AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i214_Ribosomal_Operon_1_mpneu_reg_100.orf -o214_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	RMP00221	157	Mycoplasma_pneumoniae
#2	RMP00223	45	Mycoplasma_pneumoniae
#3	RMP00226	30	Mycoplasma_pneumoniae

Motif number 1

attagttaacagcccacttaaggtggttgt	1	39	1	agcccactta	    0.992201	-119
ccacaaaatcagcccccaaacttataataa	1	79	0	agcccccaaa	    0.987955	-79
caaggggtgaaccccacaaaatcagccccc	1	92	0	accccacaaa	    0.993549	-66
ataagaaattagcccagtcaaggggtgaac	1	110	0	agcccagtca	    0.994714	-48
tactagggtcatcccagtaacaa       	2	4	0	atcccagtaa	    0.990591	-42
tactgggatgaccctagtactaaaatcaat	2	15	1	accctagtac	    0.942035	-31
          **********

Masking position 1
Map Score:   8.50045

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 = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 2

aacaaccaccttaagtgggctgttaactaa	1	40	0	ttaagtgggc	    0.992842	-118
tttattataagtttgggggctgattttgtg	1	78	1	gtttgggggc	    0.991662	-80
tgggggctgattttgtggggttcacccctt	1	91	1	ttttgtgggg	    0.989158	-67
ggttcaccccttgactgggctaatttctta	1	109	1	ttgactgggc	    0.992964	-49
        ttgttactgggatgaccctagt	2	3	1	gttactggga	    0.984933	-43
          **********

Masking position 2
Map Score:   5.22895

Number of sites scoring better than the average of aligned sites = 37
Number in coding regions = 28
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 3

ctaattaattactaataactatcaaagtcat	1	13	0	actaataata	    0.963608	-145
tgggctgttaactaattaattactaataact	1	24	0	actaattatt	    0.779836	-134
cccccaaacttataataaataaaccaaaaca	1	66	0	tataataata	    0.893273	-92
attataacaaaataagaaattagcccagtca	1	120	0	aataagaatt	    0.964227	-38
atacttgttgaattataacaaaataagaaat	1	131	0	aattataaaa	    0.914313	-27
gttataattcaacaagtattaattc      	1	143	1	aacaagtata	    0.878176	-15
tactaaaatcaataagactaaggg       	2	32	1	aataagacaa	    0.924698	-14
        taaattagaataataagcagttt	3	3	1	aattagaaaa	    0.944211	-28
          ******** **

Masking position 5
Map Score:   3.46129

Number of sites scoring better than the average of aligned sites = 291
Number in coding regions = 203
Number in noncoding regions = 88
Number of orfs with sites within 600 bp upstream = 65
Fraction of orfs with sites within 600 bp upstream = 0.0104401


Motif number 4

tactaataactatcaaagtcatct      	1	5	0	tatcaaagtc	    0.926226	-153
ataataaataaaccaaaacaaccaccttaa	1	56	0	aaccaaaaca	    0.912903	-102
ggggtgaaccccacaaaatcagcccccaaa	1	89	0	ccacaaaatc	    0.934645	-69
tgttgaattataacaaaataagaaattagc	1	127	0	taacaaaata	     0.97469	-31
atgaccctagtactaaaatcaataagacta	2	22	1	tactaaaatc	    0.935342	-24
        attaacaaaactgcttattatt	3	19	0	taacaaaact	     0.94769	-12
          **********

Masking position 5
Map Score:   0.805548

Number of sites scoring better than the average of aligned sites = 418
Number in coding regions = 358
Number in noncoding regions = 60
Number of orfs with sites within 600 bp upstream = 50
Fraction of orfs with sites within 600 bp upstream = 0.00803084


Motif number 5

          **********

No masking
Map Score:   -1.32571e-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:   -1.32571e-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:   -1.32571e-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