AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i068_Proline_Biosynthesis_ecoli_reg_300.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	     0.91378	-255
AGCGGGAGAGTCCCGTTGAAAACAGGAAAG	1	46	1	TCCCGTTGAA	    0.991017	-242
GGCTTGCTGATCCCGCGCAACAAAACGCCA	1	177	1	TCCCGCGCAA	    0.929155	-111
CCGACGACAGTCCTGCTAAAACGTTCGTTT	1	232	1	TCCTGCTAAA	    0.987387	-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

      TTTCATTCCTGATTTTAATTAACG	1	5	1	ATTCCTGATT	    0.977415	-283
GGTTAAAAACTTTCCTGTTTTCAACGGGAC	1	55	0	TTTCCTGTTT	    0.964111	-233
TTAAAGATATATTACAGATTAATAATATTC	1	93	1	ATTACAGATT	    0.978458	-195
ATTTAATAAATTACCACATTTTAAGAATAT	1	117	0	TTACCACATT	     0.90263	-171
TTACGCTTTTATTACAGATTTAATAAATTA	1	134	0	ATTACAGATT	    0.978458	-154
GCGGCAGTTGTTTACGCTTTTATTACAGAT	1	145	0	TTTACGCTTT	    0.882531	-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

ATTCGCGCGTTAATTAAAATCAGGAATGAAA  	1	9	0	TTTAAATCAG	    0.911563	-279
AACAGGAAAGTTTTTAACCTGAGATTGTTAAAG	1	66	1	TTTAACTGAG	    0.986051	-222
AACCTGAGATTGTTAAAGATATATTACAGATTA	1	81	1	TTAAAATATA	    0.852049	-207
TTTAAGAATATTATTAATCTGTAATATATCTTT	1	95	0	TTTAACTGTA	    0.987043	-193
ATTAATAATATTCTTAAAATGTGGTAATTTATT	1	110	1	TTTAAATGTG	    0.983198	-178
TGTGGTAATTTATTAAATCTGTAATAAAAGCGT	1	129	1	TTAAACTGTA	    0.983187	-159
ATATCATTTTTCCTAAAATTGAATGGCAGAGAA	1	263	1	TTAAATTGAA	    0.918794	-25
          *  **** *****

Masking position 7
Map Score:   3.68177

Number of sites scoring better than the average of aligned sites = 213
Number in coding regions = 158
Number in noncoding regions = 55
Number of orfs with sites within 600 bp upstream = 60
Fraction of orfs with sites within 600 bp upstream = 0.00963701


Motif number 4

       TTTCATTCCTGATTTTAATTAAC	1	4	1	CATTCCTGAT	    0.961037	-284
TTCAACGGGACTCTCCCGCTGAATATTCGC	1	36	0	CTCTCCCGCT	    0.997126	-252
AGGTTAAAAACTTTCCTGTTTTCAACGGGA	1	56	0	CTTTCCTGTT	    0.977525	-232
AAGCGTAAACAACTGCCGCTAGGCTTGCTG	1	156	1	AACTGCCGCT	    0.962337	-132
CAACCGACGACAGTCCTGCTAAAACGTTCG	1	229	1	CAGTCCTGCT	    0.988007	-59
      GATTCTCTGCCATTCAATTTTAGG	1	274	0	CTCTGCCATT	    0.925303	-14
          **********

Masking position 4
Map Score:   4.94143

Number of sites scoring better than the average of aligned sites = 908
Number in coding regions = 798
Number in noncoding regions = 110
Number of orfs with sites within 600 bp upstream = 122
Fraction of orfs with sites within 600 bp upstream = 0.0195952


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