AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i118_ecoli_bsub_300.orf -o118_ecoli_bsub_300.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.47 -x5 -e 
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 =  	0.47
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

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	secF	125	protein-export membrane protein
#6	yrvB	38	yrvB
#7	yrzD	115	yrzD

Motif number 1

CCCTTTTGGATAGAATATAATCG          	1	1	0	TAGAATATCG	    0.877301	-92
AAGAGGCGGGTAGTCTAGTGCCGGGGCGCTCTC	1	49	0	TAGTAGGCCG	    0.993838	-44
GACTCAGACTAAAATAAGAGGCGGGTAGTCTAG	1	64	0	AAAAAGGGCG	     0.97848	-29
TCCAACGTTTTAAACCAGCGCCGCGGAA     	2	6	0	TAAAAGGCCG	    0.993907	-50
CGTTTTCGACTAGATCAGCACCGT         	5	2	0	TAGAAGACCG	    0.993907	-124
TATCATAAGTTTGTTTAGCGCCGTTTTCGACTA	5	23	0	TTGTAGGCCG	    0.966561	-103
TCACTTCACCAAATTTATCAGCGTCTTTCAGCT	5	86	0	AAATATAGCG	    0.803422	-40
TGAAAAACAATAAAAAAGGAGCGTGGAATTC  	7	95	1	TAAAAGAGCG	     0.98739	-21
          ****  ** ****

Masking position 7
Map Score:   8.39216

Number of sites scoring better than the average of aligned sites = 400
Number in coding regions = 352
Number in noncoding regions = 48
Number of orfs with sites within 600 bp upstream = 53
Fraction of orfs with sites within 600 bp upstream = 0.00851269


Motif number 2

CCGGGGCGCTCTCCCTGCAACCTTTACCCC	1	32	0	CTCCCTGCAA	    0.989681	-61
GCAGGGAGAGCGCCCCGGCACTAGACTACC	1	44	1	CGCCCCGGCA	    0.990213	-49
CGGCACTAGACTACCCGCCTCTTATTTTAG	1	59	1	CTACCCGCCT	    0.983285	-34
TTTAAACCAGCGCCGCGGAA          	2	1	0	CGCCGCGGAA	    0.898826	-55
TATGTATATCCTCCCTTAAACCTGTGCGAA	6	19	0	CTCCCTTAAA	    0.807951	-20
     TTTTACCCCCTGCCTTCTCAAACTA	7	6	1	CCCCCTGCCT	    0.987449	-110
CCTTCTCAAACTACCTGGAATCATATACAA	7	23	1	CTACCTGGAA	    0.966164	-93
     GAATTCCACGCTCCTTTTTTATTGT	7	101	0	CCACGCTCCT	     0.79788	-15
          **********

Masking position 4
Map Score:   7.03465

Number of sites scoring better than the average of aligned sites = 2444
Number in coding regions = 2218
Number in noncoding regions = 226
Number of orfs with sites within 600 bp upstream = 218
Fraction of orfs with sites within 600 bp upstream = 0.0350145


Motif number 3

TTATATTCTATCCAAAAGGGGGTAAAGGTT	1	14	1	TCCAAAAGGG	    0.993129	-79
TTAAAATTTTTCCCTAAGGGAATTGCC   	4	11	1	TCCCTAAGGG	    0.986785	-17
GCTGATCTAGTCGAAAACGGCGCTAAACAA	5	16	1	TCGAAAACGG	    0.982304	-110
 CAGGTTGATTCGCACAGGTTTAAGGGAGG	6	10	1	TCGCACAGGT	    0.971529	-29
          **********

Masking position 7
Map Score:   0.931113

Number of sites scoring better than the average of aligned sites = 83
Number in coding regions = 67
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 4

AACGTTGGACTGTTTTTCTGACGTAGTGGA	2	30	1	TGTTTTTCTG	    0.965898	-26
TTGGCTCATTTGTTGTGCTATCATAAGTTT	5	44	0	TGTTGTGCTA	    0.943227	-82
AATTTATCAGCGTCTTTCAGCTTAATCGTG	5	78	0	CGTCTTTCAG	    0.951775	-48
TATGCGTATATGTCGTCCAAGCATGACAAG	7	59	1	TGTCGTCCAA	    0.962545	-57
CCTTTTTTATTGTTTTTCAAGAAGACTTGT	7	84	0	TGTTTTTCAA	     0.97409	-32
          **********

Masking position 6
Map Score:   0.0741986

Number of sites scoring better than the average of aligned sites = 381
Number in coding regions = 341
Number in noncoding regions = 40
Number of orfs with sites within 600 bp upstream = 49
Fraction of orfs with sites within 600 bp upstream = 0.00787022


Motif number 5

          **********

No masking
Map Score:   -5.51791e-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:   -5.51791e-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:   -5.51791e-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