AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i099_Phosphate_Transport_1_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	HI1382	90	phosphate ABC transporter, permease protein (pstC)
#2	HI1383	300	phosphate ABC transporter, periplasmic-binding protein (pstS)

Motif number 1

  AATCTCTTTATTTTATACCGCACTTTAT	1	9	1	TATTTTATAC	    0.965478	-82
TTTTATACCGCACTTTATACAAAACCTAGC	1	21	1	CACTTTATAC	    0.992375	-70
AAGATAACCGCACTTTATTAATGTTAAGTG	1	50	0	CACTTTATTA	    0.921743	-41
    CACAATTATTTTCTACACTTCGCTAC	2	7	1	TATTTTCTAC	    0.895893	-294
GATTTTTTTTCATTTTATGCATAAACATAA	2	67	0	CATTTTATGC	    0.988932	-234
TTCCCTTATCCAATTTATGCGAAGTGGGCA	2	167	1	CAATTTATGC	    0.972496	-134
ATTGATAATTAACTTTATTCCCAGTTTCTT	2	210	0	AACTTTATTC	    0.945664	-91
          **********

Masking position 2
Map Score:   7.8458

Number of sites scoring better than the average of aligned sites = 233
Number in coding regions = 199
Number in noncoding regions = 34
Number of orfs with sites within 600 bp upstream = 26
Fraction of orfs with sites within 600 bp upstream = 0.00417604


Motif number 2

TTATACCGCACTTTATACAAAACCTAGCACTT	1	23	1	CTTATCAAAA	    0.849732	-68
        AAGTATTTTCCAAAATTATTTAAG	1	77	0	GTTTTCCAAA	    0.986382	-14
AATTTGTTATGTTTATGCATAAAATGAAAAAA	2	61	1	GTTATCATAA	    0.961068	-240
ATCTTATTACGTTTTAACCTTAGGTACGTTAC	2	94	1	GTTTACCTTA	    0.947012	-207
GTGCTGGAGCGTCTTTCCCTTATCCAATTTAT	2	153	1	GTTTTCCTTA	    0.986384	-148
AAAATCAACCGTTTTTGCAATAATTTGCTGTT	2	261	0	GTTTTCAATA	    0.978755	-40
          ** *** *****

Masking position 4
Map Score:   2.73429

Number of sites scoring better than the average of aligned sites = 175
Number in coding regions = 139
Number in noncoding regions = 36
Number of orfs with sites within 600 bp upstream = 37
Fraction of orfs with sites within 600 bp upstream = 0.00594282


Motif number 3

ATTTAGATTGCGTAGCGAAGTGTAGAAAAT	2	18	0	CGTAGCGAAG	    0.940406	-283
CAAAAGGTAACGTACCTAAGGTTAAAACGT	2	102	0	CGTACCTAAG	    0.957008	-199
GTCCGCCGCCCGAACCGATGGATTGATAAT	2	231	0	CGAACCGATG	    0.992277	-70
          **********

Masking position 4
Map Score:   1.27439

Number of sites scoring better than the average of aligned sites = 8
Number in coding regions = 7
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 4

          **********

No masking
Map Score:   -6.86222e-14

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:   -6.86222e-14

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:   -6.86222e-14

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