AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i250_mgen_mpneu_300.orf -o250_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	RMG00426	270	Mycoplasma
#2	RMP00523	300	Mycoplasma_pneumoniae

Motif number 1

ATTGATCAACTGTCATCATAGCTCAATAGG	1	66	1	TGTCATCATA	    0.847066	-205
ccatccaatctttcataataccgcagtggt	2	46	0	tttcataata	    0.918561	-255
ttcattcagtttccaccaaagtaggtggca	2	116	0	ttccaccaaa	    0.957893	-185
catttgggtttttcaccagaacatttggtg	2	148	1	tttcaccaga	    0.980118	-153
ttttccgtggtttcaccaaatgttctggtg	2	161	0	tttcaccaaa	    0.990583	-140
aaatcggttttttcaaaaaaataagattct	2	236	1	tttcaaaaaa	    0.838868	-65
agattctatatttcacaaaatttcacagtg	2	259	1	tttcacaaaa	    0.978685	-42
tttcacaaaatttcacagtgtttcaccgta	2	269	1	tttcacagtg	    0.852587	-32
tttcacagtgtttcaccgtatttcaccatt	2	279	1	tttcaccgta	     0.98305	-22
tttcaccgtatttcaccatttt        	2	289	1	tttcaccatt	    0.955088	-12
          **********

Masking position 5
Map Score:   14.6793

Number of sites scoring better than the average of aligned sites = 124
Number in coding regions = 111
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 2

AAACTTTGGCACTTTTAGATTTAGATGTGATT	1	30	0	ACTTTTATTT	    0.888457	-241
TAAGTTGTAGTCATTTCATTTTGGACAAAAAG	1	227	1	TCATTTCTTT	    0.983367	-44
CTTAGCATAAAAATTTCTTTTTGTCCAAAATG	1	243	0	AAATTTCTTT	     0.85474	-28
ctcggttgcctcgtttattttttggatggtcc	2	84	0	tcgtttattt	    0.976348	-217
ctgaatgaaaacatttgggtttttcaccagaa	2	137	1	acatttgttt	    0.968923	-164
cgaaaccttgtcgtttcattttccgtggtttc	2	177	0	tcgtttcttt	    0.989363	-124
ttcttgacggtcgtttggatttttttcgcgaa	2	205	0	tcgtttgttt	     0.98458	-96
          *******  ***

Masking position 6
Map Score:   5.84233

Number of sites scoring better than the average of aligned sites = 55
Number in coding regions = 48
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 3

TGTTGGTGACGCCATTAACTTTATTTGCCTA	1	140	1	GCCATAACTT	    0.935317	-131
AACTTTATTTGCCTATCAGTTAAATAACTGG	1	156	1	GCCTTCAGTT	    0.966782	-115
CAATAAAAAAGCCTACCAGTTATTTAACTGA	1	171	0	GCCTCCAGTT	    0.990697	-100
AAAATGAAATGACTACAACTTAAATTAACCC	1	218	0	GACTCAACTT	    0.970932	-53
 gaacgcctcgactcccaatgtccaagctaa	2	10	1	gactccaatg	    0.927285	-291
ccaagctaaggacaaccactgcggtattatg	2	32	1	gacaccactg	    0.980809	-269
gcaaccgagtgccacctactttggtggaaac	2	107	1	gccactactt	    0.967805	-194
          **** ******

Masking position 8
Map Score:   5.33907

Number of sites scoring better than the average of aligned sites = 20
Number in coding regions = 18
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 4

GATGACAGTTGATCAATTATAAAACTTTGGCACT	1	49	0	GATCTAAAAA	    0.976229	-222
TTATTTAACTGATAGGCAAATAAAGTTAATGGCG	1	149	0	GATACATAAA	    0.922913	-122
ATTAACCCTTGATAAACTACAAAACAATAAAAAA	1	192	0	GATACAAAAA	    0.985254	-79
gtcacaatgggaccatccaaaaaataaacgaggc	2	75	1	gacccaaaaa	    0.983469	-226
aaacgacaaggtttcgcgaaaaaaatccaaacga	2	193	1	gtttcaaaaa	    0.942169	-108
aaatccaaacgaccgtcaagaaaatcggtttttt	2	215	1	gacccaaaaa	    0.983468	-86
aagaaaatcggttttttcaaaaaaataagattct	2	232	1	gttttaaaaa	    0.867416	-69
aataagattctatatttcacaaaatttcacagtg	2	255	1	tatataaaaa	    0.744325	-46
          ****  * * ****

Masking position 9
Map Score:   4.60205

Number of sites scoring better than the average of aligned sites = 98
Number in coding regions = 94
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 5

GAATCGAACCTGTAACCCTCAGCTCCGCAA	1	109	0	TGTAACCCTC	     0.98586	-162
atggtcccattgtgaccatccaatctttca	2	61	0	tgtgaccatc	    0.995561	-240
atggtcacaatgggaccatccaaaaaataa	2	72	1	tgggaccatc	    0.994737	-229
          **********

Masking position 5
Map Score:   1.68287

Number of sites scoring better than the average of aligned sites = 1
Number in coding regions = 1
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:   9.90086e-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:   9.90086e-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:   9.90086e-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