AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i150_mgen_mpneu_100.orf -o150_mgen_mpneu_100.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	RMG04325	74	Mycoplasma
#2	RMG03275	66	Mycoplasma
#3	RMP00239	300	Mycoplasma_pneumoniae

Motif number 1

  GGATGGTAAAGGCAAAAAAACTTGTCTTT	1	9	1	AAGCAAAAAA	    0.987706	-66
TGAGTGTAAAAAAGCTAAAAACTAATAAGCT	1	46	0	AAGCTAAAAA	    0.994614	-29
GAATTAATAGAAATCTTAAAACATATAATAA	2	18	1	AATCTTAAAA	     0.91244	-49
aaccacgcttaacgctacaaacggaaagg  	3	9	0	aagctacaaa	    0.982706	-292
tgttttgataaatgcttaaacttttcaaaaa	3	62	0	aagcttaaac	    0.981838	-239
tatttttcccattgctaaaaatagtgatatc	3	218	1	atgctaaaaa	    0.987701	-83
ttggaatatcattgcaaaaacctgatttcca	3	265	1	atgcaaaaac	    0.959202	-36
          ** ********

Masking position 9
Map Score:   10.2908

Number of sites scoring better than the average of aligned sites = 119
Number in coding regions = 109
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 2

ATATTGTTAATAAAATTATTATATGTTTTA	2	34	0	TAAAATTATT	    0.967551	-33
  ATTAAATAGAAAAATATTGTTAATAAAA	2	49	0	GAAAAATATT	    0.930323	-18
ggcaatcacatgaaaatattgcggtcttat	3	172	0	tgaaaatatt	    0.962019	-129
aaaataacgttgaaattattgtggcaatca	3	194	0	tgaaattatt	    0.979266	-107
ctaaaaatagtgatatcatttgcatggcta	3	232	1	tgatatcatt	    0.954543	-69
gctacctttggaatatcattgcaaaaacct	3	258	1	gaatatcatt	    0.917158	-43
          **********

Masking position 5
Map Score:   5.03526

Number of sites scoring better than the average of aligned sites = 141
Number in coding regions = 131
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 3

TAGTTTTTAGCTTTTTTACACTCAGCTTATT	1	53	1	CTTTTTACAC	    0.876091	-22
ATATAATAATTTTATTAACAATATTTTTCTA	2	40	1	TTTATAACAA	    0.925664	-27
gcgtggttggtttattaaaactaggggactt	3	32	1	tttataaaac	    0.920572	-269
aatgcttaaacttttcaaaaaagtcccctag	3	52	0	cttttaaaaa	    0.615833	-249
agtttaagcatttatcaaaacaacgagttac	3	71	1	tttataaaac	    0.920572	-230
atattgcggtcttataaaaaaggcgagcaat	3	156	0	cttataaaaa	    0.920572	-145
          ***** *****

Masking position 5
Map Score:   4.15014

Number of sites scoring better than the average of aligned sites = 117
Number in coding regions = 110
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 4

cgagcaatacgggaatcaggtacagcaaata	3	133	0	ggaatcaggt	    0.998121	-168
aaattattgtggcaatcacatgaaaatattg	3	181	0	ggaatcacat	    0.990637	-120
tattgagcttggaaatcaggtttttgcaatg	3	274	0	ggaatcaggt	    0.998121	-27
          ** ********

Masking position 5
Map Score:   1.96614

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

ATTTTATTAACAATATTTTTCTATTTAAT 	2	48	1	CAATATTTTT	    0.822561	-19
taaaactaggggacttttttgaaaagttta	3	47	1	ggactttttt	    0.898116	-254
aacgagttacggttttctttggttcctttt	3	92	1	ggttttcttt	    0.926638	-209
ggttttctttggttccttttttgtggcacg	3	102	1	ggttcctttt	    0.881082	-199
ccgtattgctcgccttttttataagaccgc	3	152	1	cgcctttttt	    0.952065	-149
ataatttcaacgttatttttcccattgcta	3	205	1	cgttattttt	    0.966716	-96
caaatgatatcactatttttagcaatggga	3	224	0	cactattttt	    0.912633	-77
tcatttgcatggctacctttggaatatcat	3	247	1	ggctaccttt	    0.936081	-54
          **********

Masking position 8
Map Score:   2.58533

Number of sites scoring better than the average of aligned sites = 284
Number in coding regions = 256
Number in noncoding regions = 28
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 6

          **********

No masking
Map Score:   1.01908e-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:   1.01908e-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:   1.01908e-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