AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i117_mgen_mpneu_100.orf -o117_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	RMG02265	300	Mycoplasma
#2	RMP00617	275	Mycoplasma_pneumoniae

Motif number 1

       TATTAGTATCATTTTTTTATAAAAT	1	4	1	TAGTATTTTT	    0.918108	-297
TGCTGATGTTCTTGATTATTTTATAAAAAAAT	1	21	0	CTTGATTTTT	    0.936031	-280
AACATCAGCACATGATCTTTATCACTAAATTT	1	43	1	CATGATTTAT	     0.88105	-258
TCACTAAATTTATGTTTGGTTTCAAATGAAGT	1	64	1	TATGTTGTTT	    0.848198	-237
GATTTAGAAGCTGGTTACTTTTGTTTCAGGTA	1	133	1	CTGGTTTTTT	    0.958907	-168
CTGAAAAAAACAGGTTCTTTTTTTATTTCTAT	1	194	1	CAGGTTTTTT	    0.988228	-107
GTAATGTCTATAGTCTTCTTTTTA        	1	287	1	TAGTCTTTTT	    0.803895	-14
ccaagttttgtaagatgtttttttgctatgat	2	19	0	taagattttt	    0.909361	-257
ctacattggtcaggttgattttcacgtctacc	2	127	0	caggtttttt	    0.988228	-149
tgtgaaagcttatgattattttttctttttcc	2	213	0	tatgattttt	    0.970596	-63
          ******  ****

Masking position 6
Map Score:   7.86048

Number of sites scoring better than the average of aligned sites = 235
Number in coding regions = 214
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 2

    TATTAGTATCATTTTTTTATAAAATAATCAAG	1	7	1	TATTTTATAA	    0.826833	-294
GGATTATAAATCCTGCTTTATTGTAATCATGCTTTA	1	97	1	TCTTTTGTAA	    0.993316	-204
TTTTTCAGGTTCTCAGTTTTTTGGAAATGGTACTGG	1	166	0	TCTTTTGGAA	    0.972006	-135
AGCAGTAGTTGCGATGTTTATCGTAATGTCTATAGT	1	265	1	GCTTTCGTAA	    0.950724	-36
tttgtaacaatcaccaagttttgtaagatgtttttt	2	28	0	tcgtttgtaa	    0.986414	-248
tgtcgtaaaatcagcgatttttgtaacaatcaccaa	2	47	0	tcttttgtaa	    0.993316	-229
caaaggtgagcctcagtttgtcgtaaaatcagcgat	2	65	0	cctttcgtaa	    0.950724	-211
gtttagaaagtccattggtcttataatcgtacgact	2	158	1	tcgtttataa	    0.959689	-118
tcataagctttcacaagttcatataagaatttgcaa	2	230	1	tcttatataa	    0.884622	-46
          **     ** ******

Masking position 9
Map Score:   8.31236

Number of sites scoring better than the average of aligned sites = 39
Number in coding regions = 35
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 3

GGTACTGGTTACCTGAAACAAAAGTAACCA	1	144	0	ACCTGAAACA	    0.975074	-157
AAAACTGAGAACCTGAAAAAAACAGGTTCT	1	182	1	ACCTGAAAAA	    0.988615	-119
TTAAGAATATACTTGAACATTTACTAAATA	1	223	0	ACTTGAACAT	    0.942627	-78
acatcggtagacgtgaaaatcaacctgacc	2	122	1	acgtgaaaat	    0.957552	-154
gtgaaaatcaacctgaccaatgtagtttag	2	134	1	acctgaccaa	    0.976868	-142
          **********

Masking position 6
Map Score:   3.0551

Number of sites scoring better than the average of aligned sites = 37
Number in coding regions = 35
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 4

AGAACATCAGCACATGATCTTTATCACTAAA	1	41	1	CACATGTCTT	    0.925643	-260
TGTTTGGTTTCAAATGAAGTTGGATTATAAA	1	76	1	CAAATGAGTT	    0.983218	-225
atatttagcgcaaagggacatcggtagacgt	2	105	1	caaaggacat	    0.910008	-171
atcaacctgaccaatgtagtttagaaagtcc	2	140	1	ccaatgagtt	    0.979828	-136
gattataagaccaatggactttctaaactac	2	155	0	ccaatgactt	    0.989354	-121
tgcaaattcttatatgaacttgtgaaagctt	2	234	0	tatatgactt	    0.840536	-42
          ****** ****

Masking position 4
Map Score:   1.05726

Number of sites scoring better than the average of aligned sites = 59
Number in coding regions = 52
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 5

GTTTCAAATGAAGTTGGATTATAAATCCTG	1	82	1	AAGTTGGATT	    0.969496	-219
GATTACAATAAAGCAGGATTTATAATCCAA	1	95	0	AAGCAGGATT	    0.974743	-206
TCTAAATCTAAAGCATGATTACAATAAAGC	1	111	0	AAGCATGATT	    0.866444	-190
TTAGATTTAGAAGCTGGTTACTTTTGTTTC	1	130	1	AAGCTGGTTA	    0.951873	-171
          **********

Masking position 2
Map Score:   1.44807

Number of sites scoring better than the average of aligned sites = 18
Number in coding regions = 15
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


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


Motif number 8

          **********

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