AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i099_Phosphate_Transport_1_bsub_reg_100.orf -aORF_bsub.txt -zbsub.fna -g0.435 -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 =  	0.435
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	yqgH	68	alternate gene name: yzmC; similar to phosphate ABC transporter (permease)
#2	yqgG	153	alternate gene name: yzmB; similar to phosphate ABC transporter (binding protein)

Motif number 1

TGTTAAGAGGAGAAACGGTTGTCCCCGCAC	1	28	0	AGAAACGGTT	    0.983477	-41
         AAAAAACGCTCACATGATGTG	2	2	1	AAAAACGCTC	    0.997699	-152
TTTGTATAAAAAAAACGCCCACATCATGTG	2	21	0	AAAAACGCCC	    0.996084	-133
TTTTATACAAAAAAACGCACTGATTTACAA	2	40	1	AAAAACGCAC	    0.994208	-114
GGTTCTATGTAAAAAGGGTTTGAACCGAAT	2	79	0	AAAAAGGGTT	    0.974043	-75
          **********

Masking position 5
Map Score:   8.6089

Number of sites scoring better than the average of aligned sites = 318
Number in coding regions = 259
Number in noncoding regions = 59
Number of orfs with sites within 600 bp upstream = 64
Fraction of orfs with sites within 600 bp upstream = 0.0102795


Motif number 2

GCACTCCTCTTTTTATTAAGA         	1	2	0	TTTTATTAAG	    0.676514	-67
ACTCCTATGAATGTGTTAAGAGGAGAAACG	1	41	0	ATGTGTTAAG	    0.946752	-28
ACATTCATAGGAGTGTAAAACA        	1	57	1	GAGTGTAAAA	    0.959251	-12
GTGCGTTTTTTTGTATAAAAAAAACGCCCA	2	30	0	TTGTATAAAA	    0.818459	-124
AATGTTAAGGTTTTGTAAATCAGTGCGTTT	2	52	0	TTTTGTAAAT	    0.827465	-102
GGTTTGAACCGAATGTTAAGGTTTTGTAAA	2	63	0	GAATGTTAAG	    0.911071	-91
AGTAAAGGTTCTATGTAAAAAGGGTTTGAA	2	85	0	CTATGTAAAA	    0.865345	-69
CCTACACGTATAGAGTAAAGGTTCTATGTA	2	98	0	TAGAGTAAAG	    0.913103	-56
          **********

Masking position 8
Map Score:   2.72559

Number of sites scoring better than the average of aligned sites = 1412
Number in coding regions = 1097
Number in noncoding regions = 315
Number of orfs with sites within 600 bp upstream = 321
Fraction of orfs with sites within 600 bp upstream = 0.051558


Motif number 3

GTTGTCCCCGCACTCCTCTTTTTATTAAGA	1	11	0	CACTCCTCTT	    0.994866	-58
GGACAACCGTTTCTCCTCTTAACACATTCA	1	34	1	TTCTCCTCTT	    0.965116	-35
   TGTTTTACACTCCTATGAATGTGTTAA	1	52	0	CACTCCTATG	    0.994846	-17
    AAAAAACGCTCACATGATGTGGGCGT	2	7	1	CGCTCACATG	    0.960083	-147
          **********

Masking position 4
Map Score:   1.43826

Number of sites scoring better than the average of aligned sites = 267
Number in coding regions = 162
Number in noncoding regions = 105
Number of orfs with sites within 600 bp upstream = 90
Fraction of orfs with sites within 600 bp upstream = 0.0144555


Motif number 4

          **********

No masking
Map Score:   2.15595e-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:   2.15595e-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:   2.15595e-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