AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i038_mgen_mpneu_300.orf -o038_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	RMG00209	112	Mycoplasma
#2	RMG02317	20	Mycoplasma
#3	RMG02322	24	Mycoplasma
#4	RMP00579	300	Mycoplasma_pneumoniae

Motif number 1

TGGTTATTCCAAAATACTTTGCATTGTTTTGC	1	36	0	AAAAACTTTC	    0.946383	-77
TCTTTTGAGGAAAAGCAGTTATTATCTGGTTA	1	62	0	AAAACAGTTT	    0.978399	-51
GCTTTTCCTCAAAAGAAGTTACAGTGAAAAAA	1	78	1	AAAAAAGTTC	    0.978528	-35
    CAACTTAAAATCATTTTTTCACTGTAAC	1	95	0	AAAACATTTT	    0.895305	-18
accgcaatccaaattacgtttttgagttacaa	4	47	1	aaatacgttt	     0.95103	-254
cagtattcggaacaaccgttgttagtgtgtct	4	152	0	aacaccgttt	    0.977661	-149
tcgaccatcaaaacaaagtttcagtattcgga	4	173	0	aaacaagttc	    0.923544	-128
acgcggtcgaaaaacacgttttttagaacgtt	4	221	1	aaaaacgttt	    0.851753	-80
tacacaagttgacaaacgttctaaaaaacgtg	4	235	0	gacaacgttt	    0.925453	-66
          **** ***** *

Masking position 9
Map Score:   9.48518

Number of sites scoring better than the average of aligned sites = 232
Number in coding regions = 212
Number in noncoding regions = 20
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 2

TTATTATCTGGTTATTCCAAAATACTTTGC	1	46	0	GTTATTCCAA	    0.984054	-67
         AGTTATTCCAATGCCTAATAA	3	14	0	GTTATTCCAA	    0.984054	-11
aagtgcttgtgttattgcgctatgtcgtgg	4	16	0	gttattgcgc	    0.895973	-285
taaccttttggttcgtcaaccatcgaacaa	4	120	1	gttcgtcaac	    0.918821	-181
actaacaacggttgttccgaatactgaaac	4	158	1	gttgttccga	    0.961552	-143
actttgttttgatggtcgaccgagatcttt	4	186	1	gatggtcgac	    0.846484	-115
taaaaaacgtgtttttcgaccgcgttaagc	4	216	0	gtttttcgac	    0.964788	-85
tttttagaacgtttgtcaacttgtgtaaaa	4	240	1	gtttgtcaac	    0.935028	-61
aagaatccaatttattccaaattctcttgt	4	279	1	tttattccaa	    0.858177	-22
          **********

Masking position 6
Map Score:   7.86124

Number of sites scoring better than the average of aligned sites = 112
Number in coding regions = 98
Number in noncoding regions = 14
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 3

CAGTCATTAGCAAAACAATGCAAAGTATTT	1	27	1	CAAAACAATG	    0.941848	-86
cactttaccgcaatccaaattacgtttttg	4	41	1	caatccaaat	    0.941378	-260
gatggttgacgaaccaaaaggttacgtagt	4	114	0	gaaccaaaag	      0.9613	-187
gtcaaccatcgaacaaaaagacacactaac	4	134	1	gaacaaaaag	    0.940465	-167
ggtcgaccatcaaaacaaagtttcagtatt	4	177	0	caaaacaaag	    0.967972	-124
tcactttaaagaatccaatttattccaaat	4	271	1	gaatccaatt	    0.895906	-30
          **********

Masking position 7
Map Score:   1.43601

Number of sites scoring better than the average of aligned sites = 132
Number in coding regions = 123
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 4

ATTATCTGGTTATTCCAAAATACTTTGCAT	1	44	0	TATTCCAAAA	    0.847484	-69
TAATAACTGCTTTTCCTCAAAAGAAGTTAC	1	70	1	TTTTCCTCAA	    0.972339	-43
gacatagcgcaataacacaagcactttacc	4	20	1	aataacacaa	    0.849895	-281
acacaagcactttaccgcaatccaaattac	4	34	1	tttaccgcaa	    0.968039	-267
ccgttatagttgtaactcaaaaacgtaatt	4	58	0	tgtaactcaa	    0.930833	-243
ttaaagtgaattttacacaagttgacaaac	4	250	0	ttttacacaa	    0.969793	-51
          **********

Masking position 3
Map Score:   1.3534

Number of sites scoring better than the average of aligned sites = 70
Number in coding regions = 64
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 5

          **********

No masking
Map Score:   7.2008e-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:   7.2008e-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:   7.2008e-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