AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i119_Spermidine_putrescine_Transport_mpneu_reg_100.orf -o119_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	RMP00100	300	Mycoplasma_pneumoniae

Motif number 1

ttttctcttcaacatccgattttcttccccttaatt	1	15	0	aacgattttt	    0.962051	-286
tgaagagaaaaaagaacaattttctaagggaaagaa	1	40	1	aacaatttta	     0.92466	-261
tttttctctaaaagaactatttttctttcccttaga	1	62	0	aactattttt	     0.94111	-239
tagagaaaaaaatacagaattttcaccagaaataaa	1	88	1	aagaattttc	    0.986728	-213
cctgatttaaaacttggttttatttctggtgaaaat	1	106	0	aagttttatc	    0.935971	-195
accaagttttaaatcaggtttttgtcagtttaaaaa	1	124	1	aaggtttttc	     0.99455	-177
acgtcaatttaaacacgatttttaaactgacaaaaa	1	142	0	aagattttta	    0.945646	-159
atcgtgtttaaattgacgtttttgacaagtttttta	1	159	1	aacgtttttc	    0.993507	-142
ccctatttaaaagaacgtttttttactaacgttaaa	1	201	0	aagttttttc	    0.991382	-100
aactggggcgaacgggggattttgaccctatttaaa	1	226	0	aaggattttc	     0.99353	-75
gatgaattaaaaatttcttttttgccataaataaca	1	270	0	aacttttttc	    0.989739	-31
          **    *******  *

Masking position 2
Map Score:   21.4183

Number of sites scoring better than the average of aligned sites = 105
Number in coding regions = 84
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 2

attaaggggaagaaaatcggatgttgaaga	1	16	1	agaaaatcgg	    0.927734	-285
tctttcccttagaaaattgttcttttttct	1	45	0	agaaaattgt	    0.924745	-256
ttatttctggtgaaaattctgtattttttt	1	93	0	tgaaaattct	    0.924372	-208
ttttaaactgacaaaaacctgatttaaaac	1	129	0	acaaaaacct	    0.953033	-172
tttgtcagtttaaaaatcgtgtttaaattg	1	144	1	taaaaatcgt	     0.98322	-157
aaaaaacttgtcaaaaacgtcaatttaaac	1	164	0	tcaaaaacgt	    0.979734	-137
taaaacactctaaaaaacttgtcaaaaacg	1	175	0	taaaaaactt	    0.916114	-126
taacgttagtaaaaaaacgttcttttaaat	1	203	1	aaaaaaacgt	    0.964717	-98
ttaaatagggtcaaaatcccccgttcgccc	1	227	1	tcaaaatccc	    0.955085	-74
attgatgaattaaaaatttcttttttgcca	1	279	0	taaaaatttc	    0.687997	-22
          **********

Masking position 5
Map Score:   12.0815

Number of sites scoring better than the average of aligned sites = 252
Number in coding regions = 208
Number in noncoding regions = 44
Number of orfs with sites within 600 bp upstream = 41
Fraction of orfs with sites within 600 bp upstream = 0.00658529


Motif number 3

   aaacaattaaggggaagaaaatcggatgt	1	8	1	tagggaagaa	    0.994181	-293
atcggatgttgaagagaaaaaagaacaatttt	1	31	1	gagagaaaaa	     0.96911	-270
aacaattttctaagggaaagaaaaatagttct	1	54	1	tagggaagaa	    0.994181	-247
aatagttcttttagagaaaaaaatacagaatt	1	77	1	tagagaaaaa	    0.990283	-224
caggtttttgtcagtttaaaaatcgtgtttaa	1	138	1	tagttaaaaa	    0.929699	-163
tgttttaacgttagtaaaaaaacgttctttta	1	198	1	tagtaaaaaa	    0.929608	-103
gttcttttaaatagggtcaaaatcccccgttc	1	221	1	aagggcaaaa	    0.943304	-80
acgatgttatttatggcaaaaaagaaattttt	1	266	1	tatggaaaaa	    0.965855	-35
          * **** *****

Masking position 9
Map Score:   11.4073

Number of sites scoring better than the average of aligned sites = 122
Number in coding regions = 105
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 4

          **********

No masking
Map Score:   7.91135e-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 5

          **********

No masking
Map Score:   7.91135e-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:   7.91135e-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