AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i226_Glycyl_TRNA_synthase_ecoli_reg_100.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	glyQ	300	glycine tRNA synthetase, alpha subunit

Motif number 1

TTCGTTGAATATGGAAGCGTTATGCAAGGAT	1	24	1	AGGAAGCGTT	    0.992007	-277
GAACAGTTCCAGGGAAGCTATGAAATGCGCG	1	109	1	AGGAAGCTAT	    0.997406	-192
ACTGCTCTTTACGGAAGGTATAACCGCGCAT	1	133	0	AGGAAGGTAT	    0.997417	-168
TACCCGCTGGATGGAAGATATACAGTACGAA	1	234	0	AGGAAGATAT	    0.992982	-67
TGTGGATTTAAAGGAAGGGATCAGTATACCC	1	260	0	AGGAAGGGAT	    0.997606	-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

GCCTGATCCTTGCATAACGCTTCCATATTC	1	30	0	TGCATAACGC	    0.984708	-271
AGGATCAGGCGGCAAAACGTTATAACACCG	1	50	1	GGCAAAACGT	    0.994225	-251
AACACCGGCGAGCAAAAAATCGACGTCACC	1	73	1	AGCAAAAAAT	    0.903031	-228
CATGGAAAGATGCAAAAAATGGCCATCCGC	1	181	0	TGCAAAAAAT	    0.942599	-120
GAAAAAGCAGGGCTTAACGCATGGAAAGAT	1	200	0	GGCTTAACGC	    0.972164	-101
AGTACGAAACGGGAAAAAGCAGGGCTTAAC	1	212	0	GGGAAAAAGC	    0.975291	-89
          **********

Masking position 6
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	    0.980943	-297
TTTCCCGTTTCGTACTGTATATCTTCCATC	1	226	1	CGTACTGTAT	    0.982678	-75
GATCAGTATACCCGCTGGATGGAAGATATA	1	243	0	CCCGCTGGAT	    0.995054	-58
   ATTATTTCGTGCTGGATACGTGTGGAT	1	284	0	CGTGCTGGAT	     0.99714	-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

TCCATATTCAACGAACGCAGAGGATCAA    	1	7	0	ACAAGCAGAG	    0.943725	-294
GGAAGCGTTATGCAAGGATCAGGCGGCAAAAC	1	36	1	TGAAGATCAG	    0.966959	-265
CTGGAACTGTTCGAAGGCGGTGACGTCGATTT	1	89	0	TCAAGCGGTG	    0.970142	-212
AGGGAAGCTATGAAATGCGCGGTTATACCTTC	1	119	1	TGAAGCGCGG	    0.991483	-182
TTATACCTTCCGTAAAGAGCAGTTTGTCTGTT	1	141	1	CGAAGAGCAG	     0.97702	-160
GCCATCCGCGTCAAAAGAACAGACAAACTGCT	1	158	0	TCAAGAACAG	    0.986657	-143
ACGTGTGGATTTAAAGGAAGGGATCAGTATAC	1	262	0	TTAAGAAGGG	    0.921552	-39
          ** ** ******

Masking position 5
Map Score:   2.99161

Number of sites scoring better than the average of aligned sites = 597
Number in coding regions = 540
Number in noncoding regions = 57
Number of orfs with sites within 600 bp upstream = 67
Fraction of orfs with sites within 600 bp upstream = 0.0107613


Motif number 5

CAAGGATCAGGCGGCAAAACGTTATAACAC	1	48	1	GCGGCAAAAC	    0.992313	-253
TATGAAATGCGCGGTTATACCTTCCGTAAA	1	127	1	GCGGTTATAC	    0.996317	-174
CTTCCATCCAGCGGGTATACTGATCCCTTC	1	248	1	GCGGGTATAC	    0.997516	-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

TTCCCTGGAACTGTTCGAAGGCGGTGACGT	1	95	0	CTGTTCGAAG	    0.975363	-206
ACAAACTGCTCTTTACGGAAGGTATAACCG	1	138	0	CTTTACGGAA	    0.962171	-163
GGAAGATATACAGTACGAAACGGGAAAAAG	1	223	0	CAGTACGAAA	    0.994233	-78
CACACGTATCCAGCACGAAATAAT      	1	287	1	CAGCACGAAA	     0.99019	-14
          **********

Masking position 9
Map Score:   2.1866

Number of sites scoring better than the average of aligned sites = 154
Number in coding regions = 144
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


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