AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i248_mgen_mpneu_300.orf -o248_mgen_mpneu_300.ace -a/home/amcguire/genomes/ORF_mgen.txt -z/home/amcguire/genomes/mgen.fna -g0.36 -x5 -e 
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 =  	0.36
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RMG05654	202	Mycoplasma
#2	RMG04524	17	Mycoplasma
#3	RMP00416	184	Mycoplasma_pneumoniae

Motif number 1

      AAACTTTTAAATGATATTGCTTTT	1	5	1	TTTTAAATGA	    0.876527	-198
TTAATGTAATTTTTAAATTAAATAAACTAG	1	45	1	TTTTAAATTA	    0.867444	-158
TTTTAATAGTAACTAGTTTATTTAATTTAA	1	57	0	AACTAGTTTA	    0.894424	-146
ATAGAAGCTTTTTTAAATGAAGCGTTATTA	1	88	1	TTTTAAATGA	    0.876527	-115
AATGAAGCGTTATTAGCTTATTTTTTAGTA	1	103	1	TATTAGCTTA	    0.953145	-100
CTAGGCTAATTATTAGGTTACTAAAAAATA	1	121	0	TATTAGGTTA	    0.917038	-82
AATTAGCCTAGTTTAGTTTACTTCAACTAG	1	140	1	GTTTAGTTTA	    0.816476	-63
TATTAGATTATACTAGTTGAAGTAAACTAA	1	152	0	TACTAGTTGA	     0.97999	-51
TGGATGTTGTTATTAGATTATACTAGTTGA	1	162	0	TATTAGATTA	    0.967973	-41
     TGTTTTATTAATTTGGT        	2	3	0	TATTAATTTG	     0.84894	-15
agcttaatttttttaactgaaccgctcatg	3	20	1	ttttaactga	    0.826898	-165
gtattacaagtactagtttgccaaagacaa	3	69	1	tactagtttg	    0.950219	-116
tggttggtgcaactagttgaggggcgctaa	3	100	1	aactagttga	    0.901867	-85
tactagattattctagttggctttaaggaa	3	134	0	ttctagttgg	    0.933486	-51
aatagtgcattactagattattctagttgg	3	144	0	tactagatta	    0.970402	-41
          **********

Masking position 5
Map Score:   23.6723

Number of sites scoring better than the average of aligned sites = 372
Number in coding regions = 327
Number in noncoding regions = 45
Number of orfs with sites within 600 bp upstream = 26
Fraction of orfs with sites within 600 bp upstream = 0.00417604


Motif number 2

 AAACTTTTAAATGATATTGCTTTTCTAAAAGCA	1	10	1	AATAATTTTT	    0.938884	-193
TTAATTTAAAAATTACATTAATTGCTTTTAGAAA	1	32	0	AATAATTTTG	    0.934465	-171
TTTTTAAATTAAATAAACTAGTTACTATTAAAAC	1	54	1	AAAAACTTTA	    0.715582	-149
GCTTCATTTAAAAAAGCTTCTATGTTTTAATAGT	1	77	0	AAAACTTATG	     0.88666	-126
AAAATAAGCTAATAACGCTTCATTTAAAAAAGCT	1	93	0	AATAGCTATT	    0.650005	-110
GTAACCTAATAATTAGCCTAGTTTAGTTTACTTC	1	130	1	AATACCTTTT	    0.970454	-73
GTTGTTATTAGATTATACTAGTTGAAGTAAACTA	1	153	0	GATAACTTTG	    0.826356	-50
   TTGTTCTAAAAAGCTTTAATTTGGATGTTGT	1	182	0	AAAACTTATT	    0.878751	-21
      acttaattaagcttaatttttttaactg	3	5	1	aatagctatt	    0.499578	-180
       ttaaatcaggttagattttgcaatagt	3	168	0	aatagttatt	    0.931734	-17
          *** * ***  ***

Masking position 9
Map Score:   6.49013

Number of sites scoring better than the average of aligned sites = 329
Number in coding regions = 302
Number in noncoding regions = 27
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 3

ATGATATTGCTTTTCTAAAAGCAATTAATG	1	21	1	TTTTCTAAAA	    0.890076	-182
TAATTATTAGGTTACTAAAAAATAAGCTAA	1	115	0	GTTACTAAAA	     0.95595	-88
CCTAGTTTAGTTTACTTCAACTAGTATAAT	1	146	1	TTTACTTCAA	    0.939843	-57
         TTGTTCTAAAAAGCTTTAATT	1	192	0	TGTTCTAAAA	    0.954045	-11
gcgctaaacctttccttaaagccaactaga	3	123	1	tttccttaaa	     0.95909	-62
          **********

Masking position 6
Map Score:   2.45081

Number of sites scoring better than the average of aligned sites = 69
Number in coding regions = 60
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 4

          **********

No masking
Map Score:   -6.65478e-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 5

          **********

No masking
Map Score:   -6.65478e-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:   -6.65478e-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