AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i004_bsub_mtub_300.orf -o004_bsub_mtub_300.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -x5 -e 
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 =  	0.55
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	purE	300	phosphoribosylaminoimidazole carboxylase I

Motif number 1

CGTTCGATAATATCGTTGACATTATCCATG	1	21	1	TATCGTTGAC	    0.989506	-280
TCGTTGACATTATCCATGTCCGTTGTTAAG	1	33	1	TATCCATGTC	     0.99582	-268
ATGTCAGTTTTATCGATCACTTTCCTGCAT	1	149	0	TATCGATCAC	    0.988874	-152
TTCTGCGATATATCCATGTCAGTTTTATCG	1	164	0	TATCCATGTC	     0.99582	-137
          **********

Masking position 7
Map Score:   5.86029

Number of sites scoring better than the average of aligned sites = 32
Number in coding regions = 30
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 2

        ATTTTTGTATCGTTCGATAATA	1	3	1	TTTTGTATCG	    0.963346	-298
TGAGGTCGTGTTTTGATTTCATGTTTATCT	1	61	0	TTTTGATTTC	    0.973692	-240
ACCATGCCCGGTTTGTATTGCTTCCTCATA	1	216	1	GTTTGTATTG	    0.963345	-85
AGCGGGTATTTTTTATTTTCTGAAAACAAA	1	258	1	TTTTATTTTC	    0.958906	-43
CTTCTAATGCTTTTGTTTTCAGAAAATAAA	1	269	0	TTTTGTTTTC	    0.991855	-32
          **********

Masking position 4
Map Score:   3.90459

Number of sites scoring better than the average of aligned sites = 525
Number in coding regions = 453
Number in noncoding regions = 72
Number of orfs with sites within 600 bp upstream = 77
Fraction of orfs with sites within 600 bp upstream = 0.0123675


Motif number 3

CAACGGACATGGATAATGTCAACGATATTA	1	28	0	GGATAATGTC	    0.926486	-273
TATAATCTTGGGAATATGGCCCATAAGTTT	1	91	1	GGAATATGGC	    0.950221	-210
CCCGGCAACCGTAAATTGCCGGACTATGCA	1	124	1	GTAAATTGCC	    0.945779	-177
GTAAATTGCCGGACTATGCAGGAAAGTGAT	1	134	1	GGACTATGCA	    0.983838	-167
GACGATACATGTACCATGCCCGGTTTGTAT	1	204	1	GTACCATGCC	    0.989841	-97
TTCCTCATAAGTGCAATGCAGAGCGGGTAT	1	237	1	GTGCAATGCA	    0.953618	-64
          **********

Masking position 7
Map Score:   2.35929

Number of sites scoring better than the average of aligned sites = 638
Number in coding regions = 598
Number in noncoding regions = 40
Number of orfs with sites within 600 bp upstream = 39
Fraction of orfs with sites within 600 bp upstream = 0.00626405


Motif number 4

TGTTTATCTTAACAACGGACATGGATAATG	1	40	0	AACAACGGAC	    0.994064	-261
AAGTGATCGATAAAACTGACATGGATATAT	1	157	1	TAAAACTGAC	    0.976466	-144
CGCAGAAGCGAACGACTGACGATACATGTA	1	187	1	AACGACTGAC	    0.994064	-114
          **********

Masking position 5
Map Score:   0.807304

Number of sites scoring better than the average of aligned sites = 24
Number in coding regions = 20
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


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