AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00730_bsub_reg_100.orf -o00730_bsub_100.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.44 -x5 -e 
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 =  	0.44
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	thiD	148	phosphomethylpyrimidine kinase
#2	ywbI	105	alternate gene name: ipa-24d; similar to transcriptional regulator (LysR family)

Motif number 1

AAATGCTACATAAGAAAACTAGGTAGGGGTTTTGA	1	15	0	TAGAACAGTA	    0.991691	-134
TGTATCACAATATATAGAAGATCTATAGGAATCAT	1	75	0	TAAAAAACTA	    0.970887	-74
TATATTGTGATACAGAGAAAATCTAACTATAATGA	1	96	1	TAAAAAACTA	    0.985639	-53
AGAGAGACCTTATGTACAATAAGTATATAAGGGAG	2	19	0	TAGAAAAGTA	    0.990485	-87
GGTCTCTCTATAGGTAAAATATATATTAAGAATAA	2	45	1	TAGAAAAATA	    0.843008	-61
AAATATATATTAAGAATAAGAAGTATTCCTTTTGT	2	61	1	TAGAAAAGTA	    0.997389	-45
TCACCCTTTCTATAGACAAAAGGAATACTTCTTAT	2	76	0	TAAAAAAGAA	    0.975202	-30
          ** * * ** * ***

Masking position 8
Map Score:   12.8994

Number of sites scoring better than the average of aligned sites = 53
Number in coding regions = 31
Number in noncoding regions = 22
Number of orfs with sites within 600 bp upstream = 24
Fraction of orfs with sites within 600 bp upstream = 0.0038548


Motif number 2

TTTCTCTGTATCACAATATATAGAAGATCT	1	86	0	TCACAATATA	    0.935769	-63
ACAGAGAAAATCTAACTATAATGAAAGACA	1	107	1	TCTAACTATA	    0.964853	-42
ATTGATGCCTCCCTTATATACTTATTGTAC	2	11	1	CCCTTATATA	    0.943128	-95
GTACATAAGGTCTCTCTATAGGTAAAATAT	2	37	1	TCTCTCTATA	    0.986787	-69
TACTTCTTATTCTTAATATATATTTTACCT	2	56	0	TCTTAATATA	    0.977857	-50
 GCGCTTCACCCTTTCTATAGACAAAAGGA	2	87	0	CCTTTCTATA	    0.983013	-19
          **********

Masking position 7
Map Score:   6.5583

Number of sites scoring better than the average of aligned sites = 148
Number in coding regions = 103
Number in noncoding regions = 45
Number of orfs with sites within 600 bp upstream = 51
Fraction of orfs with sites within 600 bp upstream = 0.00819146


Motif number 3

GAGATTGTCAAATGATTCCTATAGATCTTC	1	64	1	AATGATTCCT	    0.993057	-85
          ATTGATGCCTCCCTTATATA	2	1	1	ATTGATGCCT	     0.98634	-105
TAAGAATAAGAAGTATTCCTTTTGTCTATA	2	71	1	AAGTATTCCT	    0.968168	-35
          **********

Masking position 5
Map Score:   0.640166

Number of sites scoring better than the average of aligned sites = 87
Number in coding regions = 78
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 4

          **********

No masking
Map Score:   -1.1836e-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:   -1.1836e-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:   -1.1836e-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