AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i110_mgen_mpneu_300.orf -o110_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	RMG03480	125	Mycoplasma
#2	RMG04515	87	Mycoplasma
#3	RMG04514	62	Mycoplasma
#4	RMG05637	86	Mycoplasma
#5	RMG03469	113	Mycoplasma

Motif number 1

AGAACATATTCCAAATAAAAAAGAGCAGCAC	1	22	1	CAAATAAAAA	    0.949674	-104
TGGTAGATAAAAAACAAAAAAGCAGCTGTTG	1	52	0	AAACAAAAAA	    0.948167	-74
TTTTTATCTACCAAAAAACAGATTTTTAGCT	1	70	1	CAAAAAACAG	    0.859414	-56
AAAATAAGTCAGAGCTAAAAATCTGTTTTTT	1	82	0	AAGCTAAAAA	    0.939215	-44
TTAGCACTCAAACACTAAAAGTGCTAATTAA	2	19	0	ACACTAAAAG	    0.951147	-69
CTCAGTAATTATAAACAAAAATTAGCACTCA	2	40	0	AAAACAAAAA	    0.915034	-48
TTTTTTTTAGATCAATAACAATTACTCAGTA	2	64	0	ACAATAACAA	    0.807076	-24
TGTTATTGATCTAAAAAAAAAGT        	2	75	1	CAAAAAAAAA	    0.897288	-13
TACCTTTTTTAACACTAAAAACATCGTTGCT	3	30	1	ACACTAAAAA	    0.939215	-33
       AAAAAAGCTAAAAGCAACGATGTT	3	49	0	AAGCTAAAAG	    0.951147	-14
          AAAAATCAAAGTTCTGGTGGT	4	1	1	AAAATCAAAG	    0.754799	-86
CCACAAAGTAAAAACCACCAGAACTTTGATT	4	14	0	AAACCACCAG	    0.867298	-73
TGCTTACTGACAAACCACAAAGTAAAAACCA	4	28	0	CAACCACAAA	    0.901469	-59
TGGAGTTGAACAAGCTACAAGTATTGTGCTT	4	54	0	CAGCTACAAG	     0.88967	-33
TTGTTCAACTCCAACAAACAGTGCT      	4	72	1	CAACAAACAG	     0.92614	-15
TGGTAATAATAAAAATATAAATTTTAAAATT	5	12	1	AAAATATAAA	    0.672132	-102
          * *********

Masking position 10
Map Score:   16.8587

Number of sites scoring better than the average of aligned sites = 1021
Number in coding regions = 912
Number in noncoding regions = 109
Number of orfs with sites within 600 bp upstream = 56
Fraction of orfs with sites within 600 bp upstream = 0.00899454


Motif number 2

ACATATTCCAAATAAAAAAGAGCAGCACAAC	1	25	1	AATAAAAAGA	     0.88405	-101
TTTTTTGGTAGATAAAAAACAAAAAAGCAGC	1	57	0	GATAAAAACA	    0.920468	-69
CTTATTTATAAATTTTAAAAATAAGTCAGAG	1	99	0	AATTTAAAAA	    0.973621	-27
ATTACTCAGTAATTATAAACAAAAATTAGCA	2	44	0	AATATAAACA	    0.945138	-44
AATTGTTATTGATCTAAAAAAAAAGT     	2	72	1	GATTAAAAAA	    0.961799	-16
CGATGTTTTTAGTGTTAAAAAAGGTATTGGT	3	25	0	AGTTTAAAAA	    0.948233	-38
     GTGGTAATAATAAAAATATAAATTTT	5	6	1	AATATAAAAA	    0.968282	-108
TAAAAATATAAATTTTAAAATTATTGAAATT	5	21	1	AATTTAAAAT	    0.847284	-93
CATTTTACTCGGTGTAAAAAACGTTTCATTG	5	62	0	GGTTAAAAAA	    0.924809	-52
          *** *******

Masking position 7
Map Score:   8.9549

Number of sites scoring better than the average of aligned sites = 345
Number in coding regions = 305
Number in noncoding regions = 40
Number of orfs with sites within 600 bp upstream = 32
Fraction of orfs with sites within 600 bp upstream = 0.00513974


Motif number 3

ACAGCTGCTTTTTTGTTTTTTATCTACCAA	1	54	1	TTTTGTTTTT	    0.857697	-72
AAGTGCTAATTAAAGTTTGTT         	2	2	0	TAAAGTTTGT	    0.673954	-86
AATTAGCACTTTTAGTGTTTGAGTGCTAAT	2	21	1	TTTAGTGTTT	     0.95468	-67
CAACGATGTTTTTAGTGTTAAAAAAGGTAT	3	29	0	TTTAGTGTTA	    0.728005	-34
CATCGTTGCTTTTAGCTTTTTT        	3	51	1	TTTAGCTTTT	    0.954672	-12
CCACCAGAACTTTGATTTTT          	4	1	0	TTTGATTTTT	    0.855737	-86
TCAAAGTTCTGGTGGTTTTTACTTTGTGGT	4	16	1	GGTGGTTTTT	    0.877924	-71
GTTTTTACTTTGTGGTTTGTCAGTAAGCAC	4	30	1	TGTGGTTTGT	    0.959869	-57
GCACAATACTTGTAGCTTGTTCAACTCCAA	4	56	1	TGTAGCTTGT	    0.954626	-31
TTAAAATTATTGAAATTTTTGACTGTGCAA	5	35	1	TGAAATTTTT	    0.840967	-79
GACTGTGCAATGAAACGTTTTTTACACCGA	5	55	1	TGAAACGTTT	    0.674878	-59
          **********

Masking position 8
Map Score:   6.11771

Number of sites scoring better than the average of aligned sites = 869
Number in coding regions = 791
Number in noncoding regions = 78
Number of orfs with sites within 600 bp upstream = 44
Fraction of orfs with sites within 600 bp upstream = 0.00706714


Motif number 4

AACAAAAAAGCAGCTGTTGTGCTGCTCTTT	1	41	0	CAGCTGTTGT	    0.987382	-85
GAACAAGCTACAAGTATTGTGCTTACTGAC	4	48	0	CAAGTATTGT	    0.926062	-39
TGCTTGAAAGCAGCAATGGTCATTTTACTC	5	83	0	CAGCAATGGT	    0.987903	-31
     ACTTACAGCTATGCTTGAAAGCAGC	5	99	0	CAGCTATGCT	    0.987175	-15
          **********

Masking position 7
Map Score:   0.0932902

Number of sites scoring better than the average of aligned sites = 22
Number in coding regions = 19
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 5

          **********

No masking
Map Score:   5.92755e-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:   5.92755e-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 7

          **********

No masking
Map Score:   5.92755e-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