AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i279_hypothetical4_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	ywbL	156	alternate gene name: ipa-27d; similar to hypothetical proteins

Motif number 1

TCATTTTCCTTCAAAGGGCTGTTCTGTAAAA	1	15	1	TAAAGGGCTG	    0.996494	-142
GGCTGTTCTGTAAAAGGACAGCTTTTTTGCT	1	31	1	TAAAGGACAG	    0.998562	-126
TCTGAAAACCTTGATGGACAGCAAAAAAGCT	1	50	0	TGATGGACAG	    0.995626	-107
CAATTAAAATTTGAAGGTCTGAAAACCTTGA	1	67	0	TGAAGGTCTG	    0.995118	-90
ATTTTAATTGACAAAGGACAGGAACTGGCTA	1	88	1	AAAAGGACAG	    0.995284	-69
          * *********

Masking position 4
Map Score:   10.436

Number of sites scoring better than the average of aligned sites = 117
Number in coding regions = 104
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 2

TTCCTTCAAAGGGCTGTTCTGTAAAAGGAC	1	20	1	GGGCTGTTCT	     0.99011	-137
GACAGCAAAAAAGCTGTCCTTTTACAGAAC	1	35	0	AAGCTGTCCT	    0.994387	-122
GACAGCTTTTTTGCTGTCCATCAAGGTTTT	1	47	1	TTGCTGTCCA	    0.995449	-110
TCATAGCCAGTTCCTGTCCTTTGTCAATTA	1	92	0	TTCCTGTCCT	    0.995266	-65
          **********

Masking position 5
Map Score:   4.786

Number of sites scoring better than the average of aligned sites = 193
Number in coding regions = 169
Number in noncoding regions = 24
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 3

    TCGTTCATTTTCCTTCAAAGGGCTGT	1	7	1	ATTTTCCTTC	    0.971622	-150
AGACCTTCAAATTTTAATTGACAAAGGACA	1	78	1	ATTTTAATTG	    0.974115	-79
ATTGTATAACATAATCATAGCCAGTTCCTG	1	106	0	ATAATCATAG	    0.929062	-51
ATTGAAAATGATTATCATTGTATAACATAA	1	122	0	ATTATCATTG	    0.993013	-35
AATGATAATCATTTTCAATTATAGGAGGAA	1	133	1	ATTTTCAATT	     0.93683	-24
          **********

Masking position 5
Map Score:   3.00368

Number of sites scoring better than the average of aligned sites = 1138
Number in coding regions = 980
Number in noncoding regions = 158
Number of orfs with sites within 600 bp upstream = 178
Fraction of orfs with sites within 600 bp upstream = 0.0285898


Motif number 4

          **********

No masking
Map Score:   -2.03625e-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 5

          **********

No masking
Map Score:   -2.03625e-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:   -2.03625e-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