AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00340_mgen_reg_100.orf -o00340_mgen_100.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	    0.971287	-24
  CAAAATTAAAATTTTCTAATAGTGTTCTCA	3	9	1	AATTTTCTAT	    0.925383	-54
AAAAAGAGAGATATTTTCAAGAGGAACAAAAT	4	16	1	AATTTTCAAA	    0.994938	-285
AAGAGGAACAAAATTTTCAATATCATAATAAT	4	34	1	AATTTTCAAA	    0.994938	-267
AAAAAAATCAAAATTTTCAACAACAATTCACA	4	79	1	AATTTTCAAA	    0.994938	-222
ATGATAGTTAAAATTCTCGAAATTGGGATATT	4	255	0	AATTCTCGAA	    0.983492	-46
TTCTTCTATAACATTGTCAAGAATGATAGTTA	4	277	0	AATTGTCAAA	    0.986276	-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

ATAATTTCGAAATTATAATTAATGACAC   	1	11	1	AATTATATTA	    0.827493	-18
        GAAACAATTAATCAGGTGATTAT	2	13	0	AACAATAATC	    0.967298	-13
         AAACAATCATTAAGTCATCTAA	3	51	0	AACAATATTA	    0.985715	-12
TGCTGTAAGAAACCATTATTATGATATTGAA	4	49	0	AACCATATTA	    0.968831	-252
CAAAATTTTCAACAACAATTCACACAACCAC	4	87	1	AACAACATTC	    0.981171	-214
CCCAACCTAAAACAAAAATACCAGGAATAGT	4	130	1	AACAAAATAC	    0.879509	-171
CGAGAATTTTAACTATCATTCTTGACAATGT	4	268	1	AACTATATTC	    0.987075	-33
          ****** ****

Masking position 5
Map Score:   5.84049

Number of sites scoring better than the average of aligned sites = 100
Number in coding regions = 89
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 3

        ACCAAAAAAAGAGAGATATTTTCA	4	3	1	CAAAAAAAAA	    0.956068	-298
GAGATATTTTCAAGAGGAACAAAATTTTCAAT	4	23	1	CAAGAGGACA	    0.976246	-278
TTTCTTACAGCAAAAAAATCAAAATTTTCAAC	4	68	1	CAAAAAAACA	    0.982355	-233
AAATTTTCAACAACAATTCACACAACCACAGC	4	89	1	CAACAATTAA	    0.821727	-212
CAACCTAAAACAAAAATACCAGGAATAGTTCC	4	132	1	CAAAAATACG	    0.911655	-169
TCTTGGCGTTCAACAGGAACTATTCCTGGTAT	4	147	0	CAACAGGACA	    0.976246	-154
TGTTGAACGCCAAGAAAAACTAGATACAGGTG	4	164	1	CAAGAAAACA	    0.978794	-137
AAGAGTATGACAAAAAGTTAGAAATTACTCCA	4	215	1	CAAAAAGTAA	    0.926076	-86
          ******** * *

Masking position 5
Map Score:   5.78037

Number of sites scoring better than the average of aligned sites = 286
Number in coding regions = 264
Number in noncoding regions = 22
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 4

ATTAATTATAATTTCGAAATTAT         	1	2	0	ATTGAAATTA	    0.981479	-27
TGAGAACACTATTAGAAAATTTTAATTTTG  	3	9	0	ATTAAAATTT	    0.872996	-54
 ACCAAAAAAAGAGAGATATTTTCAAGAGGAA	4	10	1	AGAGATATTT	    0.906012	-291
AGAAACCATTATTATGATATTGAAAATTTTGT	4	41	0	ATTGATATTG	     0.97589	-260
GTTGTTGAAAATTTTGATTTTTTTGCTGTAAG	4	71	0	ATTGATTTTT	    0.934749	-230
TATGACAAAAAGTTAGAAATTACTCCAAAGCA	4	220	1	AGTGAAATTA	    0.972722	-81
AATTCTCGAAATTGGGATATTAACTGCTTTGG	4	244	0	ATTGATATTA	    0.985715	-57
          ***  *******

Masking position 7
Map Score:   4.50062

Number of sites scoring better than the average of aligned sites = 78
Number in coding regions = 67
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 5

          **********

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 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