AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00930_mjan_reg_300.orf -o00930_mjan_300.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	MJ0140	138	conserved hypothetical protein

Motif number 1

TGTCAAGTTAAGTTTTTATTAAATATTGATAAAA	1	22	0	AGTTATTAAT	     0.98073	-117
TTAACTTGACAGTCCCTATAATAAGTTTTAAAAT	1	45	1	AGTTATAAAA	     0.99005	-94
AGTTAGAACAAGTGAATTTTAAAACTTATTATAG	1	60	0	AGTTTTTAAA	    0.989853	-79
TATTAGATATAGTGAATATTATATTAGAGTTAGA	1	87	0	AGTTATTAAT	    0.994486	-52
ATAGTTAGAAAGTATTTATTAGATATAGTGAATA	1	103	0	AGTTATTAAT	    0.997812	-36
          ***   ***** **

Masking position 7
Map Score:   10.1929

Number of sites scoring better than the average of aligned sites = 63
Number in coding regions = 41
Number in noncoding regions = 22
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


Motif number 2

     AGTTTATTATTTTTTATCAATATTTA	1	6	1	ATTTTTTTTA	     0.93727	-133
TTATTTTTTATCAATATTTAATAAAAACTTA	1	17	1	TCATATTTAA	    0.894248	-122
GACTGTCAAGTTAAGTTTTTATTAAATATTG	1	28	0	TTAGTTTTTA	    0.894848	-111
AGTCCCTATAATAAGTTTTAAAATTCACTTG	1	55	1	ATAGTTTTAA	    0.973461	-84
TTTAAAATTCACTTGTTCTAACTCTAATATA	1	71	1	ACTGTTCTAA	    0.965289	-68
GATATAGTGAATATTATATTAGAGTTAGAAC	1	85	0	ATATATATTA	    0.819525	-54
TATAATATTCACTATATCTAATAAATACTTT	1	98	1	ACTTATCTAA	    0.946481	-41
TATCTAATAAATACTTTCTAACTATGGGAGG	1	112	1	ATATTTCTAA	    0.978869	-27
          *** *******

Masking position 11
Map Score:   7.19178

Number of sites scoring better than the average of aligned sites = 1368
Number in coding regions = 1073
Number in noncoding regions = 295
Number of orfs with sites within 600 bp upstream = 262
Fraction of orfs with sites within 600 bp upstream = 0.0420816


Motif number 3

AAATATTGATAAAAAATAATAAACT     	1	6	0	AAAAAATAAT	    0.931997	-133
ATTTTTTATCAATATTTAATAAAAACTTAA	1	19	1	AATATTTAAT	    0.724858	-120
ATATTTAATAAAAACTTAACTTGACAGTCC	1	30	1	AAAACTTAAC	    0.974506	-109
AGTGAATTTTAAAACTTATTATAGGGACTG	1	54	0	AAAACTTATT	    0.758148	-85
TCCCATAGTTAGAAAGTATTTATTAGATAT	1	111	0	AGAAAGTATT	    0.810381	-28
          **********

Masking position 4
Map Score:   1.67859

Number of sites scoring better than the average of aligned sites = 907
Number in coding regions = 652
Number in noncoding regions = 255
Number of orfs with sites within 600 bp upstream = 247
Fraction of orfs with sites within 600 bp upstream = 0.0396723


Motif number 4

TATAGGGACTGTCAAGTTAAGTTTTTATTA	1	35	0	GTCAAGTTAA	     0.97841	-104
TTAGAGTTAGAACAAGTGAATTTTAAAACT	1	68	0	AACAAGTGAA	    0.989543	-71
TATTTATTAGATATAGTGAATATTATATTA	1	95	0	ATATAGTGAA	     0.97478	-44
          **********

Masking position 5
Map Score:   0.0876568

Number of sites scoring better than the average of aligned sites = 26
Number in coding regions = 22
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 5

          **********

No masking
Map Score:   -9.70439e-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 6

          **********

No masking
Map Score:   -9.70439e-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:   -9.70439e-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