AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i194_dna_replication_mpneu_reg_300.orf -o194_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	RMP00221	157	Mycoplasma_pneumoniae
#2	RMP00223	45	Mycoplasma_pneumoniae

Motif number 1

acaaccaccttaagtgggctgttaactaat	1	39	0	taagtgggct	    0.992278	-119
ttattataagtttgggggctgattttgtgg	1	79	1	tttgggggct	    0.988075	-79
gggggctgattttgtggggttcaccccttg	1	92	1	tttgtggggt	    0.993613	-66
gttcaccccttgactgggctaatttcttat	1	110	1	tgactgggct	    0.994766	-48
       ttgttactgggatgaccctagta	2	4	1	ttactgggat	    0.990684	-42
attgattttagtactagggtcatcccagta	2	15	0	gtactagggt	    0.942582	-31
          **********

Masking position 10
Map Score:   9.17933

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

ttagttaacagcccacttaaggtggttgtt	1	40	1	gcccacttaa	    0.993592	-118
cacaaaatcagcccccaaacttataataaa	1	78	0	gcccccaaac	    0.992535	-80
aaggggtgaaccccacaaaatcagccccca	1	91	0	ccccacaaaa	    0.990291	-67
taagaaattagcccagtcaaggggtgaacc	1	109	0	gcccagtcaa	    0.993702	-49
actagggtcatcccagtaacaa        	2	3	0	tcccagtaac	    0.986501	-43
          **********

Masking position 9
Map Score:   5.79437

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

ctaattaattactaataactatcaaagtca	1	14	0	actaataact	    0.941987	-144
tgggctgttaactaattaattactaataac	1	25	0	actaattaat	    0.870135	-133
ccaaacttataataaataaaccaaaacaac	1	64	0	aataaataaa	    0.911211	-94
attataacaaaataagaaattagcccagtc	1	121	0	aataagaaat	    0.909406	-37
atacttgttgaattataacaaaataagaaa	1	132	0	aattataaca	    0.921255	-26
         gaattaatacttgttgaatta	1	147	0	aattaatact	    0.918695	-11
tgaccctagtactaaaatcaataagactaa	2	23	1	actaaaatca	    0.873926	-23
          **********

Masking position 5
Map Score:   3.81629

Number of sites scoring better than the average of aligned sites = 327
Number in coding regions = 229
Number in noncoding regions = 98
Number of orfs with sites within 600 bp upstream = 77
Fraction of orfs with sites within 600 bp upstream = 0.0123675


Motif number 4

          **********

No masking
Map Score:   -4.73059e-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:   -4.73059e-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:   -4.73059e-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