AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i111_Amino_Acid_Transport_2_mpneu_reg_100.orf -o111_mpneu_100.ace -a/home/amcguire/alignace/lib/ORF_mpneu.txt -z/skink1/amcguire/genomes/mpneu.fna -g0.40 -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 =  	0.4
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RMP00155	300	Mycoplasma_pneumoniae
#2	RMP00158	67	Mycoplasma_pneumoniae

Motif number 1

agtatttatttagtattatgcta       	1	4	0	tagtattatg	    0.981013	-297
ttaatattattagtatttatttagtattat	1	15	0	tagtatttat	    0.962831	-286
taaatactaataatattaagctattagtag	1	26	1	taatattaag	    0.969738	-275
agtaggtaaataatattaagataatattat	1	51	1	taatattaag	    0.969738	-250
aatattaagataatattatgttaaagaaaa	1	62	1	taatattatg	    0.930489	-239
atcttctatatagtatagagaaactttttc	1	87	0	tagtatagag	    0.828699	-214
tatagaagattagtatttaatagtaaacgg	1	107	1	tagtatttaa	    0.918485	-194
aaaaagaaagtggtatataggaaaatggaa	1	151	0	tggtatatag	    0.907126	-150
gctaccaacgtggtattaaaatgtgcccaa	1	186	0	tggtattaaa	    0.956786	-115
aataccatcagggtattaagatgctaccaa	1	208	0	gggtattaag	    0.946622	-93
aataccctgatggtattaatttcgtcggta	1	221	1	tggtattaat	     0.98073	-80
agtattattccggtattatttaccgacgaa	1	241	0	cggtattatt	    0.770419	-60
aatatttatttagtattattccggtattat	1	252	0	tagtattatt	    0.959002	-49
gcttaaattctaatatttatttagtattat	1	263	0	taatatttat	    0.870386	-38
          **********

Masking position 5
Map Score:   26.1625

Number of sites scoring better than the average of aligned sites = 166
Number in coding regions = 135
Number in noncoding regions = 31
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 2

agctattagtaggtaaataatattaagata	1	44	1	aggtaaataa	     0.94761	-257
gataatattatgttaaagaaaaagtttctc	1	70	1	tgttaaagaa	    0.904344	-231
taatagtaaacggcaaacaaatttgttttc	1	124	1	cggcaaacaa	    0.984895	-177
tataggaaaatggaaaacaaatttgtttgc	1	136	0	tggaaaacaa	    0.971768	-165
tgcccaaccgcgaaaaagaaagtggtatat	1	163	0	cgaaaaagaa	    0.936973	-138
ttaatttcgtcggtaaataataccggaata	1	236	1	cggtaaataa	    0.986275	-65
          **********

Masking position 5
Map Score:   4.8404

Number of sites scoring better than the average of aligned sites = 149
Number in coding regions = 134
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 3

attattagtatttatttagtattatgcta 	1	10	0	tttatttagt	    0.989819	-291
atactaatcttctatatagtatagagaaac	1	93	0	tctatatagt	    0.865799	-208
cctgatggtattaatttcgtcggtaaataa	1	226	1	ttaatttcgt	    0.959151	-75
aattctaatatttatttagtattattccgg	1	258	0	tttatttagt	    0.989819	-43
          **********

Masking position 5
Map Score:   3.34886

Number of sites scoring better than the average of aligned sites = 55
Number in coding regions = 10
Number in noncoding regions = 45
Number of orfs with sites within 600 bp upstream = 38
Fraction of orfs with sites within 600 bp upstream = 0.00610344


Motif number 4

          **********

No masking
Map Score:   6.63809e-14

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 5

          **********

No masking
Map Score:   6.63809e-14

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:   6.63809e-14

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