AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i279_hypothetical4_bsub_reg_300.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
#2	ywbI	105	alternate gene name: ipa-24d; similar to transcriptional regulator (LysR family)

Motif number 1

ACAGCCCTTTGAAGGAAAATGAACGA    	1	7	0	GAAGGAAAAT	    0.913522	-150
ATTTTCCTTCAAAGGGCTGTTCTGTAAAAG	1	17	1	AAAGGGCTGT	    0.970387	-140
CTGTTCTGTAAAAGGACAGCTTTTTTGCTG	1	33	1	AAAGGACAGC	    0.996185	-124
TGAAAACCTTGATGGACAGCAAAAAAGCTG	1	49	0	GATGGACAGC	    0.985007	-108
ATTAAAATTTGAAGGTCTGAAAACCTTGAT	1	66	0	GAAGGTCTGA	    0.938438	-91
TTTAATTGACAAAGGACAGGAACTGGCTAT	1	90	1	AAAGGACAGG	    0.989977	-67
TCTATAGACAAAAGGAATACTTCTTATTCT	2	73	0	AAAGGAATAC	    0.938024	-33
          **********

Masking position 2
Map Score:   7.97818

Number of sites scoring better than the average of aligned sites = 1102
Number in coding regions = 933
Number in noncoding regions = 169
Number of orfs with sites within 600 bp upstream = 126
Fraction of orfs with sites within 600 bp upstream = 0.0202377


Motif number 2

AGGGCTGTTCTGTAAAAGGACAGCTTTTTT	1	29	1	TGTAAAAGGA	    0.921195	-128
ATGATTATGTTATACAATGATAATCATTTT	1	118	1	TATACAATGA	    0.934088	-39
CATTTTCAATTATAGGAGGAACATG     	1	142	1	TATAGGAGGA	    0.982203	-15
GTACAATAAGTATATAAGGGAGGCATCAAT	2	11	0	TATATAAGGG	    0.978298	-95
ATATTTTACCTATAGAGAGACCTTATGTAC	2	37	0	TATAGAGAGA	    0.967246	-69
AGGTAAAATATATATTAAGAATAAGAAGTA	2	56	1	TATATTAAGA	    0.913063	-50
TCCTTTTGTCTATAGAAAGGGTGAAGCGC 	2	87	1	TATAGAAAGG	    0.984754	-19
          **********

Masking position 4
Map Score:   6.2718

Number of sites scoring better than the average of aligned sites = 368
Number in coding regions = 263
Number in noncoding regions = 105
Number of orfs with sites within 600 bp upstream = 121
Fraction of orfs with sites within 600 bp upstream = 0.0194346


Motif number 3

GTCCTTTTACAGAACAGCCCTTTGAAGGAA	1	20	0	AGAACAGCCC	    0.982423	-137
GTTCTGTAAAAGGACAGCTTTTTTGCTGTC	1	35	1	AGGACAGCTT	    0.990138	-122
AAAACCTTGATGGACAGCAAAAAAGCTGTC	1	47	0	TGGACAGCAA	     0.99198	-110
TAATTGACAAAGGACAGGAACTGGCTATGA	1	92	1	AGGACAGGAA	    0.991546	-65
          **********

Masking position 6
Map Score:   2.67966

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 4

TGTCCTTTGTCAATTAAAATTTGAAGGTCT	1	78	0	CAATTAAAAT	    0.932492	-79
CAGGAACTGGCTATGATTATGTTATACAAT	1	106	1	CTATGATTAT	    0.963321	-51
TTATGTTATACAATGATAATCATTTTCAAT	1	122	1	CAATGATAAT	    0.985191	-35
ACCTTATGTACAATAAGTATATAAGGGAGG	2	18	0	CAATAAGTAT	    0.953484	-88
          **********

Masking position 6
Map Score:   0.650095

Number of sites scoring better than the average of aligned sites = 140
Number in coding regions = 117
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 27
Fraction of orfs with sites within 600 bp upstream = 0.00433665


Motif number 5

          **********

No masking
Map Score:   3.22176e-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:   3.22176e-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:   3.22176e-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