AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i118_ecoli_mtub_100.orf -o118_ecoli_mtub_100.ace -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.58 -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 =  	0.58
 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	secD	109	secD

Motif number 1

CCGGGGCGCTCTCCCTGCAACCTTTACCCC	1	32	0	CTCCCTGCAA	    0.959261	-61
GCAGGGAGAGCGCCCCGGCACTAGACTACC	1	44	1	CGCCCCGGCA	     0.58084	-49
CGGCACTAGACTACCCGCCTCTTATTTTAG	1	59	1	CTACCCGCCT	    0.971684	-34
TTTAAACCAGCGCCGCGGAA          	2	1	0	CGCCGCGGAA	    0.548343	-55
      CCGGCAACCGGCCGACCGGAACCG	5	5	1	CAACCGGCCG	    0.914032	-105
CGACCGGAACCGACGAGCCGCTTGCGCGAC	5	23	1	CGACGAGCCG	    0.811783	-87
CGCCGGGGCGCGTCGCGCAAGCGGCTCGTC	5	34	0	CGTCGCGCAA	    0.960843	-76
TTGCGCGACGCGCCCCGGCGCGACACGTAG	5	44	1	CGCCCCGGCG	    0.501634	-66
CCGACAGAGCCTACGTGTCGCGCCGGGGCG	5	54	0	CTACGTGTCG	    0.590028	-56
          **********

Masking position 4
Map Score:   14.7855

Number of sites scoring better than the average of aligned sites = 4002
Number in coding regions = 3803
Number in noncoding regions = 199
Number of orfs with sites within 600 bp upstream = 184
Fraction of orfs with sites within 600 bp upstream = 0.0295535


Motif number 2

TTACCCCCTTTTGGATAGAATATAATCG  	1	9	0	TTGGATAGAA	    0.889731	-84
CTATCCAAAAGGGGGTAAAGGTTGCAGGGA	1	21	1	GGGGGTAAAG	     0.98383	-72
GGTAAAGGTTGCAGGGAGAGCGCCCCGGCA	1	34	1	GCAGGGAGAG	    0.954268	-59
TTCTGACGTAGTGGAGAAAAA         	2	45	1	GTGGAGAAAA	    0.964465	-11
 TATTAATAATGAGGGAAATTTA       	3	10	1	TGAGGGAAAT	    0.897109	-13
GGCAATTCCCTTAGGGAAAAATTTTAA   	4	8	0	TTAGGGAAAA	    0.944787	-20
AGGCTCTGTCGGGGGTAGAAAACTGATTCT	5	72	1	GGGGGTAGAA	    0.990924	-38
TGATTCTCGAGGAGATACAAGGAAC     	5	95	1	GGAGATACAA	    0.909399	-15
          **********

Masking position 7
Map Score:   6.64286

Number of sites scoring better than the average of aligned sites = 1519
Number in coding regions = 1224
Number in noncoding regions = 295
Number of orfs with sites within 600 bp upstream = 254
Fraction of orfs with sites within 600 bp upstream = 0.0407967


Motif number 3

GAGGCGGGTAGTCTAGTGCCGGGGCGCTCTCC	1	48	0	GTTAGGCCGG	    0.986047	-45
CTCTTATTTTAGTCTGAGTCAGTGTC      	1	77	1	AGCTGGTCAG	    0.959805	-16
GCGGCTCGTCGGTTCCGGTCGGCCGGTTGCCG	5	12	0	GGTCCGTCGG	    0.996392	-98
CAGAGCCTACGTGTCGCGCCGGGGCGCGTCGC	5	48	0	GTTCGGCCGG	    0.994752	-62
CGCGACACGTAGGCTCTGTCGGGGGTAGAAAA	5	62	1	AGCTCGTCGG	    0.988446	-48
          ** *** *****

Masking position 8
Map Score:   0.604643

Number of sites scoring better than the average of aligned sites = 756
Number in coding regions = 718
Number in noncoding regions = 38
Number of orfs with sites within 600 bp upstream = 31
Fraction of orfs with sites within 600 bp upstream = 0.00497912


Motif number 4

          **********

No masking
Map Score:   -5.44113e-14

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:   -5.44113e-14

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:   -5.44113e-14

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