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

Motif number 1

ATAAAGTGCGGTATAAAATAAAGAGATT  	1	9	0	GTATAAAATA	    0.962993	-82
GCTAGGTTTTGTATAAAGTGCGGTATAAAA	1	21	0	GTATAAAGTG	     0.99181	-70
CACTTAACATTAATAAAGTGCGGTTATCTT	1	50	1	TAATAAAGTG	    0.916386	-41
GTAGCGAAGTGTAGAAAATAATTGTG    	2	7	0	GTAGAAAATA	    0.888976	-294
TTATGTTTATGCATAAAATGAAAAAAAATC	2	67	1	GCATAAAATG	    0.988114	-234
TGCCCACTTCGCATAAATTGGATAAGGGAA	2	167	0	GCATAAATTG	    0.970501	-134
AAGAAACTGGGAATAAAGTTAATTATCAAT	2	210	1	GAATAAAGTT	    0.941839	-91
          **********

Masking position 5
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

ACATTAATAAAGTGCGGTTATCTTAAATAATTTT	1	56	1	AGGGTTTCTT	    0.989772	-35
AAACGTAATAAGATTTTTTTTCATTTTATGCATA	2	74	0	AGTTTTTCAT	    0.983037	-227
TTTTAACCTTAGGTACGTTACCTTTTGCTCAAGC	2	105	1	AGTGTTCCTT	    0.989763	-196
CTGGTGCTGGAGCGTCTTTCCCTTATCCAATTTA	2	150	1	AGGTTTCCTT	    0.989768	-151
CTTTATTCCCAGTTTCTTTCTCATATAAAGATGC	2	194	0	AGTTTTTCAT	    0.983037	-107
          ** *  *** ****

Masking position 8
Map Score:   2.12303

Number of sites scoring better than the average of aligned sites = 81
Number in coding regions = 68
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 3

ATTTAGATTGCGTAGCGAAGTGTAGAAAAT	2	18	0	CGTAGCGAAG	    0.940893	-283
CAAAAGGTAACGTACCTAAGGTTAAAACGT	2	102	0	CGTACCTAAG	    0.957306	-199
GTCCGCCGCCCGAACCGATGGATTGATAAT	2	231	0	CGAACCGATG	    0.992201	-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