AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i120_Xanthine_Transport_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	xpt	300	xanthine phosphoribosyltransferase

Motif number 1

AAAAATTCCCGAACTTTAATTTTGTTTTTTTA	1	48	0	GAACTTATTT	    0.977676	-253
TAAAGTTCGGGAATTTTTATTTTCAGCCTATG	1	62	1	GAATTTATTT	    0.980916	-239
CAAGAGATTAGAATCTTGATATAATTTATTAC	1	94	1	GAATTTATAT	    0.981422	-207
AATATAATAGGAACACTCATATAATCGCGTGG	1	126	1	GAACCTATAT	    0.985705	-175
AAAGAGCAAGCAATGCTGATATCACAAAAAAC	1	231	0	CAATCTATAT	    0.977491	-70
TTTGAGCGGGCAATGCTTTTTTTATTCTCATA	1	264	1	CAATCTTTTT	    0.914686	-37
          **** ** ****

Masking position 7
Map Score:   5.53989

Number of sites scoring better than the average of aligned sites = 171
Number in coding regions = 148
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 2

TCAAGATTCTAATCTCTTGCATAGGCTGAA	1	83	0	AATCTCTTGC	    0.949275	-218
ACACTCATATAATCGCGTGGATATGGCACG	1	138	1	AATCGCGTGG	    0.967338	-163
CCCGGTAGAAACTTGCGTGCCATATCCACG	1	153	0	ACTTGCGTGC	    0.982884	-148
CGTGCGGTTCCATTGCTCACCCATAGTCGG	1	195	0	CATTGCTCAC	    0.967134	-106
GTGATATCAGCATTGCTTGCTCTTTATTTG	1	238	1	CATTGCTTGC	     0.99566	-63
ATAAAAAAAGCATTGCCCGCTCAAATAAAG	1	259	0	CATTGCCCGC	    0.991116	-42
          **********

Masking position 3
Map Score:   5.32544

Number of sites scoring better than the average of aligned sites = 503
Number in coding regions = 478
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 28
Fraction of orfs with sites within 600 bp upstream = 0.00449727


Motif number 3

AAATACGAATGATATCTAAAAAAACAAAATTAAA	1	32	1	GATATAAAAA	    0.994823	-269
GTGTTCCTATTATATTGTAATAAATTATATCAAG	1	108	0	TATATAAAAA	    0.697266	-193
TAATCGCGTGGATATGGCACGCAAGTTTCTACCG	1	147	1	GATATACCAA	    0.975624	-154
AAGCAATGCTGATATCACAAAAAACCGTACACGT	1	222	0	GATATAAAAA	    0.994823	-79
GTCTACCTCCGTTATGAGAATAAAAAAAGCATTG	1	274	0	GTTATAAAAA	    0.947901	-27
          *****   ** ***

Masking position 9
Map Score:   3.66629

Number of sites scoring better than the average of aligned sites = 102
Number in coding regions = 76
Number in noncoding regions = 26
Number of orfs with sites within 600 bp upstream = 31
Fraction of orfs with sites within 600 bp upstream = 0.00497912


Motif number 4

AGATATCATTCGTATTTCAAGGGGATTCGATATA	1	15	0	CGATTAGGGG	    0.990935	-286
CACCCATAGTCGGACATTTACGGTGCCCGGTAGA	1	174	0	CGAATACGGT	    0.994776	-127
GCAATGGAACCGCACGTGTACGGTTTTTTGTGAT	1	209	1	CGAGTACGGT	    0.998078	-92
ATTCTCATAACGGAGGTAGACAGG          	1	287	1	CGAGTACAGG	    0.995077	-14
          ** * **  *****

Masking position 7
Map Score:   0.38354

Number of sites scoring better than the average of aligned sites = 41
Number in coding regions = 32
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 5

GGTAGAAACTTGCGTGCCATATCCACGCGA	1	150	0	TGCGTGCCAT	    0.967218	-151
GCGGTTCCATTGCTCACCCATAGTCGGACA	1	192	0	TGCTCACCCA	     0.96218	-109
ATATCAGCATTGCTTGCTCTTTATTTGAGC	1	241	1	TGCTTGCTCT	    0.988639	-60
AAAAAAGCATTGCCCGCTCAAATAAAGAGC	1	256	0	TGCCCGCTCA	    0.961048	-45
          **********

Masking position 1
Map Score:   0.660352

Number of sites scoring better than the average of aligned sites = 263
Number in coding regions = 242
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 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