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

Motif number 1

CAGATTTTAATTGTCGAACTAGTCAGACAAGTTATTA	1	14	1	TTCGATCAGA	    0.998042	-287
AGACAAGTTATTATAGAAATTTCCAGAAAAAAAGACA	1	38	1	TTAGATCAGA	    0.987515	-263
AAAGATCAGATTAACGCGTTTTCCAGACTGCGCTCGA	1	88	0	TTCGGTCAGA	    0.997645	-213
TAATCTGATCTTTCCGTGATCGACAGGGGAACGGTTG	1	112	1	TTCGGTCAGG	    0.997163	-189
CTACTACGAATTTGCGGAACAGTCAGGCGGGACATCA	1	235	0	TTCGACCAGG	    0.994616	-66
CCTCCTTCTTTTGTCATATAAAGCAGATGCGGCTACT	1	267	0	TTCAAACAGA	    0.960082	-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

ATCGACAGGGGAACGGTTGTTGACCATGGCAAG	1	130	1	GAACGGGTGA	    0.997882	-171
GTTGACCATGGCAAGGCTGATGAAGAAACGGCA	1	148	1	GCAAGGGTGA	    0.997912	-153
ATGCCGCTTTGAAAGGCATCTTACCGTATGACC	1	180	1	GAAAGGTTTA	    0.981149	-121
CATTCTCGAAGAAAGGGAGGTGATGTCCCGCCT	1	215	1	GAAAGGGTGA	    0.998756	-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

GATTTTAATTGTCGAACTAGTCAGACAAGTT	1	16	1	GTCGACTAGT	    0.947425	-285
TGTTATCTTAGTCGAGCGCAGTCTGGAAAAC	1	77	1	GTCGACGCAG	    0.986459	-224
CCGTTCCCCTGTCGATCACGGAAAGATCAGA	1	115	0	GTCGACACGG	    0.998459	-186
GGGAACGGTTGTTGACCATGGCAAGGCTGAT	1	138	1	GTTGACATGG	    0.987698	-163
CCTCCCTTTCTTCGAGAATGGGGGTCATACG	1	204	0	TTCGAAATGG	     0.93897	-97
          ***** *****

Masking position 5
Map Score:   1.68647

Number of sites scoring better than the average of aligned sites = 236
Number in coding regions = 213
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 4

CCTGTCGATCACGGAAAGATCAGATTAACG	1	109	0	ACGGAAAGAT	    0.995513	-192
TGGGGGTCATACGGTAAGATGCCTTTCAAA	1	187	0	ACGGTAAGAT	    0.995317	-114
          **********

Masking position 6
Map Score:   0.50812

Number of sites scoring better than the average of aligned sites = 18
Number in coding regions = 15
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 5

CGTGATCGACAGGGGAACGGTTGTTGACCA	1	126	1	AGGGGAACGG	    0.981057	-175
TCTTCGAGAATGGGGGTCATACGGTAAGAT	1	197	0	TGGGGGTCAT	     0.98403	-104
GGAACAGTCAGGCGGGACATCACCTCCCTT	1	227	0	GGCGGGACAT	    0.992417	-74
ACTACGAATTTGCGGAACAGTCAGGCGGGA	1	240	0	TGCGGAACAG	    0.993618	-61
          **********

Masking position 5
Map Score:   1.07025

Number of sites scoring better than the average of aligned sites = 228
Number in coding regions = 209
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


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


Motif number 8

          **********

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