AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i064_Histidine_Biosynthesis_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	hisZ	250	histidyl-tRNA synthetase

Motif number 1

          CTTTATCTCCTTGTTCTCTATT	1	1	1	CTTTACTCTT	    0.980819	-250
TCTCCTTGTTCTCTATTTGATTTGTATTATAG	1	16	1	CTCTATTGTT	    0.939555	-235
TACGTAATATCTCAAATTCTTTATGTTTGGCA	1	50	0	CTCAATTCTT	    0.971269	-201
TATTACGTACCTTTAATACATTATTCATGATT	1	73	1	CTTTATACTT	    0.971832	-178
GTAAGGATATTTTTAGTTCAAATATCCTTCTC	1	118	0	TTTTATTCAA	    0.823849	-133
AAAATCAACGCTTAACTTCAGTAAGGATATTT	1	138	0	CTTAATTCGT	    0.955118	-113
TAAGCGTTGATTTTCATTCTTTCATCTGCTAA	1	156	1	TTTTCTTCTT	     0.97227	-95
ATTCCGAATCCTTTAGTTCGCTAATATGATAA	1	192	0	CTTTATTCCT	    0.985368	-59
GGATTCGGAATTTTCCTTCATAAGATAACAGC	1	213	1	TTTTCTTCTA	    0.917216	-38
          ***** *** **

Masking position 2
Map Score:   7.09854

Number of sites scoring better than the average of aligned sites = 1182
Number in coding regions = 966
Number in noncoding regions = 216
Number of orfs with sites within 600 bp upstream = 228
Fraction of orfs with sites within 600 bp upstream = 0.0366206


Motif number 2

ATTCTTTATGTTTGGCATGCTATAATACAAATCAAAT	1	30	0	TTCATTTAAA	    0.942428	-221
TATGAAAAAATCATGAATAATGTATTAAAGGTACGTA	1	76	0	TCAATTTATA	    0.895994	-175
AATATCCTTCTCCTCATTATGAAAAAATCATGAATAA	1	93	0	TCATTGAAAA	    0.923824	-158
TGATTTTCATTCTTTCATCTGCTAACATATTATCATA	1	163	1	TCCATGTAAA	    0.996656	-88
ATCCTTTAGTTCGCTAATATGATAATATGTTAGCAGA	1	180	0	TCAATGTAAA	    0.995006	-71
TTCGGAATTTTCCTTCATAAGATAACAGCGGAGGTGC	1	216	1	TCCATGTAAA	    0.996625	-35
          **   ***  * *** *

Masking position 8
Map Score:   2.74502

Number of sites scoring better than the average of aligned sites = 165
Number in coding regions = 130
Number in noncoding regions = 35
Number of orfs with sites within 600 bp upstream = 38
Fraction of orfs with sites within 600 bp upstream = 0.00610344


Motif number 3

      CTTTATCTCCTTGTTCTCTATTTG	1	5	1	ATCTCCTTGT	     0.98618	-246
TTTAGTTCAAATATCCTTCTCCTCATTATG	1	109	0	ATATCCTTCT	    0.978493	-142
TGAACTAAAAATATCCTTACTGAAGTTAAG	1	130	1	ATATCCTTAC	    0.988043	-121
TCATTCTTTCATCTGCTAACATATTATCAT	1	169	1	ATCTGCTAAC	     0.95097	-82
          **********

Masking position 4
Map Score:   0.980586

Number of sites scoring better than the average of aligned sites = 154
Number in coding regions = 117
Number in noncoding regions = 37
Number of orfs with sites within 600 bp upstream = 38
Fraction of orfs with sites within 600 bp upstream = 0.00610344


Motif number 4

          **********

No masking
Map Score:   -2.7468e-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:   -2.7468e-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:   -2.7468e-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