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

Motif number 1

AAAAATTCCCGAACTTTAATTTTGTTTTTTTA	1	48	0	GAACTTATTT	    0.979035	-253
TAAAGTTCGGGAATTTTTATTTTCAGCCTATG	1	62	1	GAATTTATTT	    0.982017	-239
CAAGAGATTAGAATCTTGATATAATTTATTAC	1	94	1	GAATTTATAT	    0.982556	-207
AATATAATAGGAACACTCATATAATCGCGTGG	1	126	1	GAACCTATAT	    0.986584	-175
AAAGAGCAAGCAATGCTGATATCACAAAAAAC	1	231	0	CAATCTATAT	    0.978861	-70
TTTGAGCGGGCAATGCTTTTTTTATTCTCATA	1	264	1	CAATCTTTTT	    0.919572	-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

TTCAGCCTATGCAAGAGATTAGAATCTTGA	1	83	1	GCAAGAGATT	    0.943585	-218
CGTGCCATATCCACGCGATTATATGAGTGT	1	138	0	CCACGCGATT	    0.963671	-163
CGTGGATATGGCACGCAAGTTTCTACCGGG	1	153	1	GCACGCAAGT	    0.980899	-148
CCGACTATGGGTGAGCAATGGAACCGCACG	1	195	1	GTGAGCAATG	     0.96337	-106
CAAATAAAGAGCAAGCAATGCTGATATCAC	1	238	0	GCAAGCAATG	    0.995146	-63
CTTTATTTGAGCGGGCAATGCTTTTTTTAT	1	259	1	GCGGGCAATG	    0.990071	-42
          **********

Masking position 8
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	    0.994464	-269
GTGTTCCTATTATATTGTAATAAATTATATCAAG	1	108	0	TATATAAAAA	    0.704418	-193
TAATCGCGTGGATATGGCACGCAAGTTTCTACCG	1	147	1	GATATACCAA	    0.973886	-154
AAGCAATGCTGATATCACAAAAAACCGTACACGT	1	222	0	GATATAAAAA	    0.994464	-79
GTCTACCTCCGTTATGAGAATAAAAAAAGCATTG	1	274	0	GTTATAAAAA	    0.949031	-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	CGTATAGGGG	    0.991745	-286
CACCCATAGTCGGACATTTACGGTGCCCGGTAGA	1	174	0	CGGATACGGT	    0.998259	-127
GCAATGGAACCGCACGTGTACGGTTTTTTGTGAT	1	209	1	CGCATACGGT	    0.996799	-92
ATTCTCATAACGGAGGTAGACAGG          	1	287	1	CGGATACAGG	    0.995527	-14
          ****  *  *****

Masking position 7
Map Score:   0.38354

Number of sites scoring better than the average of aligned sites = 46
Number in coding regions = 37
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 5

GGTAGAAACTTGCGTGCCATATCCACGCGA	1	150	0	TGCGTGCCAT	     0.97002	-151
GCGGTTCCATTGCTCACCCATAGTCGGACA	1	192	0	TGCTCACCCA	    0.961813	-109
ATATCAGCATTGCTTGCTCTTTATTTGAGC	1	241	1	TGCTTGCTCT	    0.989555	-60
AAAAAAGCATTGCCCGCTCAAATAAAGAGC	1	256	0	TGCCCGCTCA	    0.958898	-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