AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i218_Ribosomal_Operon_5_mpneu_reg_300.orf -o218_mpneu_300.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	RMP00219	21	Mycoplasma_pneumoniae
#2	RMP00220	157	Mycoplasma_pneumoniae

Motif number 1

gttttattctttaatcgggtcagttcccca	2	35	1	ttaatcgggt	    0.993338	-123
ttggggtgttttagtcgggggtttgaatat	2	66	1	ttagtcgggg	     0.99725	-92
ttgaatattatttatttggttttgttggtg	2	88	1	tttatttggt	    0.947834	-70
tttatttggttttgttggtggaattcaccc	2	98	1	tttgttggtg	    0.977873	-60
taattaatcaattgtcgggtgaattccacc	2	114	0	attgtcgggt	    0.993211	-44
          **********

Masking position 5
Map Score:   6.39121

Number of sites scoring better than the average of aligned sites = 86
Number in coding regions = 78
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 2

        cgaaacaatgttaataaacta 	1	3	1	aaacaatgtt	    0.993134	-19
ttaaagaataaaacaatattaagttgttca	2	19	0	aaacaatatt	    0.989072	-139
aaaaccaaataaataatattcaaacccccg	2	81	0	aaataatatt	    0.976238	-77
atcattaattaatcaattgtcgggtgaatt	2	119	0	aatcaattgt	    0.956264	-39
acaattgattaattaatgattattgatagt	2	129	1	aattaatgat	    0.947043	-29
          **********

Masking position 5
Map Score:   5.70006

Number of sites scoring better than the average of aligned sites = 84
Number in coding regions = 75
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 3

ccaagtggggaactgacccgattaaagaat	2	40	0	aactgacccg	    0.992238	-118
acccccgactaaaacaccccaagtggggaa	2	58	0	aaaacacccc	    0.993468	-100
aaataatattcaaacccccgactaaaacac	2	71	0	caaacccccg	    0.992921	-87
ttgttggtggaattcacccgacaattgatt	2	109	1	aattcacccg	    0.995694	-49
          **********

Masking position 2
Map Score:   3.50022

Number of sites scoring better than the average of aligned sites = 41
Number in coding regions = 33
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 4

  cgaaacaatgttaataaacta       	1	9	1	tgttaataaa	    0.973959	-13
aatattaagttgttcataattaag      	2	5	0	tgttcataat	    0.960241	-153
aacaaaaccaaataaataatattcaaaccc	2	84	0	aataaataat	     0.93178	-74
aataatcattaattaatcaattgtcgggtg	2	123	0	aattaatcaa	    0.915965	-35
ctactgaaactatcaataatcattaattaa	2	137	0	tatcaataat	    0.966811	-21
          **********

Masking position 6
Map Score:   1.61457

Number of sites scoring better than the average of aligned sites = 127
Number in coding regions = 96
Number in noncoding regions = 31
Number of orfs with sites within 600 bp upstream = 32
Fraction of orfs with sites within 600 bp upstream = 0.00513974


Motif number 5

          **********

No masking
Map Score:   3.08538e-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:   3.08538e-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:   3.08538e-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