AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00340_mgen_reg_300.orf -o00340_mgen_300.ace -a/home/amcguire/genomes/ORF_mgen.txt -z/home/amcguire/genomes/mgen.fna -g0.32 -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 =  	0.32
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	MG035	28	histidyl-tRNA synthetase
#2	MG466	25	ribosomal protein L34 (rpL34)
#3	MG468.1	62	ABC transporter, ATP-binding protein
#4	MG469	300	chromosomal replication initiator protein (dnaA)

Motif number 1

GTCATTAATTATAATTTCGAAATTAT      	1	5	0	AAATTTCGAA	    0.970007	-24
  CAAAATTAAAATTTTCTAATAGTGTTCTCA	3	9	1	AATTTTCTAT	    0.922222	-54
AAAAAGAGAGATATTTTCAAGAGGAACAAAAT	4	16	1	AATTTTCAAA	    0.994706	-285
AAGAGGAACAAAATTTTCAATATCATAATAAT	4	34	1	AATTTTCAAA	    0.994706	-267
AAAAAAATCAAAATTTTCAACAACAATTCACA	4	79	1	AATTTTCAAA	    0.994706	-222
ATGATAGTTAAAATTCTCGAAATTGGGATATT	4	255	0	AATTCTCGAA	    0.982747	-46
TTCTTCTATAACATTGTCAAGAATGATAGTTA	4	277	0	AATTGTCAAA	    0.985654	-24
          * ******** *

Masking position 3
Map Score:   11.9393

Number of sites scoring better than the average of aligned sites = 26
Number in coding regions = 21
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 2

ATTAAGTCATCTAAAAAAATACCCTGAGAAC	3	34	0	CTAAAAAATA	    0.834401	-29
   ACCAAAAAAAGAGAGATATTTTCAAGAG	4	8	1	AAAGAGGATA	    0.851627	-293
GAGATATTTTCAAGAGGAACAAAATTTTCAA	4	23	1	CAAGAGAACA	    0.980863	-278
TTTCTTACAGCAAAAAAATCAAAATTTTCAA	4	68	1	CAAAAAATCA	    0.734273	-233
TCAAAATTTTCAACAACAATTCACACAACCA	4	86	1	CAACAAAATT	    0.948699	-215
CCCCAACCTAAAACAAAAATACCAGGAATAG	4	129	1	AAACAAAATA	     0.92015	-172
TCTTGGCGTTCAACAGGAACTATTCCTGGTA	4	148	0	CAACAGAACT	    0.934492	-153
TGTTGAACGCCAAGAAAAACTAGATACAGGT	4	164	1	CAAGAAAACT	    0.970235	-137
ATAACATTGTCAAGAATGATAGTTAAAATTC	4	271	0	CAAGAAGATA	    0.966182	-30
TGACAATGTTATAGAAGAATA          	4	290	1	ATAGAAAATA	    0.839011	-11
          ****** ****

Masking position 5
Map Score:   7.91906

Number of sites scoring better than the average of aligned sites = 512
Number in coding regions = 476
Number in noncoding regions = 36
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 3

AAACAATTAATCAGGTGATTATAA      	2	5	0	TCAGGTGATT	    0.949787	-21
AATAGTGTTCTCAGGGTATTTTTTTAGATG	3	28	1	TCAGGGTATT	    0.991344	-35
GAAACCATTATTATGATATTGAAAATTTTG	4	42	0	TTATGATATT	    0.935835	-259
CAGGAACTATTCCTGGTATTTTTGTTTTAG	4	136	0	TCCTGGTATT	    0.967549	-165
ATTCTCGAAATTGGGATATTAACTGCTTTG	4	245	0	TTGGGATATT	     0.95068	-56
          **********

Masking position 8
Map Score:   1.16792

Number of sites scoring better than the average of aligned sites = 23
Number in coding regions = 19
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 4

AATCACCTGATTAATTGTTTC         	2	15	1	TTAATTGTTT	    0.954438	-11
AGATGACTTAATGATTGTTT          	3	53	1	ATGATTGTTT	    0.988772	-10
CAATATCATAATAATGGTTTCTTACAGCAA	4	51	1	ATAATGGTTT	    0.946249	-250
GTTGAAAATTTTGATTTTTTTGCTGTAAGA	4	70	0	TTGATTTTTT	     0.87955	-231
TATTCCTGGTATTTTTGTTTTAGGTTGGGG	4	129	0	ATTTTTGTTT	    0.845408	-172
ATTGTCAAGAATGATAGTTAAAATTCTCGA	4	267	0	ATGATAGTTA	    0.868483	-34
          **********

Masking position 5
Map Score:   2.61039

Number of sites scoring better than the average of aligned sites = 184
Number in coding regions = 175
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 5

TAATTATAATTTCGAAATTAT         	1	2	0	TTCGAAATTA	    0.982005	-27
GAGAACACTATTAGAAAATTTTAATTTTG 	3	10	0	TTAGAAAATT	    0.906928	-53
TTTTGTTCCTCTTGAAAATATCTCTCTTTT	4	17	0	CTTGAAAATA	    0.937783	-284
TGACAAAAAGTTAGAAATTACTCCAAAGCA	4	222	1	TTAGAAATTA	    0.972436	-79
AGTTAAAATTCTCGAAATTGGGATATTAAC	4	252	0	CTCGAAATTG	    0.971875	-49
          **********

Masking position 5
Map Score:   2.53416

Number of sites scoring better than the average of aligned sites = 17
Number in coding regions = 13
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 6

          **********

No masking
Map Score:   -8.92852e-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:   -8.92852e-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:   -8.92852e-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