AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i215_Ribosomal_Operon_2_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	obg	33	GTPase activity
#2	spo0B	300	sporulation initiation phosphoprotein
#3	rplU	146	ribosomal protein L21 (BL20)

Motif number 1

CTAAACCGTTAAAAACTCCG          	1	1	0	AAAAACTCCG	    0.971668	-33
ATATTGCAAAAAAAACTCCAGTCATCATC 	2	10	0	AAAAACTCCA	    0.926326	-291
GTATGTGCGAGCAGACCCCGCCAAGAATGA	2	70	1	GCAGACCCCG	    0.973903	-231
TTTTTCTAACAAAGCCTTCTCTGTTATAAT	2	222	1	AAAGCCTTCT	    0.881744	-79
ACACACTTATACAGACTCCTAAATAAGAAA	2	259	1	ACAGACTCCT	    0.994364	-42
 AACTGATTGACAAACGCCTTGTATTTTGG	3	10	1	ACAAACGCCT	    0.974676	-137
AAGAGCTTTTACAGCCCCCTGGTATCTGGC	3	98	1	ACAGCCCCCT	    0.989942	-49
          **********

Masking position 3
Map Score:   6.89879

Number of sites scoring better than the average of aligned sites = 407
Number in coding regions = 299
Number in noncoding regions = 108
Number of orfs with sites within 600 bp upstream = 86
Fraction of orfs with sites within 600 bp upstream = 0.013813


Motif number 2

TGCAAAAAAAACTCCAGTCATCATC      	2	5	0	ACCCAGTCAT	    0.949178	-296
TGCGGAGTAAACACCTAGAATGAAATGCAGA	2	39	1	ACCCTAGAAT	    0.940292	-262
CGAGCAGACCCCGCCAAGAATGAGAATAAAC	2	77	1	CCCCAAGAAT	    0.978023	-224
CTGGATATGTTCCCCAAGCAGTAATACATAA	2	120	1	TCCCAAGCAG	    0.951078	-181
GGTTGATTTGCAGCCAGGCAGAACATTTTAT	2	147	0	CACCAGGCAG	    0.736463	-154
   TTTCGCACTCCCAATCATTTAATTTCTT	2	283	0	CTCCAATCAT	    0.847912	-18
TGATTGACAAACGCCTTGTATTTTGGTATAT	3	14	1	ACCCTTGTAT	    0.848638	-133
GCTTTTACAGCCCCCTGGTATCTGGCGAGTC	3	102	1	CCCCTGGTAT	    0.975396	-45
  TCTCTGCACCTCCTATTAGACTAAGACTC	3	128	0	CCCCTATTAG	    0.941774	-19
          ** ********

Masking position 10
Map Score:   6.21337

Number of sites scoring better than the average of aligned sites = 815
Number in coding regions = 727
Number in noncoding regions = 88
Number of orfs with sites within 600 bp upstream = 86
Fraction of orfs with sites within 600 bp upstream = 0.013813


Motif number 3

TAGGTGTTTACTCCGCATATTGCAAAAAAA	2	26	0	CTCCGCATAT	    0.988753	-275
CTCGCACATACTCTGCATTTCATTCTAGGT	2	51	0	CTCTGCATTT	    0.987704	-250
ATCTCAAACCCACTGGATATGTTCCCCAAG	2	108	1	CACTGGATAT	    0.957266	-193
         TCTCTGCACCTCCTATTAGAC	3	136	0	CTCTGCACCT	     0.98663	-11
          **********

Masking position 7
Map Score:   1.30944

Number of sites scoring better than the average of aligned sites = 90
Number in coding regions = 69
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 4

TGCATTTCATTCTAGGTGTTTACTCCGCATAT	2	36	0	TAGGTGTTTA	    0.994927	-265
TCCAGTGGGTTTGAGATGTTTATTCTCATTCT	2	93	0	TAGATGTTTA	    0.975593	-208
TAGGAGTCTGTATAAGTGTGTATTATGAATTA	2	248	0	TAAGTGTGTA	    0.966277	-53
AACCGCTCAGTACAGGTGTTAAGAGCTTTTAC	3	78	1	TAGGTGTTAA	    0.981906	-69
          *  *********

Masking position 7
Map Score:   0.198907

Number of sites scoring better than the average of aligned sites = 33
Number in coding regions = 29
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 5

TTAATGTTATGGATGTAGCACCATTGCTAC	3	48	1	GGATGTAGCA	    0.993158	-99
TGTACTGAGCGGTTGTAGCAATGGTGCTAC	3	62	0	GGTTGTAGCA	    0.991118	-85
GATACCAGGGGGCTGTAAAAGCTCTTAACA	3	94	0	GGCTGTAAAA	     0.96932	-53
          **********

Masking position 7
Map Score:   0.415326

Number of sites scoring better than the average of aligned sites = 15
Number in coding regions = 12
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 6

          **********

No masking
Map Score:   -3.03101e-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:   -3.03101e-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:   -3.03101e-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