AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i119_Spermidine_putrescine_Transport_mpneu_reg_300.orf -o119_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	RMP00100	300	Mycoplasma_pneumoniae

Motif number 1

ttttctcttcaacatccgattttcttcccctta	1	18	0	aaccgatttt	    0.600309	-283
tgaagagaaaaaagaacaattttctaagggaaa	1	40	1	aaacaatttt	    0.589298	-261
tttttctctaaaagaactatttttctttccctt	1	65	0	aaactatttt	    0.601427	-236
ttctggtgaaaattctgtatttttttctctaaa	1	86	0	aatgtatttt	    0.941123	-215
cctgatttaaaacttggttttatttctggtgaa	1	109	0	aacgttttat	    0.888794	-192
accaagttttaaatcaggtttttgtcagtttaa	1	124	1	aaaggttttt	    0.799854	-177
acgtcaatttaaacacgatttttaaactgacaa	1	145	0	aaagattttt	     0.56214	-156
atcgtgtttaaattgacgtttttgacaagtttt	1	159	1	aatcgttttt	     0.96629	-142
accctatttaaaagaacgtttttttactaacgt	1	205	0	aaacgttttt	    0.606687	-96
aactggggcgaacgggggattttgaccctattt	1	229	0	aacggatttt	    0.987558	-72
cccagtttttaacgatgttatttatggcaaaaa	1	255	1	aacgttattt	    0.872605	-46
gatgaattaaaaatttcttttttgccataaata	1	273	0	aaactttttt	    0.581697	-28
          ***   *******

Masking position 2
Map Score:   23.9425

Number of sites scoring better than the average of aligned sites = 199
Number in coding regions = 142
Number in noncoding regions = 57
Number of orfs with sites within 600 bp upstream = 39
Fraction of orfs with sites within 600 bp upstream = 0.00626405


Motif number 2

cttcaacatccgattttcttccccttaatt	1	15	0	cgattttctt	     0.89045	-286
gaaaattgttcttttttctcttcaacatcc	1	34	0	cttttttctc	     0.96071	-267
tctaaaagaactatttttctttcccttaga	1	62	0	ctatttttct	    0.806134	-239
tgaaaattctgtatttttttctctaaaaga	1	83	0	gtattttttt	    0.860713	-218
aaaaaatacagaattttcaccagaaataaa	1	94	1	gaattttcac	    0.835428	-207
ttaaaacttggttttatttctggtgaaaat	1	106	0	gttttatttc	     0.74288	-195
ttttaaatcaggtttttgtcagtttaaaaa	1	130	1	ggtttttgtc	    0.977325	-171
aatttaaacacgatttttaaactgacaaaa	1	143	0	cgatttttaa	    0.766464	-158
tttaaattgacgtttttgacaagtttttta	1	165	1	cgtttttgac	    0.977325	-136
ttaaaagaacgtttttttactaacgttaaa	1	201	0	gtttttttac	    0.961457	-100
ggcgaacgggggattttgaccctatttaaa	1	226	0	ggattttgac	    0.977323	-75
ttaaaaatttcttttttgccataaataaca	1	270	0	cttttttgcc	    0.955776	-31
          **********

Masking position 5
Map Score:   14.0303

Number of sites scoring better than the average of aligned sites = 456
Number in coding regions = 393
Number in noncoding regions = 63
Number of orfs with sites within 600 bp upstream = 46
Fraction of orfs with sites within 600 bp upstream = 0.00738837


Motif number 3

catccgattttcttccccttaattgttt   	1	8	0	tcttccctta	     0.98806	-293
aaattgttcttttttctcttcaacatccgat	1	31	0	ttttctcttc	    0.900469	-270
gaactatttttctttcccttagaaaattgtt	1	54	0	tcttccctta	     0.98806	-247
attctgtatttttttctctaaaagaactatt	1	77	0	ttttctctaa	    0.943955	-224
aaatacagaattttcaccagaaataaaacca	1	97	1	ttttaccaga	    0.912187	-204
taaacacgatttttaaactgacaaaaacctg	1	138	0	ttttaactga	    0.882637	-163
ttttagagtgttttaacgttagtaaaaaaac	1	190	1	ttttacgtta	    0.934475	-111
gaacgggggattttgaccctatttaaaagaa	1	222	0	ttttacccta	    0.958133	-79
aaaatttcttttttgccataaataacatcgt	1	266	0	ttttccataa	    0.889995	-35
          **** ******

Masking position 4
Map Score:   8.42665

Number of sites scoring better than the average of aligned sites = 266
Number in coding regions = 228
Number in noncoding regions = 38
Number of orfs with sites within 600 bp upstream = 31
Fraction of orfs with sites within 600 bp upstream = 0.00497912


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