AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i324_mixed9_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	pspA	151	phage shock protein, inner membrane protein
#2	pspB	53	phage shock protein
#3	pspE	74	phage shock protein
#4	ycjM	185	putative polysaccharide hydrolase
#5	ycjQ	30	putative oxidoreductase

Motif number 1

CAATCCTGAACGCAGAAATCAAGAGGACAA	1	128	1	CGCAGAAATC	    0.952618	-24
CCGAACGCGCCGCCGCTCATCGTCTAAGGA	2	28	1	CGCCGCTCAT	    0.977427	-26
 GGGGAGTTTCGCAAAAATTGTTAAATCTC	3	10	1	CGCAAAAATT	    0.946877	-65
GGCGCATAAGCGCCGCTCATGGTGAATTCT	4	12	0	CGCCGCTCAT	    0.977427	-174
TGTGAGCTGACGCAAATAATCTATGGGGAT	4	70	0	CGCAAATAAT	    0.969199	-116
GTTTTAGTCACGCAGGAAATCATTTTTTAC	4	117	0	CGCAGGAAAT	    0.985436	-69
GAGACTACTCCGCAGAAAATAAACTGTCAA	4	159	0	CGCAGAAAAT	    0.993386	-27
          **********

Masking position 3
Map Score:   8.46786

Number of sites scoring better than the average of aligned sites = 1000
Number in coding regions = 942
Number in noncoding regions = 58
Number of orfs with sites within 600 bp upstream = 63
Fraction of orfs with sites within 600 bp upstream = 0.0101189


Motif number 2

AAATCAAAAAGATAAAAAATTGGCACGCAAATTG	1	75	1	GATAAAAAGC	    0.985814	-77
CCTGAACGCAGAAATCAAGAGGACAACATT    	1	132	1	GAAATAAGGC	     0.98294	-20
AGGTGTGACAGAAAAAAAAACGGCGCATAAGCGC	4	29	0	GAAAAAAAGC	    0.996464	-157
CTATGGGGATGTAAATAAGGTGTGACAGAAAAAA	4	46	0	GTAAAAAGGG	     0.96634	-140
CTACTCCGCAGAAAATAAACTGTCAATTGAGCAC	4	151	0	GAAAAAAAGC	    0.996393	-35
AAAACTCCTTGTAAAGAAACTGGCCGCT      	5	5	0	GTAAAAAAGC	    0.993422	-26
          ***** ***  * *

Masking position 7
Map Score:   7.48562

Number of sites scoring better than the average of aligned sites = 88
Number in coding regions = 68
Number in noncoding regions = 20
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 3

TCAACAGCAACATGCCAGGATGAGTTAGCG	1	25	0	CATGCCAGGA	    0.951728	-127
GTATTAACAGTTCAGCAGGACAATCCTGAA	1	108	1	TTCAGCAGGA	    0.981011	-44
AATTTTCATCCATAGAAGGACGCTTAC   	3	58	1	CATAGAAGGA	    0.904972	-17
     AAGAATTCACCATGAGCGGCGCTTA	4	6	1	TTCACCATGA	    0.939627	-180
GAAATCATTTTTTACCAGGGAAAAAGCGTA	4	102	0	TTTACCAGGG	     0.97796	-84
GGCCAGTTTCTTTACAAGGAGTTTTAA   	5	14	1	TTTACAAGGA	    0.976194	-17
          **********

Masking position 7
Map Score:   2.45679

Number of sites scoring better than the average of aligned sites = 667
Number in coding regions = 570
Number in noncoding regions = 97
Number of orfs with sites within 600 bp upstream = 116
Fraction of orfs with sites within 600 bp upstream = 0.0186315


Motif number 4

TAAATCTCAGGCGTATAATGGATGGCAATTT	3	32	1	GCGTAAATGG	    0.972484	-43
AAAAAAAACGGCGCATAAGCGCCGCTCATGG	4	20	0	GCGCAAAGCG	    0.997396	-166
TTTTTTACCAGGGAAAAAGCGTATTTGTGAG	4	94	0	GGGAAAAGCG	    0.987065	-92
ACTGTCAATTGAGCACAAGGGTTTTAGTCAC	4	136	0	GAGCAAAGGG	     0.99293	-50
          ***** *****

Masking position 5
Map Score:   0.560602

Number of sites scoring better than the average of aligned sites = 109
Number in coding regions = 93
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 5

          **********

No masking
Map Score:   -6.51267e-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:   -6.51267e-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:   -6.51267e-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