AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i217_Ribosomal_Operon_4_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	spoIIIJ	144	alternate gene name: spo0J87
#2	rpmH	217	ribosomal protein L34

Motif number 1

ATCAACCAGAAAGGAAGCGCTTTTAAAAGTTGTAAGA	1	26	0	AAGGACTTAA	    0.986001	-119
TTGATCAGAAAAAGACACCATTTAAAACTGAAAGATG	1	58	1	AAAGACTAAA	    0.990502	-87
TTTAAAACTGAAAGATGCTAAAATACATACAAGTATG	1	78	1	AAAGACATAA	    0.966327	-67
AAATACATACAAGTATGCTTTGCAATAAAAGAGTGTA	1	98	1	AAGTACTAAA	    0.963556	-47
AAAAGAGTGTAAAGATTAATTATAGGAGGAA      	1	124	1	AAAGAATAGA	    0.925385	-21
TTTACGGAAAAAAGACAAATTCAAACAATTTGCCCCT	2	29	0	AAAGAATAAA	    0.981509	-189
CCGTAAAATTAAGGAATCTAAAAAATAAGGTTTCGAA	2	59	1	AAGGACAAAA	    0.986001	-159
TAGGTAACGCAAATATAATAAGTAAGACTGTCTTTAA	2	163	1	AAATAAAAAA	    0.845751	-55
CACCTCCCTCGAGGAATAGCTGTTAAAGACAGTCTTA	2	185	0	GAGGAATTAA	    0.893342	-33
          *****  *  *  ** *

Masking position 5
Map Score:   7.51025

Number of sites scoring better than the average of aligned sites = 1066
Number in coding regions = 920
Number in noncoding regions = 146
Number of orfs with sites within 600 bp upstream = 148
Fraction of orfs with sites within 600 bp upstream = 0.0237713


Motif number 2

CTTTTAAAAGTTGTAAGAAAGCAGTGGTGA	1	14	0	TTGTAAGAAA	    0.986892	-131
CAAGTATGCTTTGCAATAAAAGAGTGTAAA	1	107	1	TTGCAATAAA	    0.986892	-38
CCTATTATGGTTGCAAGAAATAAAAGCACT	2	115	1	TTGCAAGAAA	    0.984955	-103
          **********

Masking position 5
Map Score:   3.05158

Number of sites scoring better than the average of aligned sites = 22
Number in coding regions = 19
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 3

AAAGGAAGCGCTTTTAAAAGTTGTAAGAAAG	1	23	0	CTTTAAAAGT	    0.941148	-122
AAAAAGACACCATTTAAAACTGAAAGATGCT	1	66	1	CTTTAAAACT	    0.979742	-79
GGATACCATACCTTTTCAACTTTCGAAACCT	2	86	0	CTTTTCAACT	    0.969169	-132
GTTACCTATTCATTGTCAACTTCACTAGTGC	2	140	0	CTTGTCAACT	    0.974895	-78
GTAAGACTGTCTTTAACAGCTATTCCTCGAG	2	184	1	CTTAACAGCT	    0.960446	-34
          * *********

Masking position 4
Map Score:   2.50642

Number of sites scoring better than the average of aligned sites = 237
Number in coding regions = 207
Number in noncoding regions = 30
Number of orfs with sites within 600 bp upstream = 35
Fraction of orfs with sites within 600 bp upstream = 0.00562159


Motif number 4

TTTTAAATGGTGTCTTTTTCTGATCAACCAG	1	54	0	TGTTTTTTCT	    0.864251	-91
AAAGCATACTTGTATGTATTTTAGCATCTTT	1	88	0	TGTTGTATTT	      0.9808	-57
   ATCCACATGCGTGATTTTAGGGGCAAAT	2	8	1	TGCTGATTTT	    0.977299	-210
AGGGGCAAATTGTTTGAATTTGTCTTTTTTC	2	29	1	TGTTGAATTT	    0.980799	-189
ATTTTTTAGATTCCTTAATTTTACGGAAAAA	2	54	0	TTCTTAATTT	    0.887674	-164
ACTTCACTAGTGCTTTTATTTCTTGCAACCA	2	122	0	TGCTTTATTT	      0.9808	-96
          *** *******

Masking position 5
Map Score:   3.43183

Number of sites scoring better than the average of aligned sites = 689
Number in coding regions = 553
Number in noncoding regions = 136
Number of orfs with sites within 600 bp upstream = 135
Fraction of orfs with sites within 600 bp upstream = 0.0216833


Motif number 5

          **********

No masking
Map Score:   7.55607e-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:   7.55607e-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:   7.55607e-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