AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00450_mjan_reg_100.orf -o00450_mjan_100.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.31 -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 =  	0.31
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	MJ1263	130	methionyl-tRNA synthetase (metS)
#2	MJ1388	300	adenosylhomocysteinase (ahcY)

Motif number 1

TTAATAAACTTTAATACCTTTTTTGAAAGACA      	1	5	0	TTATTTTTGA	    0.970023	-126
GTATTAAAGTTTATTAAGGAAATTTGAATGCCTTCTAT	1	26	1	TTATGAATTA	    0.938346	-105
AAGGCGTTCATTAATACATTAATAGTTATTACAAAATA	1	67	1	TTATTTATGA	    0.972992	-64
TTAATAGTTATTACAAAATATTTTGAAAGACACTATTA	1	85	1	TTAATATTGA	    0.737211	-46
ACTTATTTACTTACTTAATTAATCTTAATTTTTAAGTG	2	18	0	TTATTTATTA	     0.98398	-283
CGGTCTGATTTTAATCTTGTAGTTTCCAAAGAAGGACA	2	116	0	TTATGTATTA	    0.977184	-185
AAAATAAACCTTAAATTTTTATTCTGAATCGGTCTGAT	2	145	0	TTAATTATTA	    0.964405	-156
TATTTTCTTTTTATTAATTTAATTTATATATTTGAATT	2	177	1	TTATTTATTA	    0.987108	-124
AGAAAAGCTTTTATTATTTATAAATTCAAATATATAAA	2	199	0	TTATTATATA	    0.759227	-102
GATATATAAATTACTATTTTTTAGTGAAGAAAAGCTTT	2	226	0	TTATTTTATA	    0.907344	-75
ATTTTAAAAATTAGTAGGGTAGCAGAGATATATAAATT	2	252	0	TTATGTACGA	    0.880212	-49
TCATTTCACCTTAAAGAATTAATTTTAAAAATTAGTAG	2	273	0	TTAATTATTA	    0.933176	-28
          *** *   *** * *  *

Masking position 3
Map Score:   14.1427

Number of sites scoring better than the average of aligned sites = 588
Number in coding regions = 397
Number in noncoding regions = 191
Number of orfs with sites within 600 bp upstream = 176
Fraction of orfs with sites within 600 bp upstream = 0.0282686


Motif number 2

 TGTCACACACTTAAAAATTAAGATTAATT	2	10	1	CTTAAAAATT	    0.953982	-291
ACCGATTCAGAATAAAAATTTAAGGTTTAT	2	150	1	AATAAAAATT	    0.910123	-151
TTATTTTCTTTTTATTAATTTAATTTATAT	2	176	1	TTTATTAATT	    0.938729	-125
TAAATTCAAATATATAAATTAAATTAATAA	2	187	0	TATATAAATT	    0.981625	-114
GCTTTTATTATTTATAAATTCAAATATATA	2	201	0	TTTATAAATT	    0.986593	-100
GTAGCAGAGATATATAAATTACTATTTTTT	2	242	0	TATATAAATT	    0.981625	-59
AAGAATTAATTTTAAAAATTAGTAGGGTAG	2	268	0	TTTAAAAATT	    0.982662	-33
          **********

Masking position 4
Map Score:   11.9064

Number of sites scoring better than the average of aligned sites = 476
Number in coding regions = 296
Number in noncoding regions = 180
Number of orfs with sites within 600 bp upstream = 169
Fraction of orfs with sites within 600 bp upstream = 0.0271442


Motif number 3

TTTAATACCTTTTTTGAAAGACA       	1	4	0	TTTTTGAAAG	    0.979486	-127
TTATTAAGGAAATTTGAATGCCTTCTATAA	1	36	1	AATTTGAATG	    0.956491	-95
CTTTCAAAATATTTTGTAATAACTATTAAT	1	84	0	ATTTTGTAAT	    0.815153	-47
ATTACAAAATATTTTGAAAGACACTATTAG	1	94	1	ATTTTGAAAG	    0.976442	-37
AATAAGTTATGTTGTGAATGATTGTCCTAT	2	49	1	GTTGTGAATG	     0.88561	-252
AATCAGACTGATTTGGAATGGAAACATTAG	2	82	1	ATTTGGAATG	    0.944314	-219
TTAATTTATATATTTGAATTTATAAATAAT	2	195	1	TATTTGAATT	    0.873151	-106
ACCCTACTAATTTTTAAAATTAATTCTTTA	2	270	1	TTTTTAAAAT	    0.574801	-31
          **********

Masking position 8
Map Score:   5.35935

Number of sites scoring better than the average of aligned sites = 790
Number in coding regions = 640
Number in noncoding regions = 150
Number of orfs with sites within 600 bp upstream = 134
Fraction of orfs with sites within 600 bp upstream = 0.0215226


Motif number 4

AACTTTAATACCTTTTTTGAAAGACA    	1	7	0	CCTTTTTTGA	    0.964298	-124
TTAATGAACGCCTTCTTATAGAAGGCATTC	1	51	0	CCTTCTTATA	    0.964861	-80
    CCTCTCCCTCCTTTTGACTAATAGTG	1	115	0	CCTCCTTTTG	    0.984359	-16
TAGCTGGTGTCCTTCTTTGGAAACTACAAG	2	109	1	CCTTCTTTGG	    0.993877	-192
          **********

Masking position 6
Map Score:   2.06617

Number of sites scoring better than the average of aligned sites = 98
Number in coding regions = 88
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 5

TTTTAATAGGACAATCATTCACAACATAAC	2	54	0	ACAATCATTC	    0.959824	-247
TTGTCCTATTAAAATCAGACTGATTTGGAA	2	70	1	AAAATCAGAC	    0.992739	-231
CTACAAGATTAAAATCAGACCGATTCAGAA	2	132	1	AAAATCAGAC	    0.992739	-169
          **********

Masking position 4
Map Score:   0.916882

Number of sites scoring better than the average of aligned sites = 175
Number in coding regions = 16
Number in noncoding regions = 159
Number of orfs with sites within 600 bp upstream = 18
Fraction of orfs with sites within 600 bp upstream = 0.0028911


Motif number 6

          **********

No masking
Map Score:   9.48026e-14

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:   9.48026e-14

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:   9.48026e-14

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