AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i099_Phosphate_Transport_1_ecoli_reg_300.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.5 -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 =  	0.5
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	BIME185	97	BIME
#2	pstC	86	high-affinity phosphate-specific transport system, cytoplasmic membrane component
#3	pstS	300	high-affinity phosphate-specific transport system; periplasmic phosphate-binding protein

Motif number 1

AGGCGCTCGGTCGGTCCCCTCGCCCCTCTG	1	51	0	TCGGTCCCCT	    0.966657	-47
AAGATGACGGTTTGTCACATGGAGTTGGCA	3	60	0	TTTGTCACAT	    0.978253	-241
CTACTTTTTCTCTGTCACAGAATGAAAATT	3	93	1	TCTGTCACAG	    0.983744	-208
TGAAAATTTTTCTGTCATCTCTTCGTTATT	3	115	1	TCTGTCATCT	    0.991839	-186
ACTTTATCTCTCTGTCATAAAACTGTCATA	3	194	1	TCTGTCATAA	    0.962606	-107
CTGTCATAAAACTGTCATATTCCTTACATA	3	205	1	ACTGTCATAT	    0.978445	-96
CTTACATATAACTGTCACCTGTTTGTCCTA	3	227	1	ACTGTCACCT	    0.986028	-74
CTGTCACCTGTTTGTCCTATTTTGCTTCTC	3	238	1	TTTGTCCTAT	     0.94138	-63
          **********

Masking position 5
Map Score:   13.1688

Number of sites scoring better than the average of aligned sites = 201
Number in coding regions = 166
Number in noncoding regions = 35
Number of orfs with sites within 600 bp upstream = 37
Fraction of orfs with sites within 600 bp upstream = 0.00594282


Motif number 2

ACACGGTTTTCCCCTCACCCTAACCCTCTC	1	19	1	CCCCTCACCC	     0.99869	-79
CCTCACCCTAACCCTCTCCCCAGAGGGGCG	1	31	1	ACCCTCTCCC	       0.988	-67
CTCGGTCGGTCCCCTCGCCCCTCTGGGGAG	1	46	0	CCCCTCGCCC	    0.997769	-52
CGGCGTAAAACACCGTACCCGGCCTGGAGT	2	15	0	CACCGTACCC	    0.972638	-72
CGGTGTTTTACGCCGCATCCGGCATTACAA	2	30	1	CGCCGCATCC	    0.991375	-57
AAGAAAAATGCCCCGCTTACGCA       	3	4	0	CCCCGCTTAC	    0.977651	-297
          **********

Masking position 4
Map Score:   9.76822

Number of sites scoring better than the average of aligned sites = 419
Number in coding regions = 334
Number in noncoding regions = 85
Number of orfs with sites within 600 bp upstream = 56
Fraction of orfs with sites within 600 bp upstream = 0.00899454


Motif number 3

TAACCGTGTACAGAGTCAAAAAGGCGCTCGG	1	71	0	CAGATCAAAA	    0.978464	-27
AAAAACATAACAGGAAGAAAAATGCCCCGCT	3	17	0	CAGGAGAAAA	    0.983191	-284
CATTCTGTGACAGAGAAAAAGTAGCCGAAGA	3	86	0	CAGAAAAAAG	    0.918091	-215
TTCTCTGTCACAGAATGAAAATTTTTCTGTC	3	100	1	CAGATGAAAA	    0.993788	-201
TTATTTAAATCAGACTGAAGACTTTATCTCT	3	174	1	CAGATGAAGA	    0.983191	-127
AGTTTTATGACAGAGAGATAAAGTCTTCAGT	3	187	0	CAGAAGATAA	    0.975288	-114
          **** ******

Masking position 8
Map Score:   5.649

Number of sites scoring better than the average of aligned sites = 315
Number in coding regions = 258
Number in noncoding regions = 57
Number of orfs with sites within 600 bp upstream = 65
Fraction of orfs with sites within 600 bp upstream = 0.0104401


Motif number 4

        AAGTGTTAACCGTGTACAGAGT	1	86	0	GTGTTAACCG	     0.92436	-12
GCCGGGTACGGTGTTTTACGCCGCATCCGG	2	22	1	GTGTTTTACG	    0.966973	-65
AGTTACTCTTCAGTTAAACGCGTTTACAAA	2	66	0	CAGTTAAACG	    0.945893	-21
AGGAATATGACAGTTTTATGACAGAGAGAT	3	199	0	CAGTTTTATG	    0.962975	-102
AAACAGGTGACAGTTATATGTAAGGAATAT	3	221	0	CAGTTATATG	    0.950735	-80
          **********

Masking position 5
Map Score:   1.85778

Number of sites scoring better than the average of aligned sites = 251
Number in coding regions = 233
Number in noncoding regions = 18
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 5

CCCCTCGCCCCTCTGGGGAGAGGGTTAGGGT	1	35	0	CTCTGGGAGA	    0.987536	-63
GTCAAAAAGGCGCTCGGTCGGTCCCCTCGCC	1	57	0	CGCTGGTCGG	    0.990537	-41
     TAAAACTCCAGGCCGGGTACGGTGTT	2	6	1	CTCCGGCCGG	     0.99756	-81
     AATGTCTCCTGGGAGGATTCATAAAG	3	285	0	CTCCGGGAGG	    0.997925	-16
          **** ******

Masking position 6
Map Score:   1.71379

Number of sites scoring better than the average of aligned sites = 138
Number in coding regions = 120
Number in noncoding regions = 18
Number of orfs with sites within 600 bp upstream = 18
Fraction of orfs with sites within 600 bp upstream = 0.0028911


Motif number 6

          **********

No masking
Map Score:   -6.1574e-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 7

          **********

No masking
Map Score:   -6.1574e-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 8

          **********

No masking
Map Score:   -6.1574e-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