AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i218_mgen_mpneu_300.orf -o218_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	RMG02025	188	Mycoplasma
#2	RMP00219	21	Mycoplasma_pneumoniae
#3	RMP00220	157	Mycoplasma_pneumoniae

Motif number 1

         TAATTAATAAACACGTTGAATTA	1	2	1	AATAATAACA	    0.779949	-187
CCAAGGTTAGAAGTAATAAATTCTCCTACTTA	1	60	1	AATAATAATT	    0.722957	-129
TATTTATTATAAGTAATAAGTAAGTAGGAGAA	1	80	0	AATAATAGTA	    0.876247	-109
TTTATTAATAAAAATAAAAACTATATTTATTA	1	103	0	AAATAAAACT	    0.750888	-86
ATATCGAGAGAATTTATTAATAAAAATAAAAA	1	115	0	AATTATAATA	    0.565437	-74
TATACATCTAAACAAATTAACAAAGCCATTTA	1	163	1	AAAAATAACA	    0.968344	-26
         tagtttattaacattgtttcg  	2	9	0	agttataaca	     0.67235	-13
        cttaattatgaacaacttaatatt	3	3	1	tattataaca	    0.872558	-155
ccgattaaagaataaaacaatattaagttgtt	3	21	0	aaaaaaaata	    0.909657	-137
caacaaaaccaaataaataatattcaaacccc	3	83	0	aataaaaata	    0.960041	-75
aataatcattaattaatcaattgtcgggtgaa	3	121	0	aataataatt	    0.638247	-37
   tctactgaaactatcaataatcattaatt	3	139	0	aactataata	    0.923456	-19
          ** **** ****

Masking position 6
Map Score:   15.4907

Number of sites scoring better than the average of aligned sites = 483
Number in coding regions = 420
Number in noncoding regions = 63
Number of orfs with sites within 600 bp upstream = 49
Fraction of orfs with sites within 600 bp upstream = 0.00787022


Motif number 2

ATCGAAAATATCGAGAGAATTTATTAATAAA	1	123	0	TCGAGAGATT	    0.965458	-66
tattctttaatcgggtcagttccccacttgg	3	39	1	tcgggtcatt	    0.990537	-119
gttccccacttggggtgttttagtcgggggt	3	57	1	tggggtgttt	    0.986495	-101
ggtgttttagtcgggggtttgaatattattt	3	70	1	tcgggggttg	      0.9855	-88
taatcaattgtcgggtgaattccaccaacaa	3	109	0	tcgggtgatt	    0.997294	-49
          ******** **

Masking position 10
Map Score:   4.35553

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 3

AGCCGTTTTCTAATTTTGTTATAATTCAAC	1	25	0	TAATTTTGTT	     0.98293	-164
  AAGTTAAATGGCTTTGTTAATTTGTTTA	1	171	0	TGGCTTTGTT	    0.986383	-18
  tagtttattaacattgtttcg       	2	4	0	taacattgtt	    0.977465	-18
atgaacaacttaatattgttttattcttta	3	18	1	taatattgtt	    0.975717	-140
attatttatttggttttgttggtggaattc	3	94	1	tggttttgtt	    0.985316	-64
          **********

Masking position 6
Map Score:   6.94868

Number of sites scoring better than the average of aligned sites = 137
Number in coding regions = 127
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 4

gtggggaactgacccgattaaagaataaaa	3	36	0	gacccgatta	    0.964835	-122
aatattcaaacccccgactaaaacacccca	3	67	0	cccccgacta	    0.997794	-91
cgggtgaattccaccaacaaaaccaaataa	3	99	0	ccaccaacaa	    0.966313	-59
tggtggaattcacccgacaattgattaatt	3	113	1	cacccgacaa	    0.996594	-45
          **********

Masking position 7
Map Score:   2.59187

Number of sites scoring better than the average of aligned sites = 4
Number in coding regions = 3
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 5

          **********

No masking
Map Score:   3.43493e-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:   3.43493e-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:   3.43493e-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