AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i319_mixed4_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	HI0299	115	prepilin peptidase dependent protein D

Motif number 1

ATCGCAAAAAAAAGGAAAAATGT       	1	4	0	AAAGGAAAAA	    0.997244	-112
TGCGATCCTGATCGCAAAAAAAAGGAAAAA	1	14	0	ATCGCAAAAA	    0.994684	-102
TGCGATCAGGATCGCAGAAAAAGTGCGGTC	1	28	1	ATCGCAGAAA	    0.988276	-88
GACATTGTGAAAAGGAAAAATTTGTTTGTA	1	63	0	AAAGGAAAAA	    0.997244	-53
AGGCTTAATAAAAGGAAAATGA        	1	104	1	AAAGGAAAAT	    0.990988	-12
          **********

Masking position 6
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	    0.970227	-107
AAAGTGCGGTCAATTTTACAAACAAATTTTT	1	47	1	CAATTTACAA	    0.955823	-69
ACAAATTTTTCCTTTTCACAATGTCGTTGCC	1	68	1	CCTTTTACAA	     0.99542	-48
   TCATTTTCCTTTTATTAAGCCTTTGTTG	1	98	0	CCTTTTTTAA	     0.99293	-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

CATTTTTCCTTTTTTTTGCGATCAGGATCG	1	12	1	TTTTTTTGCG	     0.99661	-104
TTGACCGCACTTTTTCTGCGATCCTGATCG	1	30	0	TTTTTCTGCG	    0.994235	-86
AAAGGAAAAATTTGTTTGTAAAATTGACCG	1	53	0	TTTGTTTGTA	    0.986666	-63
TTATTAAGCCTTTGTTGGCAACGACATTGT	1	85	0	TTTGTTGGCA	    0.994235	-31
          **********

Masking position 5
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