AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i068_Proline_Biosynthesis_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	proB	287	gamma-glutamate kinase

Motif number 1

AACGGGACTCTCCCGCTGAATATTCGCGCG	1	33	0	TCCCGCTGAA	    0.918732	-255
AGCGGGAGAGTCCCGTTGAAAACAGGAAAG	1	46	1	TCCCGTTGAA	    0.991009	-242
GGCTTGCTGATCCCGCGCAACAAAACGCCA	1	177	1	TCCCGCGCAA	     0.93305	-111
CCGACGACAGTCCTGCTAAAACGTTCGTTT	1	232	1	TCCTGCTAAA	    0.986552	-56
          **********

Masking position 9
Map Score:   6.89324

Number of sites scoring better than the average of aligned sites = 74
Number in coding regions = 62
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 2

CGTTAATTAAAATCAGGAATGAAA      	1	5	0	AATCAGGAAT	    0.977178	-283
GTCCCGTTGAAAACAGGAAAGTTTTTAACC	1	55	1	AAACAGGAAA	    0.963603	-233
GAATATTATTAATCTGTAATATATCTTTAA	1	93	0	AATCTGTAAT	    0.978152	-195
ATATTCTTAAAATGTGGTAATTTATTAAAT	1	117	1	AATGTGGTAA	    0.901339	-171
TAATTTATTAAATCTGTAATAAAAGCGTAA	1	134	1	AATCTGTAAT	    0.978152	-154
ATCTGTAATAAAAGCGTAAACAACTGCCGC	1	145	1	AAAGCGTAAA	    0.881009	-143
          **********

Masking position 2
Map Score:   5.00377

Number of sites scoring better than the average of aligned sites = 498
Number in coding regions = 419
Number in noncoding regions = 79
Number of orfs with sites within 600 bp upstream = 91
Fraction of orfs with sites within 600 bp upstream = 0.0146161


Motif number 3

        TTTCATTCCTGATTTTAATTAA	1	3	1	TCATTCCTGA	     0.96402	-285
TTTCAACGGGACTCTCCCGCTGAATATTCG	1	37	0	ACTCTCCCGC	    0.990225	-251
CAGGTTAAAAACTTTCCTGTTTTCAACGGG	1	57	0	ACTTTCCTGT	    0.986049	-231
GCAACCGACGACAGTCCTGCTAAAACGTTC	1	228	1	ACAGTCCTGC	    0.975718	-60
          **********

Masking position 5
Map Score:   1.5724

Number of sites scoring better than the average of aligned sites = 210
Number in coding regions = 191
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


Motif number 4

TAACCTGAGATTGTTAAAGATATATTACAG	1	80	1	TTGTTAAAGA	    0.968713	-208
TGTTAAAGATATATTACAGATTAATAATAT	1	91	1	ATATTACAGA	     0.98426	-197
GTTTACGCTTTTATTACAGATTTAATAAAT	1	136	0	TTATTACAGA	    0.990763	-152
          **********

Masking position 6
Map Score:   1.29766

Number of sites scoring better than the average of aligned sites = 31
Number in coding regions = 16
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 5

          **********

No masking
Map Score:   2.93755e-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:   2.93755e-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:   2.93755e-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