AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i218_Ribosomal_Operon_5_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	rpmB	276	ribosomal protein L28

Motif number 1

AGCTGTAACTCTATGCATTCGAAGGAGGAA	1	16	0	CTATGCATTC	    0.982195	-261
CTATTCTACTATATGGTTTCCATTATGAAA	1	44	1	ATATGGTTTC	     0.99353	-233
ACGTTTGCAACTATTGTTTCATCATCTTTC	1	155	0	CTATTGTTTC	    0.969546	-122
GATGCTTTCGATATGGATACTTTAAATAAT	1	201	0	ATATGGATAC	    0.966922	-76
ATATAATCTTAGATGCTTTCGATATGGATA	1	212	0	AGATGCTTTC	    0.979349	-65
          **********

Masking position 4
Map Score:   5.55883

Number of sites scoring better than the average of aligned sites = 151
Number in coding regions = 130
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 29
Fraction of orfs with sites within 600 bp upstream = 0.00465789


Motif number 2

CATAGAGTTACAGCTATTCTACTATATGGT	1	31	1	CAGCTATTCT	    0.990124	-246
GAGGTACGGCCAGCGATTATTGCCTGGTCT	1	74	0	CAGCGATTAT	    0.959519	-203
CGTACCTCTACATATACTATAGCGCTGCTG	1	96	1	CATATACTAT	    0.956338	-181
AAAACGTTTGCAACTATTGTTTCATCATCT	1	158	0	CAACTATTGT	    0.952296	-119
TTTTAACATTCATATAATCTTAGATGCTTT	1	223	0	CATATAATCT	    0.925493	-54
TTGCACAAAACATCTACTTTTTAACATTCA	1	241	0	CATCTACTTT	    0.973514	-36
          **********

Masking position 6
Map Score:   3.21766

Number of sites scoring better than the average of aligned sites = 291
Number in coding regions = 243
Number in noncoding regions = 48
Number of orfs with sites within 600 bp upstream = 53
Fraction of orfs with sites within 600 bp upstream = 0.00851269


Motif number 3

ATGGTTTCCATTATGAAAAGACCAGGCAAT	1	56	1	TTATGAAAAG	    0.936147	-221
GCGCTATAGTATATGTAGAGGTACGGCCAG	1	91	0	ATATGTAGAG	      0.9705	-186
TGTTTCCGCAAGATGTCAAGTGAATTTTCT	1	124	1	AGATGTCAAG	    0.964653	-153
TTGTTTCATCATCTTTCAAGAAAATTCACT	1	142	0	ATCTTTCAAG	    0.923732	-135
CTGTGGTAAATTATTTAAAGTATCCATATC	1	192	1	TTATTTAAAG	    0.955376	-85
TAAAGTATCCATATCGAAAGCATCTAAGAT	1	207	1	ATATCGAAAG	    0.937893	-70
          **********

Masking position 4
Map Score:   1.60003

Number of sites scoring better than the average of aligned sites = 520
Number in coding regions = 402
Number in noncoding regions = 118
Number of orfs with sites within 600 bp upstream = 148
Fraction of orfs with sites within 600 bp upstream = 0.0237713


Motif number 4

TAGTAGAATAGCTGTAACTCTATGCATTCGAA	1	23	0	GCGTACTCTA	    0.997996	-254
ATAATCGCTGGCCGTACCTCTACATATACTAT	1	84	1	GCGTACTCTA	    0.997996	-193
TCTTGCGGAAACAGCAGCGCTATAGTATATGT	1	105	0	ACGCACGCTA	    0.992307	-172
          ** *** *****

Masking position 6
Map Score:   0.128291

Number of sites scoring better than the average of aligned sites = 12
Number in coding regions = 9
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 5

        ACTAGTTCCTCCTTCGAATGCA	1	3	1	TAGTTCCTCC	    0.967281	-274
ATAGCGCTGCTGTTTCCGCAAGATGTCAAG	1	114	1	TGTTTCCGCA	    0.990801	-163
TTGCAACTATTGTTTCATCATCTTTCAAGA	1	151	0	TGTTTCATCA	     0.96894	-126
         TTGTTTCCCTCCTCACTTGCA	1	266	0	TGTTTCCCTC	    0.976935	-11
          **********

Masking position 5
Map Score:   0.021532

Number of sites scoring better than the average of aligned sites = 574
Number in coding regions = 468
Number in noncoding regions = 106
Number of orfs with sites within 600 bp upstream = 101
Fraction of orfs with sites within 600 bp upstream = 0.0162223


Motif number 6

          **********

No masking
Map Score:   1.09013e-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:   1.09013e-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:   1.09013e-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