACCGCCATTATGATGACCA	1	106	0	TACCGCCATT	    0.969052	-195
AATGAAAAATAACCGCACTTTATCCGTAAT	1	138	0	AACCGCACTT	    0.992248	-163
CGTAAAGAAATACCGAAATTTCCCGAGCTT	1	192	1	TACCGAAATT	    0.966115	-109
TACCGAAATTTCCCGAGCTTGTCAAACAGA	1	202	1	TCCCGAGCTT	    0.979798	-99
CGGTTAGTTTACACGAAATTTATTGACTAA	1	258	0	ACACGAAATT	    0.912829	-43
CGTGTAAACTAACCGCACTTTTTTATAAAG	1	273	1	AACCGCACTT	    0.992248	-28
          **********

Masking position 4
Map Score:   18.6088

Number of sites scoring better than the average of aligned sites = 1190
Number in coding regions = 835
Number in noncoding regions = 355
Number of orfs with sites within 600 bp upstream = 218
Fraction of orfs with sites within 600 bp upstream = 0.0350145


Motif number 2

AATAGCGGGTTTTTTTATAAATTTAAAAA 	1	10	0	TTTTTTATAA	    0.898035	-291
TGAATCGCGGGTTTTCTGTATCTTGTTTTT	1	44	1	GTTTTCTGTA	    0.851989	-257
ACCCGCACCATTAATCATAATAATGGTCAT	1	83	1	TTAATCATAA	    0.912327	-218
CATAATAATGGTCATCATAATGGCGGTAAT	1	98	1	GTCATCATAA	      0.8685	-203
CACTTTATCCGTAATCATTAGCACGATTAC	1	123	0	GTAATCATTA	    0.864506	-178
AGTGCGGTTATTTTTCATTGTGTTTTATCT	1	149	1	TTTTTCATTG	    0.896476	-152
TTCATTGTGTTTTATCTTGAAAAATGAATG	1	162	1	TTTATCTTGA	    0.852622	-139
GAAATTTCGGTATTTCTTTACGCATTCATT	1	184	0	TATTTCTTTA	    0.725677	-117
AAGTGACAAATTTTTCAGAAATTTTCTTAG	1	232	1	TTTTTCAGAA	    0.956179	-69
CTAACCGCACTTTTTTATAAAGGAAAACCT	1	281	1	TTTTTTATAA	    0.898035	-20
          **********

Masking position 5
Map Score:   4.858

Number of sites scoring better than the average of aligned sites = 1850
Number in coding regions = 1508
Number in noncoding regions = 342
Number of orfs with sites within 600 bp upstream = 274
Fraction of orfs with sites within 600 bp upstream = 0.044009


Motif number 3

GGTTAGTGCAGCAAAAACAAGATACAGAAA	1	56	0	GCAAAAACAA	    0.981819	-245
TTTTTCAAGATAAAACACAATGAAAAATAA	1	156	0	TAAAACACAA	    0.919891	-145
GTTTTATCTTGAAAAATGAATGCGTAAAGA	1	170	1	GAAAAATGAA	    0.913876	-131
AAAAATGAATGCGTAAAGAAATACCGAAAT	1	181	1	GCGTAAAGAA	     0.91504	-120
CCCGAGCTTGTCAAACAGAAAGTGACAAAT	1	213	1	TCAAACAGAA	    0.974152	-88
          **********

Masking position 5
Map Score:   0.189159

Number of sites scoring better than the average of aligned sites = 498
Number in coding regions = 416
Number in noncoding regions = 82
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