AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_mpneu.txt -z/home/amcguire/genomes/mpneu.fna -ifadR_mpneu_opreg_300.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

ACTTAAGCTAACTTAAGTGTTTAATTTGCG	1	68	0	ACTTAAGTGT	    0.971005	-233
ACTTAAGTTAGCTTAAGTCTAATATTTAAG	1	80	1	GCTTAAGTCT	    0.994754	-221
TAAGTCTAATATTTAAGTGAAAACAAGCCT	1	93	1	ATTTAAGTGA	    0.954779	-208
TTAAGCGAATGTTTAAGTCAGTTTTGCCTC	1	148	0	GTTTAAGTCA	    0.991705	-153
TTAAACATTCGCTTAAGTCAATTCAAGGAA	1	162	1	GCTTAAGTCA	    0.997181	-139
TAAGGTTGTGGCTAAACTCAAAAAAGAAGT	1	221	0	GCTAAACTCA	     0.95241	-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

TGCTACCTGCCCTTTTATTAGTAGCAATTCC	1	15	0	CCTTTTTTAG	    0.979195	-286
TTAATTTGCGTTTCGTGTTCGTAGGTCAACT	1	47	0	TTTCGTTTCG	    0.969802	-254
TATTTCTTTACTTCTTTTTTGAGTTTAGCCA	1	212	1	CTTCTTTTTG	    0.988924	-89
TTCTTAGTGGTTTTTTGTTTGCTTTAAACTA	1	265	0	TTTTTTTTTG	    0.973054	-36
CTCTTTTTCGTTTTTTCTTAGTGGTTTTTTG	1	279	0	TTTTTTTTAG	    0.973053	-22
          CCTCTTTTTCGTTTTTTCTTA	1	290	0	CCTCTTTTCG	    0.991342	-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

    TAGGGGAATTGCTACTAATAAAAGGG	1	7	1	AATTGCTACT	    0.946671	-294
CGTAGGTCAACTCTGCTACCTGCCCTTTTA	1	29	0	CTCTGCTACC	    0.985413	-272
TCAGTTTTGCCTCTGCAACTATCTGTGTTT	1	131	0	CTCTGCAACT	    0.976523	-170
TAATTCGCTCATTTACTGCTTATTCCTTGA	1	184	0	ATTTACTGCT	    0.941306	-117
CGAATTATTTCTTTACTTCTTTTTTGAGTT	1	207	1	CTTTACTTCT	    0.960672	-94
          **********

Masking position 4
Map Score:   1.01202

Number of sites scoring better than the average of aligned sites = 99
Number in coding regions = 85
Number in noncoding regions = 14
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 4

TCAAAAAGGCTTGTTTTCACTTAAATATTA	1	99	0	TTGTTTTCAC	    0.976718	-202
ACAAGCCTTTTTGAATAAACACAGATAGTT	1	115	1	TTGAATAAAC	    0.924432	-186
TGCTTATTCCTTGAATTGACTTAAGCGAAT	1	168	0	TTGAATTGAC	    0.963958	-133
CAACCTTATGTTGTTTGCACGATAGTTTAA	1	243	1	TTGTTTGCAC	    0.981521	-58
          **********

Masking position 6
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 5

CTACTAATAAAAGGGCAGGTAGCAGAGTTG	1	22	1	AAGGGCAGGT	    0.952766	-279
TACGAACACGAAACGCAAATTAAACACTTA	1	55	1	AAACGCAAAT	     0.97436	-246
AACGCAAATTAAACACTTAAGTTAGCTTAA	1	66	1	AAACACTTAA	    0.737769	-235
GTTTATTCAAAAAGGCTTGTTTTCACTTAA	1	105	0	AAAGGCTTGT	    0.923222	-196
CTTTTTGAATAAACACAGATAGTTGCAGAG	1	121	1	AAACACAGAT	    0.941342	-180
GAATTGACTTAAGCGAATGTTTAAGTCAGT	1	156	0	AAGCGAATGT	    0.923549	-145
CACTAAGAAAAAACGAAAAAGAGG      	1	287	1	AAACGAAAAA	    0.818623	-14
          **********

Masking position 2
Map Score:   1.09982

Number of sites scoring better than the average of aligned sites = 431
Number in coding regions = 384
Number in noncoding regions = 47
Number of orfs with sites within 600 bp upstream = 41
Fraction of orfs with sites within 600 bp upstream = 0.00658529


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