AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i170_Urease_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	ureA	300	urease (gamma subunit)

Motif number 1

CAGATTTTAATTGTCGAACTAGTCAGACAAGTTATTA	1	14	1	TTCGATCAGA	    0.997834	-287
AGACAAGTTATTATAGAAATTTCCAGAAAAAAAGACA	1	38	1	TTAGATCAGA	    0.986193	-263
AAAGATCAGATTAACGCGTTTTCCAGACTGCGCTCGA	1	88	0	TTCGGTCAGA	    0.997393	-213
TAATCTGATCTTTCCGTGATCGACAGGGGAACGGTTG	1	112	1	TTCGGTCAGG	    0.996859	-189
CTACTACGAATTTGCGGAACAGTCAGGCGGGACATCA	1	235	0	TTCGACCAGG	    0.994077	-66
CCTCCTTCTTTTGTCATATAAAGCAGATGCGGCTACT	1	267	0	TTCAAACAGA	    0.955981	-34
          **  ** * *   ****

Masking position 15
Map Score:   6.94998

Number of sites scoring better than the average of aligned sites = 109
Number in coding regions = 100
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 2

CTTGCCATGGTCAACAACCGTTCCCCTGTCGAT	1	130	0	TCACCCGTTC	    0.997705	-171
TGCCGTTTCTTCATCAGCCTTGCCATGGTCAAC	1	148	0	TCACCCTTGC	    0.997732	-153
GGTCATACGGTAAGATGCCTTTCAAAGCGGCAT	1	180	0	TAAACCTTTC	     0.97953	-121
AGGCGGGACATCACCTCCCTTTCTTCGAGAATG	1	215	0	TCACCCTTTC	    0.998652	-86
          *** *  ******

Masking position 3
Map Score:   3.25652

Number of sites scoring better than the average of aligned sites = 50
Number in coding regions = 38
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 3

GAAATTTCCAGAAAAAAAGACATTTGTTAT	1	53	1	GAAAAAAAGA	    0.963059	-248
CAAGGCTGATGAAGAAACGGCATGCCGCTT	1	159	1	GAAGAAACGG	    0.992629	-142
CCCCATTCTCGAAGAAAGGGAGGTGATGTC	1	212	1	GAAGAAAGGG	    0.992629	-89
CTTTATATGACAAAAGAAGGAGGACTACAG	1	281	1	CAAAAGAAGG	    0.957743	-20
          **********

Masking position 5
Map Score:   1.20485

Number of sites scoring better than the average of aligned sites = 462
Number in coding regions = 382
Number in noncoding regions = 80
Number of orfs with sites within 600 bp upstream = 84
Fraction of orfs with sites within 600 bp upstream = 0.0134918


Motif number 4

ATGGTCAACAACCGTTCCCCTGTCGATCAC	1	127	0	ACCGTTCCCC	    0.989911	-174
CATCTTACCGTATGACCCCCATTCTCGAAG	1	196	1	TATGACCCCC	    0.974351	-105
AAAGGGAGGTGATGTCCCGCCTGACTGTTC	1	226	1	GATGTCCCGC	    0.992371	-75
GTCCCGCCTGACTGTTCCGCAAATTCGTAG	1	239	1	ACTGTTCCGC	    0.992687	-62
          **********

Masking position 4
Map Score:   1.07025

Number of sites scoring better than the average of aligned sites = 204
Number in coding regions = 183
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 5

          **********

No masking
Map Score:   7.91135e-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:   7.91135e-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:   7.91135e-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