AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_mpneu.txt -z/home/amcguire/genomes/mpneu.fna -isoxS_mpneu_opreg_100.orf -g0.400 -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 =  	0.4
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	araD	300	L-ribulose-5-phosphate 4-epimerase; similar to Swiss-Prot Accession Number P08203, from E. coli
#2	rpl21	146	ribosomal protein L21; similar to Swiss-Prot Accession Number P26908, from B. subtilis

Motif number 1

CCAAAGAGCACCCTGATTTTGTGATGTTATCG	1	64	0	CCCTGATTGT	    0.988605	-237
GGCTTCCGGACCCCAATTCTTAATTAAATGAT	1	94	1	CCCCAATTTA	    0.925476	-207
GGGACATTGACCCTAAGGATTTAGGTATTTGT	1	136	0	CCCTAAGTTT	    0.984785	-165
GGTCAATGTCCCCTAAAACTGTTCTTACAAAT	1	156	1	CCCTAAATGT	    0.988635	-145
ATTGAAATAACCCTAATAATGTGTAAGCTACT	1	226	1	CCCTAATTGT	    0.996484	-75
GTAAGTCTAGCCTTAAGCATGACTTTAGCAGG	2	32	1	CCTTAAGTGA	    0.965694	-115
TTCTGCGGTTCCTAAATTTTGTTTATACAAAA	2	99	1	CCTAAATTGT	    0.950483	-48
          *******  ***

Masking position 6
Map Score:   6.92593

Number of sites scoring better than the average of aligned sites = 58
Number in coding regions = 53
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 2

ACCCTAAGGATTTAGGTATTTGTGACTGTC	1	129	0	TTTAGGTATT	    0.979318	-172
TTAAATGGTTTAAGTGTATTGAAATAACCC	1	209	1	TAAGTGTATT	    0.918226	-92
TATATGTATTTATATGTATTA         	2	2	0	TATATGTATT	    0.983648	-145
CTAGACTTACTATATGTATTTATATGTATT	2	12	0	TATATGTATT	    0.983648	-135
AAACCGTTTCTTTTGGTATTTTGTATAAAC	2	119	0	TTTTGGTATT	     0.94944	-28
          **********

Masking position 7
Map Score:   4.45483

Number of sites scoring better than the average of aligned sites = 21
Number in coding regions = 16
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 3

TCGTGACAGTCACAAATACCTAAATCCTTA	1	125	1	CACAAATACC	    0.905795	-176
AGTTTTAGGGGACATTGACCCTAAGGATTT	1	146	0	GACATTGACC	    0.889969	-155
TATTTCAATACACTTAAACCATTTAACGTC	1	205	0	CACTTAAACC	    0.964538	-96
TAAGTGTATTGAAATAACCCTAATAATGTG	1	219	1	GAAATAACCC	    0.947472	-82
CTGTTAATGGCAAATTATCCAGTAGCTTAC	1	248	0	CAAATTATCC	    0.949233	-53
GAAATTATAACAAATTAACCCCTGCTAAAG	2	54	0	CAAATTAACC	    0.986979	-93
TTTGTTTATACAAAATACCAAAAGAAACGG	2	116	1	CAAAATACCA	     0.78025	-31
       TTTCAATAAAACCGTTTCTTTTG	2	134	0	CAATAAAACC	    0.945346	-13
          **********

Masking position 2
Map Score:   3.91872

Number of sites scoring better than the average of aligned sites = 435
Number in coding regions = 398
Number in noncoding regions = 37
Number of orfs with sites within 600 bp upstream = 31
Fraction of orfs with sites within 600 bp upstream = 0.00497912


Motif number 4

          **********

No masking
Map Score:   5.92755e-14

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 5

          **********

No masking
Map Score:   5.92755e-14

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:   5.92755e-14

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