AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i335_2_7_7_40_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	HI0673	122	conserved hypothetical protein

Motif number 1

AAATTCTTTTATTTTAACCGCACTTTTTTG	1	19	0	ATTTTAACCG	    0.997893	-104
AATAAAAGAATTTTTAACCGCACTTTCTTT	1	36	1	TTTTTAACCG	    0.997187	-87
ACTTTCTTTCATTTTATCGTTTTTCCTAAT	1	57	1	ATTTTATCGT	    0.979245	-66
TTTTTCCTAATTTTTCACGGTAAACAGGTT	1	76	1	TTTTTCACGG	    0.991029	-47
TGTGAGTAAAATTTTAACCTGTTTACCGTG	1	91	0	ATTTTAACCT	    0.993942	-32
          **********

Masking position 5
Map Score:   11.8763

Number of sites scoring better than the average of aligned sites = 206
Number in coding regions = 134
Number in noncoding regions = 72
Number of orfs with sites within 600 bp upstream = 52
Fraction of orfs with sites within 600 bp upstream = 0.00835207


Motif number 2

CTTTTATTTTAACCGCACTTTTTTGTATAA	1	14	0	AACCGCACTT	    0.890687	-109
AAGAATTTTTAACCGCACTTTCTTTCATTT	1	41	1	AACCGCACTT	    0.890687	-82
          **********

Masking position 7
Map Score:   4.32938

Number of sites scoring better than the average of aligned sites = 449
Number in coding regions = 280
Number in noncoding regions = 169
Number of orfs with sites within 600 bp upstream = 123
Fraction of orfs with sites within 600 bp upstream = 0.0197559


Motif number 3

AGTGCGGTTAAAATAAAAGAATTTTTAACCG	1	25	1	AAATAAAGAA	    0.995323	-98
AAAAACGATAAAATGAAAGAAAGTGCGGTTA	1	50	0	AAATAAAGAA	    0.995323	-73
TTTACCGTGAAAAATTAGGAAAAACGATAAA	1	69	0	AAAATAGGAA	    0.982929	-54
          **** ******

Masking position 7
Map Score:   1.57617

Number of sites scoring better than the average of aligned sites = 63
Number in coding regions = 47
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 4

          **********

No masking
Map Score:   1.23224e-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:   1.23224e-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:   1.23224e-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