AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i226_ecoli_mtub_100.orf -o226_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	glyQ	300	glycine tRNA synthetase, alpha subunit

Motif number 1

ATCCTTGCATAACGCTTCCATATTCAACGAA	1	24	0	AACGCTTCCT	    0.991954	-277
CGCGCATTTCATAGCTTCCCTGGAACTGTTC	1	109	0	ATAGCTTCCT	    0.997388	-192
ATGCGCGGTTATACCTTCCGTAAAGAGCAGT	1	133	1	ATACCTTCCT	    0.997399	-168
TTCGTACTGTATATCTTCCATCCAGCGGGTA	1	234	1	ATATCTTCCT	    0.992933	-67
GGGTATACTGATCCCTTCCTTTAAATCCACA	1	260	1	ATCCCTTCCT	    0.997589	-41
          ********* *

Masking position 6
Map Score:   11.5188

Number of sites scoring better than the average of aligned sites = 48
Number in coding regions = 42
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 2

GAATATGGAAGCGTTATGCAAGGATCAGGC	1	30	1	GCGTTATGCA	    0.983501	-271
CGGTGTTATAACGTTTTGCCGCCTGATCCT	1	50	0	ACGTTTTGCC	    0.993764	-251
GGTGACGTCGATTTTTTGCTCGCCGGTGTT	1	73	0	ATTTTTTGCT	    0.896055	-228
GCGGATGGCCATTTTTTGCATCTTTCCATG	1	181	1	ATTTTTTGCA	    0.938275	-120
ATCTTTCCATGCGTTAAGCCCTGCTTTTTC	1	200	1	GCGTTAAGCC	    0.970096	-101
GTTAAGCCCTGCTTTTTCCCGTTTCGTACT	1	212	1	GCTTTTTCCC	    0.973361	-89
          **********

Masking position 5
Map Score:   4.88962

Number of sites scoring better than the average of aligned sites = 1737
Number in coding regions = 1597
Number in noncoding regions = 140
Number of orfs with sites within 600 bp upstream = 158
Fraction of orfs with sites within 600 bp upstream = 0.0253774


Motif number 3

ATTCAACGAACGCAGAGGATCAA       	1	4	0	CGCAGAGGAT	    0.979162	-297
TTTCCCGTTTCGTACTGTATATCTTCCATC	1	226	1	CGTACTGTAT	    0.981056	-75
GATCAGTATACCCGCTGGATGGAAGATATA	1	243	0	CCCGCTGGAT	    0.994584	-58
   ATTATTTCGTGCTGGATACGTGTGGAT	1	284	0	CGTGCTGGAT	    0.996868	-17
          **********

Masking position 9
Map Score:   2.78338

Number of sites scoring better than the average of aligned sites = 777
Number in coding regions = 747
Number in noncoding regions = 30
Number of orfs with sites within 600 bp upstream = 30
Fraction of orfs with sites within 600 bp upstream = 0.0048185


Motif number 4

CGTCACCGCCTTCGAACAGTTCCAGGGAAG	1	96	1	TTCGAACAGT	     0.98418	-205
TTTTTCCCGTTTCGTACTGTATATCTTCCA	1	224	1	TTCGTACTGT	    0.994754	-77
     ATTATTTCGTGCTGGATACGTGTGG	1	286	0	TTCGTGCTGG	    0.992728	-15
          **********

Masking position 2
Map Score:   1.24351

Number of sites scoring better than the average of aligned sites = 49
Number in coding regions = 44
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 5

CAAGGATCAGGCGGCAAAACGTTATAACAC	1	48	1	GCGGCAAAAC	    0.992633	-253
TATGAAATGCGCGGTTATACCTTCCGTAAA	1	127	1	GCGGTTATAC	     0.99647	-174
CTTCCATCCAGCGGGTATACTGATCCCTTC	1	248	1	GCGGGTATAC	     0.99762	-53
          **********

Masking position 7
Map Score:   2.6404

Number of sites scoring better than the average of aligned sites = 25
Number in coding regions = 21
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 6

TGGAAGCGTTATGCAAGGATCAGGCGGCAA	1	35	1	ATGCAAGGAT	    0.972917	-266
AAGCTATGAAATGCGCGGTTATACCTTCCG	1	123	1	ATGCGCGGTT	      0.9593	-178
ACTGCTCTTTACGGAAGGTATAACCGCGCA	1	134	0	ACGGAAGGTA	    0.948882	-167
GCAGGGCTTAACGCATGGAAAGATGCAAAA	1	194	0	ACGCATGGAA	    0.985842	-107
CGTGCTGGATACGTGTGGATTTAAAGGAAG	1	274	0	ACGTGTGGAT	     0.96506	-27
          **********

Masking position 1
Map Score:   1.52547

Number of sites scoring better than the average of aligned sites = 570
Number in coding regions = 539
Number in noncoding regions = 31
Number of orfs with sites within 600 bp upstream = 33
Fraction of orfs with sites within 600 bp upstream = 0.00530035


Motif number 7

          **********

No masking
Map Score:   7.91135e-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:   7.91135e-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 9

          **********

No masking
Map Score:   7.91135e-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