AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_mpneu.txt -z/home/amcguire/genomes/mpneu.fna -igalR_mpneu_opreg_300.orf -g0.400 -x5 
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 = 	0

Input sequences:
#1	1674278	300	MG116 homolog, from M. genitalium

Motif number 1

GACCCGCTACCCCACTGCAGGCCACGGCAAT	1	82	0	CCCACTGAGG	    0.899725	-219
AAACAAGCTACCAACTGCTTGGTTTTCCAAT	1	120	0	CCAACTGTTG	    0.717496	-181
GTTTCTAGAGCCAGCTGGTAGTTTTGTTTCA	1	186	0	CCAGCTGTAG	    0.945209	-115
ACGAATTGCGCCAGCTTTTTGTGCAAAAAAT	1	215	1	CCAGCTTTTG	    0.969258	-86
TAAAATGTGTTCAACTGTTTGCAAGATTTTT	1	240	0	TCAACTGTTG	    0.968482	-61
          ******* ***

Masking position 6
Map Score:   5.96734

Number of sites scoring better than the average of aligned sites = 54
Number in coding regions = 50
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 2

GTGCTGTATCGCGTTATTGTGTTCGTGAAA	1	17	1	GCGTTATTGT	    0.967817	-284
TATCAACATTGAGTTTTTGCATTAAACCTA	1	53	0	GAGTTTTTGC	    0.958498	-248
GCTACCAACTGCTTGGTTTTCCAATGCATC	1	115	0	GCTTGGTTTT	    0.957493	-186
GCAGTTGGTAGCTTGTTTTTCTGTGTGATT	1	133	1	GCTTGTTTTT	    0.954268	-168
TTGTTTTTCTGTGTGATTGTTGCCAACAAG	1	145	1	GTGTGATTGT	    0.941589	-156
CCAGCTGGTAGTTTTGTTTCAAAGTCATAA	1	177	0	GTTTTGTTTC	     0.90907	-124
CTGTTTGCAAGATTTTTTGCACAAAAAGCT	1	227	0	GATTTTTTGC	    0.950311	-74
          **********

Masking position 4
Map Score:   4.92967

Number of sites scoring better than the average of aligned sites = 292
Number in coding regions = 250
Number in noncoding regions = 42
Number of orfs with sites within 600 bp upstream = 34
Fraction of orfs with sites within 600 bp upstream = 0.00546097


Motif number 3

TGAAATGGCGTTAGGTTTAATGCAAAAACT	1	42	1	TTAGGTTTAA	    0.982466	-259
TGAACACATTTTAAGTGAAATTTCTTAGGT	1	258	1	TTAAGTGAAA	    0.951735	-43
GTGAAATTTCTTAGGTTAAATAAGGTTTAA	1	272	1	TTAGGTTAAA	    0.992102	-29
TTAGGTTAAATAAGGTTTAAGAGAACAAG 	1	282	1	TAAGGTTTAA	    0.981411	-19
          **********

Masking position 6
Map Score:   4.35827

Number of sites scoring better than the average of aligned sites = 38
Number in coding regions = 29
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 4

AACATTGAGTTTTTGCATTAAACCTAACGCC	1	48	0	TTTTGCATAA	     0.97543	-253
CATAAGCCTTGTTGGCAACAATCACACAGAA	1	151	0	GTTGGCAAAA	    0.985895	-150
AGGCTTATGACTTTGAAACAAAACTACCAGC	1	173	1	CTTTGAAAAA	    0.941764	-128
TTGCAAGATTTTTTGCACAAAAAGCTGGCGC	1	222	0	TTTTGCACAA	     0.97904	-79
GTGTTCAACTGTTTGCAAGATTTTTTGCACA	1	234	0	GTTTGCAAAT	    0.979265	-67
          ******** **

Masking position 7
Map Score:   1.82152

Number of sites scoring better than the average of aligned sites = 89
Number in coding regions = 69
Number in noncoding regions = 20
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 5

GTATCGCGTTATTGTGTTCGTGAAATGGCG	1	22	1	ATTGTGTTCG	    0.974949	-279
TGTTCGTGAAATGGCGTTAGGTTTAATGCA	1	36	1	ATGGCGTTAG	    0.980499	-265
ACATTGAGTTTTTGCATTAAACCTAACGCC	1	48	0	TTTGCATTAA	    0.796328	-253
TTGGTTTTCCAATGCATCAGGACCCGCTAC	1	103	0	AATGCATCAG	     0.95425	-198
CTAGAAACGAATTGCGCCAGCTTTTTGTGC	1	209	1	ATTGCGCCAG	    0.973376	-92
TTTCACTTAAAATGTGTTCAACTGTTTGCA	1	248	0	AATGTGTTCA	    0.875751	-53
          **********

Masking position 4
Map Score:   0.223593

Number of sites scoring better than the average of aligned sites = 204
Number in coding regions = 182
Number in noncoding regions = 22
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


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


Motif number 7

          **********

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 8

          **********

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