AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i343_weak4_bsub_reg_100.orf -aORF_bsub.txt -zbsub.fna -g0.435 -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 =  	0.435
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	gbsA	198	glycine betaine aldehyde dehydrogenase
#2	ywiA	133	similar to hypothetical proteins

Motif number 1

CTGACCCTCTTTTCCTTTAGAAAATTAAATT	1	12	1	TTTCTTTAGA	    0.985398	-187
AGAAAATTAAATTCGTTAAGTTATTTCTTTA	1	30	1	ATTCTTAAGT	    0.904862	-169
CGTTAAGTTATTTCTTTATGTTCTTTATCTT	1	43	1	TTTCTTATGT	    0.961158	-156
TTTCCTCATGTTTCGTTAAGATAAAGAACAT	1	60	0	TTTCTTAAGA	    0.993344	-139
CATTTTGATTTTTCTTTTTGACTTTTCCTCA	1	83	0	TTTCTTTTGA	    0.961157	-116
ACATTAAATTTTTATTTAACAAACTTTATTT	1	161	1	TTTATTAACA	    0.924495	-38
TTTAACAAACTTTATTTACGTCAAGGAGGCT	1	175	1	TTTATTACGT	    0.898743	-24
AAAATTGTAATTTACTTAAAAAGGGCATAGT	2	39	0	TTTATTAAAA	    0.953708	-95
AGAGGTAGATTTTAGTTAAAAATTGTAATTT	2	57	0	TTTATTAAAA	    0.953708	-77
CACAACCGTTTTTCATTTGAATCATATGTAT	2	100	1	TTTCTTTGAA	    0.871369	-34
          **** ******

Masking position 6
Map Score:   13.3802

Number of sites scoring better than the average of aligned sites = 995
Number in coding regions = 831
Number in noncoding regions = 164
Number of orfs with sites within 600 bp upstream = 180
Fraction of orfs with sites within 600 bp upstream = 0.028911


Motif number 2

          ACTGACCCTCTTTTCCTTTAGAA	1	1	1	ACTACCCTTT	     0.97321	-198
TTTCTTTTTGACTTTTCCTCATGTTTCGTTAAG	1	71	0	ACTTCCCATG	     0.96284	-128
TTAAACTGTCAAAGTCCCATTTTGATTTTTCTT	1	98	0	AAATCCTTTT	    0.962325	-101
TAACAACCTTAATCTAACATATGGTTTTTAAAC	1	125	0	AATTACTATG	      0.7286	-74
GTTGTTAAAAACATTAAATTTTTATTTAACAAA	1	151	1	ACATAATTTT	    0.789607	-48
TAGTAGAATGACTATGCCCTTTTGGGAGATCC 	2	10	0	ACTTCCTTTT	    0.994206	-124
TAGTCATTCTACTATGCCCTTTTTAAGTAAATT	2	29	1	ACTTCCTTTT	    0.994206	-105
CTTTTTAAGTAAATTACAATTTTTAACTAAAAT	2	47	1	AAATCATTTT	    0.901483	-87
TTTTAACTAAAATCTACCTCTTGGATATACATA	2	67	1	AATTCCCTTG	    0.975475	-67
GGATATACATACACAACCGTTTTTCATTTGAAT	2	89	1	ACAACCTTTT	    0.972153	-45
          *** * ** ****

Masking position 12
Map Score:   12.5562

Number of sites scoring better than the average of aligned sites = 1369
Number in coding regions = 1149
Number in noncoding regions = 220
Number of orfs with sites within 600 bp upstream = 239
Fraction of orfs with sites within 600 bp upstream = 0.0383874


Motif number 3

TAGTAGAATGACTATGCCCTTTTGGGAGAT	2	13	0	ACTATGCCCT	    0.998415	-121
TAGTCATTCTACTATGCCCTTTTTAAGTAA	2	29	1	ACTATGCCCT	    0.998415	-105
       AATACCATCCCCTATACATATGA	2	121	0	ACCATCCCCT	    0.996537	-13
          **********

Masking position 4
Map Score:   5.42894

Number of sites scoring better than the average of aligned sites = 7
Number in coding regions = 2
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 4

TTAAATTCGTTAAGTTATTTCTTTATGTTC	1	36	1	TAAGTTATTT	    0.943463	-163
GTTATTTCTTTATGTTCTTTATCTTAACGA	1	49	1	TATGTTCTTT	    0.930009	-150
TAATCTAACATATGGTTTTTAAACTGTCAA	1	119	0	TATGGTTTTT	     0.97892	-80
TATGTTAGATTAAGGTTGTTAAAAACATTA	1	137	1	TAAGGTTGTT	    0.986269	-62
AATAAAAATTTAATGTTTTTAACAACCTTA	1	147	0	TAATGTTTTT	    0.930555	-52
TGACGTAAATAAAGTTTGTTAAATAAAAAT	1	168	0	AAAGTTTGTT	    0.918445	-31
          **********

Masking position 6
Map Score:   4.99919

Number of sites scoring better than the average of aligned sites = 335
Number in coding regions = 234
Number in noncoding regions = 101
Number of orfs with sites within 600 bp upstream = 107
Fraction of orfs with sites within 600 bp upstream = 0.017186


Motif number 5

          **********

No masking
Map Score:   -2.46258e-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:   -2.46258e-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:   -2.46258e-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