AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_mpneu.txt -z/home/amcguire/genomes/mpneu.fna -ifadR_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	1673934	300	D02_orf100 Protein

Motif number 1

CGCAAATTAAACACTTAAGTTAGCTTAAGT	1	68	1	ACACTTAAGT	    0.970908	-233
CTTAAATATTAGACTTAAGCTAACTTAAGT	1	80	0	AGACTTAAGC	    0.994736	-221
AGGCTTGTTTTCACTTAAATATTAGACTTA	1	93	0	TCACTTAAAT	    0.954629	-208
GAGGCAAAACTGACTTAAACATTCGCTTAA	1	148	1	TGACTTAAAC	    0.991676	-153
TTCCTTGAATTGACTTAAGCGAATGTTTAA	1	162	0	TGACTTAAGC	    0.997172	-139
ACTTCTTTTTTGAGTTTAGCCACAACCTTA	1	221	1	TGAGTTTAGC	    0.952253	-80
          **********

Masking position 5
Map Score:   10.2676

Number of sites scoring better than the average of aligned sites = 59
Number in coding regions = 50
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 2

GGAATTGCTACTAATAAAAGGGCAGGTAGCA	1	15	1	CTAAAAAAGG	    0.978172	-286
AGTTGACCTACGAACACGAAACGCAAATTAA	1	47	1	CGAAACGAAA	    0.968332	-254
TGGCTAAACTCAAAAAAGAAGTAAAGAAATA	1	212	0	CAAAAAGAAG	    0.988373	-89
TAGTTTAAAGCAAACAAAAAACCACTAAGAA	1	265	1	CAAAAAAAAA	    0.971737	-36
CAAAAAACCACTAAGAAAAAACGAAAAAGAG	1	279	1	CTAAAAAAAA	    0.971737	-22
TAAGAAAAAACGAAAAAGAGG          	1	290	1	CGAAAAGAGG	     0.99091	-11
          **** ******

Masking position 6
Map Score:   5.95029

Number of sites scoring better than the average of aligned sites = 125
Number in coding regions = 107
Number in noncoding regions = 18
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 3

ACTTAAGTGTTTAATTTGCGTTTCGTGTTC	1	58	0	TTAATTTGCG	    0.937725	-243
TGTTTTCACTTAAATATTAGACTTAAGCTA	1	88	0	TAAATATTAG	    0.896699	-213
AAAACTGACTTAAACATTCGCTTAAGTCAA	1	153	1	TAAACATTCG	    0.979953	-148
GAATAAGCAGTAAATGAGCGAATTATTTCT	1	189	1	TAAATGAGCG	    0.966736	-112
TTGTTTGCTTTAAACTATCGTGCAAACAAC	1	252	0	TAAACTATCG	    0.971892	-49
          **********

Masking position 4
Map Score:   1.34973

Number of sites scoring better than the average of aligned sites = 61
Number in coding regions = 44
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 4

          TAGGGGAATTGCTACTAATA	1	1	1	TAGGGGAATT	    0.972501	-300
ATATTAGACTTAAGCTAACTTAAGTGTTTA	1	75	0	TAAGCTAACT	    0.959778	-226
TGAATTGACTTAAGCGAATGTTTAAGTCAG	1	157	0	TAAGCGAATG	    0.989539	-144
AAGCAGTAAATGAGCGAATTATTTCTTTAC	1	193	1	TGAGCGAATT	    0.989549	-108
          **********

Masking position 7
Map Score:   1.0189

Number of sites scoring better than the average of aligned sites = 30
Number in coding regions = 26
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 5

TAATATTTAAGTGAAAACAAGCCTTTTTGA	1	99	1	GTGAAAACAA	    0.976427	-202
AACTATCTGTGTTTATTCAAAAAGGCTTGT	1	115	0	GTTTATTCAA	    0.921905	-186
ATTCGCTTAAGTCAATTCAAGGAATAAGCA	1	168	1	GTCAATTCAA	    0.963162	-133
TTAAACTATCGTGCAAACAACATAAGGTTG	1	243	0	GTGCAAACAA	    0.980762	-58
          **********

Masking position 5
Map Score:   0.620279

Number of sites scoring better than the average of aligned sites = 38
Number in coding regions = 33
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 6

          **********

No masking
Map Score:   7.91135e-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:   7.91135e-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:   7.91135e-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