AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i326_not_clear1_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	lsp	102	signal peptidase II
#2	yqfP	122	similar to penicillin tolerance

Motif number 1

CCTGATATTTCTTTACTCCAGTGCTTTTTA	1	33	1	CTTTACTCCA	    0.997222	-70
TTTACGGTTACTTTAATCCATTATGCATTT	1	69	0	CTTTAATCCA	    0.991823	-34
       AAACGTTCCTCCAGTTTACGGTT	1	90	0	CGTTCCTCCA	    0.992596	-13
ATATAAAAAGCCGTAATCAAACGGCTCTAT	2	66	0	CCGTAATCAA	    0.938679	-57
TTTATATTGCCTTTACTCACTTCAGTATTG	2	89	1	CTTTACTCAC	    0.977951	-34
    TTTCGGTTGTCCTCCAATACTGAAGT	2	107	0	TTGTCCTCCA	    0.974417	-16
          **********

Masking position 4
Map Score:   8.26563

Number of sites scoring better than the average of aligned sites = 370
Number in coding regions = 322
Number in noncoding regions = 48
Number of orfs with sites within 600 bp upstream = 54
Fraction of orfs with sites within 600 bp upstream = 0.00867331


Motif number 2

AGAAATATCAGGCATATTAACCGGACAGAC	1	15	0	GGCATATTAA	     0.96985	-88
TTTACTCCAGTGCTTTTTATTGATAAAATG	1	44	1	TGCTTTTTAT	    0.992537	-59
TAATCCATTATGCATTTTATCAATAAAAAG	1	56	0	TGCATTTTAT	    0.992535	-47
GTTTGATTACGGCTTTTTATATTGCCTTTA	2	74	1	GGCTTTTTAT	    0.995163	-49
          **********

Masking position 5
Map Score:   6.0689

Number of sites scoring better than the average of aligned sites = 141
Number in coding regions = 106
Number in noncoding regions = 35
Number of orfs with sites within 600 bp upstream = 34
Fraction of orfs with sites within 600 bp upstream = 0.00546097


Motif number 3

TATAGCCAATCTCACTTAAGATATCAAAGA	2	14	0	CTCACTTAAG	    0.969872	-109
TTCTTCTGATCTCATTATAGCCAATCTCAC	2	29	0	CTCATTATAG	    0.977872	-94
ATTGCCTTTACTCACTTCAGTATTGGAGGA	2	94	1	CTCACTTCAG	     0.97118	-29
          **********

Masking position 4
Map Score:   2.44789

Number of sites scoring better than the average of aligned sites = 14
Number in coding regions = 12
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 4

ATATTTCTTTACTCCAGTGCTTTTTATTGA	1	37	1	ACTCCAGTGC	    0.992534	-66
CGGTTACTTTAATCCATTATGCATTTTATC	1	65	0	AATCCATTAT	    0.906494	-38
   AAACGTTCCTCCAGTTTACGGTTACTT	1	86	0	CCTCCAGTTT	    0.989216	-17
TTTCGGTTGTCCTCCAATACTGAAGTGAGT	2	103	0	CCTCCAATAC	    0.989266	-20
          **********

Masking position 6
Map Score:   1.30053

Number of sites scoring better than the average of aligned sites = 223
Number in coding regions = 161
Number in noncoding regions = 62
Number of orfs with sites within 600 bp upstream = 59
Fraction of orfs with sites within 600 bp upstream = 0.00947639


Motif number 5

          **********

No masking
Map Score:   3.08538e-14

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:   3.08538e-14

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:   3.08538e-14

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