AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i319_mixed4_hinf_reg_300.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	HI0299	115	prepilin peptidase dependent protein D

Motif number 1

       ACATTTTTCCTTTTTTTTGCGAT	1	4	1	TTTTTCCTTT	    0.997159	-112
TTTTTCCTTTTTTTTGCGATCAGGATCGCA	1	14	1	TTTTTGCGAT	    0.994521	-102
GACCGCACTTTTTCTGCGATCCTGATCGCA	1	28	0	TTTCTGCGAT	    0.987918	-88
TACAAACAAATTTTTCCTTTTCACAATGTC	1	63	1	TTTTTCCTTT	    0.997159	-53
        TCATTTTCCTTTTATTAAGCCT	1	104	0	ATTTTCCTTT	    0.990712	-12
          **********

Masking position 5
Map Score:   11.7871

Number of sites scoring better than the average of aligned sites = 182
Number in coding regions = 132
Number in noncoding regions = 50
Number of orfs with sites within 600 bp upstream = 58
Fraction of orfs with sites within 600 bp upstream = 0.00931577


Motif number 2

  ACATTTTTCCTTTTTTTTGCGATCAGGAT	1	9	1	CCTTTTTTTG	    0.971298	-107
AAAGTGCGGTCAATTTTACAAACAAATTTTT	1	47	1	CAATTTACAA	     0.95739	-69
ACAAATTTTTCCTTTTCACAATGTCGTTGCC	1	68	1	CCTTTTACAA	    0.995589	-48
   TCATTTTCCTTTTATTAAGCCTTTGTTG	1	98	0	CCTTTTTTAA	     0.99319	-18
          ****** ****

Masking position 6
Map Score:   1.54758

Number of sites scoring better than the average of aligned sites = 113
Number in coding regions = 93
Number in noncoding regions = 20
Number of orfs with sites within 600 bp upstream = 26
Fraction of orfs with sites within 600 bp upstream = 0.00417604


Motif number 3

CGATCCTGATCGCAAAAAAAAGGAAAAATG	1	12	0	CGCAAAAAAA	    0.996301	-104
CGATCAGGATCGCAGAAAAAGTGCGGTCAA	1	30	1	CGCAGAAAAA	    0.993711	-86
CGGTCAATTTTACAAACAAATTTTTCCTTT	1	53	1	TACAAACAAA	    0.985464	-63
ACAATGTCGTTGCCAACAAAGGCTTAATAA	1	85	1	TGCCAACAAA	     0.99371	-31
          **********

Masking position 6
Map Score:   6.46518

Number of sites scoring better than the average of aligned sites = 150
Number in coding regions = 131
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 4

          **********

No masking
Map Score:   1.3033e-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:   1.3033e-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:   1.3033e-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