AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i004_4_1_1_21_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	purE	300	phosphoribosylaminoimidazole carboxylase I

Motif number 1

CATGGATAATGTCAACGATATTATCGAACG	1	21	0	GTCAACGATA	    0.989201	-280
CTTAACAACGGACATGGATAATGTCAACGA	1	33	0	GACATGGATA	    0.995698	-268
ATGCAGGAAAGTGATCGATAAAACTGACAT	1	149	1	GTGATCGATA	    0.988551	-152
CGATAAAACTGACATGGATATATCGCAGAA	1	164	1	GACATGGATA	    0.995698	-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

TATTATCGAACGATACAAAAAT        	1	3	0	CGATACAAAA	    0.962975	-298
AGATAAACATGAAATCAAAACACGACCTCA	1	61	1	GAAATCAAAA	    0.973424	-240
TATGAGGAAGCAATACAAACCGGGCATGGT	1	216	0	CAATACAAAC	    0.962974	-85
TTTGTTTTCAGAAAATAAAAAATACCCGCT	1	258	0	GAAAATAAAA	    0.958492	-43
TTTATTTTCTGAAAACAAAAGCATTAGAAG	1	269	1	GAAAACAAAA	     0.99177	-32
          **********

Masking position 7
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

CATTATCCATGTCCGTTGTTAAGATAAACA	1	40	1	GTCCGTTGTT	    0.993782	-261
ATATATCCATGTCAGTTTTATCGATCACTT	1	157	0	GTCAGTTTTA	    0.975365	-144
TACATGTATCGTCAGTCGTTCGCTTCTGCG	1	187	0	GTCAGTCGTT	    0.993782	-114
          **********

Masking position 6
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