AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i218_Ribosomal_Operon_5_bsub_reg_300.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

TTCCTCCTTCGAATGCATAGAGTTACAGCT	1	16	1	GAATGCATAG	    0.982221	-261
TTTCATAATGGAAACCATATAGTAGAATAG	1	44	0	GAAACCATAT	    0.993554	-233
GAAAGATGATGAAACAATAGTTGCAAACGT	1	155	1	GAAACAATAG	    0.969657	-122
ATTATTTAAAGTATCCATATCGAAAGCATC	1	201	1	GTATCCATAT	    0.967018	-76
TATCCATATCGAAAGCATCTAAGATTATAT	1	212	1	GAAAGCATCT	    0.979424	-65
          **********

Masking position 7
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	    0.988292	-246
GAGGTACGGCCAGCGATTATTGCCTGGTCT	1	74	0	CAGCGATTAT	     0.95228	-203
CGTACCTCTACATATACTATAGCGCTGCTG	1	96	1	CATATACTAT	    0.948562	-181
AAAACGTTTGCAACTATTGTTTCATCATCT	1	158	0	CAACTATTGT	    0.943851	-119
TTTTAACATTCATATAATCTTAGATGCTTT	1	223	0	CATATAATCT	    0.912725	-54
TTGCACAAAACATCTACTTTTTAACATTCA	1	241	0	CATCTACTTT	    0.968698	-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	     0.93188	-221
GCGCTATAGTATATGTAGAGGTACGGCCAG	1	91	0	ATATGTAGAG	    0.968452	-186
TGTTTCCGCAAGATGTCAAGTGAATTTTCT	1	124	1	AGATGTCAAG	    0.962212	-153
TTGTTTCATCATCTTTCAAGAAAATTCACT	1	142	0	ATCTTTCAAG	    0.918705	-135
CTGTGGTAAATTATTTAAAGTATCCATATC	1	192	1	TTATTTAAAG	    0.952329	-85
TAAAGTATCCATATCGAAAGCATCTAAGAT	1	207	1	ATATCGAAAG	    0.933747	-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	    0.997786	-254
ATAATCGCTGGCCGTACCTCTACATATACTAT	1	84	1	GCGTACTCTA	    0.997786	-193
TCTTGCGGAAACAGCAGCGCTATAGTATATGT	1	105	0	ACGCACGCTA	    0.991506	-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

TGCATTCGAAGGAGGAACTAGT        	1	3	0	GGAGGAACTA	    0.968686	-274
CTTGACATCTTGCGGAAACAGCAGCGCTAT	1	114	0	TGCGGAAACA	    0.991197	-163
TCTTGAAAGATGATGAAACAATAGTTGCAA	1	151	1	TGATGAAACA	    0.970161	-126
TGCAAGTGAGGAGGGAAACAA         	1	266	1	GAGGGAAACA	    0.977935	-11
          **********

Masking position 6
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