AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i118_SecDF_ecoli_hinf_reg_100.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 =  	0.46
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	queA	92	synthesis of queuine in tRNA; probably S-adenosylmethionine:tRNA ribosyltransferase-isomerase
#2	tgt	55	tRNA-guanine transglycosylase
#3	yajC	22	orf, hypothetical protein
#4	secD	27	protein secretion; membrane protein, part of the channel
#5	HI0240	69	protein-export membrane protein (secD)
#6	HI0241	107	conserved hypothetical protein

Motif number 1

GTTGCAGGGAGAGCGCCCCGGCACTAGACT	1	41	1	GAGCGCCCCG	    0.996948	-52
CGTTTTAAACCAGCGCCGCGGAA       	2	4	0	CAGCGCCGCG	    0.998477	-52
AATTATTTTCCAGAGCCACGCATTGTGGCT	5	22	1	CAGAGCCACG	    0.998245	-48
TTCTAACGCACAGAGCCACAATGCGTGGCT	5	35	0	CAGAGCCACA	    0.995979	-35
          **********

Masking position 2
Map Score:   8.33706

Number of sites scoring better than the average of aligned sites = 257
Number in coding regions = 250
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 2

TTCTCCACTACGTCAGAAAAACAGTCCAACG	2	32	0	CGTAGAAAAA	    0.976328	-24
TTTCTGACGTAGTGGAGAAAAA         	2	44	1	AGTGAGAAAA	    0.919787	-12
   TATTAATAATGAGGGAAATTTA      	3	8	1	AATAGGGAAA	    0.934748	-15
 GGCAATTCCCTTAGGGAAAAATTTTAA   	4	8	0	CTTGGGAAAA	    0.978699	-20
TGGCTCTGTGCGTTAGAAAAGAAAAGGAAAA	5	47	1	CGTAGAAAAG	    0.965138	-23
TAAATTGCTTCATTGGGAAAGGCGAACTAAG	6	40	0	CATGGGAAAG	    0.987277	-68
AACTTAAATTAATAAGGAAAACACA      	6	93	1	AATAGGAAAA	    0.978972	-15
          *** *******

Masking position 9
Map Score:   5.60381

Number of sites scoring better than the average of aligned sites = 707
Number in coding regions = 621
Number in noncoding regions = 86
Number of orfs with sites within 600 bp upstream = 104
Fraction of orfs with sites within 600 bp upstream = 0.0167041


Motif number 3

CGGGGCGCTCTCCCTGCAACCTTTACCCCC	1	31	0	TCCCTGCAAC	    0.961361	-62
CAGGGAGAGCGCCCCGGCACTAGACTACCC	1	45	1	GCCCCGGCAC	    0.979435	-48
GGCACTAGACTACCCGCCTCTTATTTTAGT	1	60	1	TACCCGCCTC	    0.984625	-33
         TTCCGCGGCGCTGGTTTAAAA	2	2	1	TCCGCGGCGC	    0.989333	-54
AGAGCCACAATGCGTGGCTCTGGAAAATAA	5	24	0	TGCGTGGCTC	     0.97977	-46
          **********

Masking position 6
Map Score:   2.69884

Number of sites scoring better than the average of aligned sites = 926
Number in coding regions = 871
Number in noncoding regions = 55
Number of orfs with sites within 600 bp upstream = 49
Fraction of orfs with sites within 600 bp upstream = 0.00787022


Motif number 4

TCTGGAAAATAATTTAATGTTATTC     	5	6	0	AATTTAATGT	    0.947737	-64
CCAATGAAGCAATTTATGGTATTTTACGCA	6	55	1	AATTTATGGT	    0.980016	-53
TTTCCTTATTAATTTAAGTTAAAAATTTTG	6	83	0	AATTTAAGTT	    0.793296	-25
          **********

Masking position 6
Map Score:   0.446433

Number of sites scoring better than the average of aligned sites = 15
Number in coding regions = 11
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 5

ATTATATTCTATCCAAAAGGGGGTAAAGGT	1	13	1	ATCCAAAAGG	    0.958687	-80
     TTTTTCTCCACTACGTCAGAAAAAC	2	41	0	CTCCACTACG	    0.986162	-15
TAACGCACAGAGCCACAATGCGTGGCTCTG	5	32	0	AGCCACAATG	    0.985087	-38
   AATTAATCGCCATAACGTAGGATATTG	6	8	1	CGCCATAACG	    0.988911	-100
          **********

Masking position 5
Map Score:   0.349751

Number of sites scoring better than the average of aligned sites = 443
Number in coding regions = 418
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 29
Fraction of orfs with sites within 600 bp upstream = 0.00465789


Motif number 6

          **********

No masking
Map Score:   -6.29951e-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:   -6.29951e-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:   -6.29951e-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