AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i117_mgen_mpneu_300.orf -o117_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	RMG02265	300	Mycoplasma
#2	RMP00617	275	Mycoplasma_pneumoniae

Motif number 1

TTATTTTATAAAAAAATGATACTAATA       	1	4	0	AAAAAAACTA	    0.877795	-297
TCATTTTTTTATAAAATAATCAAGAACATCAGCA	1	19	1	AAAAAACAAG	    0.957562	-282
ATAAATTTAGTGATAAAGATCATGTGCTGATGTT	1	43	0	TATAAACATG	    0.846809	-258
CAACTTCATTTGAAACCAAACATAAATTTAGTGA	1	64	0	TAAACACATA	    0.823514	-237
GTTACCTGAAACAAAAGTAACCAGCTTCTAAATC	1	133	0	AAAAAACCAG	    0.977229	-168
AAATAGAAATAAAAAAAGAACCTGTTTTTTTCAG	1	194	0	AAAAAACCTG	    0.988059	-107
          TAAAAAGAAGACTATAGACATTAC	1	287	0	TAAAAAACTA	    0.877795	-14
tgatcatagcaaaaaaacatcttacaaaacttgg	2	17	1	aaaaaactta	    0.870226	-259
gcgatttttgtaacaatcaccaagttttgtaaga	2	36	0	tacaaacaag	    0.809496	-240
ccctttgcgctaaatattagccaaaggtgagcct	2	88	0	taataaccaa	    0.756436	-188
tcggtagacgtgaaaatcaacctgaccaatgtag	2	125	1	taaaaacctg	    0.988059	-151
aaggaaaaagaaaaaataatcataagctttcaca	2	211	1	aaaaaacata	    0.964515	-65
          * ****  * ****

Masking position 9
Map Score:   9.19106

Number of sites scoring better than the average of aligned sites = 353
Number in coding regions = 325
Number in noncoding regions = 28
Number of orfs with sites within 600 bp upstream = 18
Fraction of orfs with sites within 600 bp upstream = 0.0028911


Motif number 2

TAAAGCATGATTACAATAAAGCAGGATTTATAATC	1	98	0	TTACAAAAGG	    0.986702	-203
ATGGTACTGGTTACCTGAAACAAAAGTAACCAGCT	1	141	0	TTACTAAACA	    0.925088	-160
CCAGTACCATTTCCAAAAAACTGAGAACCTGAAAA	1	166	1	TTCCAAAACG	     0.99162	-135
ACTATAGACATTACGATAAACATCGCAACTACTGC	1	266	0	TTACAAAACG	    0.996908	-35
ttggtgattgttacaaaaatcgctgattttacgac	2	47	1	ttacaaatcg	    0.987629	-229
atcgctgattttacgacaaactgaggctcaccttt	2	65	1	ttacaaaacg	    0.996915	-211
          **** * ****   *

Masking position 8
Map Score:   6.55279

Number of sites scoring better than the average of aligned sites = 12
Number in coding regions = 11
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 3

ATAAAATAATCAAGAACATCAGCACATGAT	1	29	1	CAAGAACATC	    0.922063	-272
ATTTAGTGATAAAGATCATGTGCTGATGTT	1	43	0	AAAGATCATG	    0.817452	-258
ATTTATAATCCAACTTCATTTGAAACCAAA	1	78	0	CAACTTCATT	    0.962975	-223
AGTAAATGTTCAAGTATATTCTTAAACGAT	1	228	1	CAAGTATATT	    0.888904	-73
tggactttctaaactacattggtcaggttg	2	142	0	aaactacatt	    0.925497	-134
tgtagtttagaaagtccattggtcttataa	2	154	1	aaagtccatt	     0.94344	-122
taagctttcacaagttcatataagaatttg	2	233	1	caagttcata	    0.948808	-43
          **********

Masking position 3
Map Score:   1.55962

Number of sites scoring better than the average of aligned sites = 134
Number in coding regions = 126
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 4

aaatcaacctgaccaatgtagtttagaaag	2	138	1	gaccaatgta	    0.973941	-138
acgattataagaccaatggactttctaaac	2	158	0	gaccaatgga	    0.982308	-118
tggaccaagagtccagggagtcgtacgatt	2	182	0	gtccagggag	    0.969532	-94
tggactcttggtccaaggaaaaagaaaaaa	2	197	1	gtccaaggaa	    0.987434	-79
          **********

Masking position 5
Map Score:   0.171138

Number of sites scoring better than the average of aligned sites = 10
Number in coding regions = 3
Number in noncoding regions = 7
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:   -1.14154e-12

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:   -1.14154e-12

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:   -1.14154e-12

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