AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i004_bsub_mtub_100.orf -o004_bsub_mtub_100.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

CATGGATAATGTCAACGATATTATCGAACG	1	21	0	GTCAACGATA	    0.988013	-280
CTTAACAACGGACATGGATAATGTCAACGA	1	33	0	GACATGGATA	    0.995221	-268
ATGCAGGAAAGTGATCGATAAAACTGACAT	1	149	1	GTGATCGATA	    0.987292	-152
CGATAAAACTGACATGGATATATCGCAGAA	1	164	1	GACATGGATA	    0.995221	-137
          **********

Masking position 4
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	    0.959565	-298
TGAGGTCGTGTTTTGATTTCATGTTTATCT	1	61	0	TTTTGATTTC	    0.970946	-240
ACCATGCCCGGTTTGTATTGCTTCCTCATA	1	216	1	GTTTGTATTG	    0.959564	-85
AGCGGGTATTTTTTATTTTCTGAAAACAAA	1	258	1	TTTTATTTTC	    0.954688	-43
CTTCTAATGCTTTTGTTTTCAGAAAATAAA	1	269	0	TTTTGTTTTC	    0.990987	-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	    0.923874	-273
TATAATCTTGGGAATATGGCCCATAAGTTT	1	91	1	GGAATATGGC	    0.948994	-210
CCCGGCAACCGTAAATTGCCGGACTATGCA	1	124	1	GTAAATTGCC	    0.943966	-177
GTAAATTGCCGGACTATGCAGGAAAGTGAT	1	134	1	GGACTATGCA	    0.983241	-167
GACGATACATGTACCATGCCCGGTTTGTAT	1	204	1	GTACCATGCC	    0.989455	-97
TTCCTCATAAGTGCAATGCAGAGCGGGTAT	1	237	1	GTGCAATGCA	    0.951915	-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	    0.993782	-261
AAGTGATCGATAAAACTGACATGGATATAT	1	157	1	TAAAACTGAC	    0.975365	-144
CGCAGAAGCGAACGACTGACGATACATGTA	1	187	1	AACGACTGAC	    0.993782	-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