AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i043_5_1_3_1_mjan_reg_300.orf -o043_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	RMJ03270	23	M_jannaschii_chromosome
#2	RMJ00927	156	M_jannaschii_chromosome
#3	RMJ06922	26	M_jannaschii_chromosome
#4	RMJ13401	29	M_jannaschii_chromosome
#5	RMJ08184	47	M_jannaschii_chromosome

Motif number 1

TAAATCACCAAAAAATAAAATT        	1	3	0	AAAAATAAAA	    0.985234	-21
ACTTACACCTAAAAATAATAGATAGTAAAT	2	20	0	AAAAATAATA	    0.987732	-137
GATGTTATGCTAAAATAATTGTTAGTCATA	2	56	0	TAAAATAATT	    0.911381	-101
TAAAAAAAGCAAAAACAAAAAATCCATAAT	2	86	0	AAAAACAAAA	    0.974229	-71
TCAATGAATTAATAAAAAAAGCAAAAACAA	2	98	0	AATAAAAAAA	    0.879081	-59
TTAAGATTTAAAAAATAATATCATTACTCA	2	125	0	AAAAATAATA	    0.987732	-32
         TAAAAACACATTAATGGTGAT	3	2	1	AAAAACACAT	    0.937495	-25
ATTATTAATTAATAATACTTTTCGTGGTGG	5	17	0	AATAATACTT	    0.941396	-31
ATTATTAATTAATAATAATTCCTTTTA   	5	31	1	AATAATAATT	    0.937244	-17
          **********

Masking position 5
Map Score:   15.7307

Number of sites scoring better than the average of aligned sites = 1216
Number in coding regions = 778
Number in noncoding regions = 438
Number of orfs with sites within 600 bp upstream = 338
Fraction of orfs with sites within 600 bp upstream = 0.0542885


Motif number 2

      TTAAATCACCAAAAAATAAAATT 	1	10	0	ATCACCAAAA	    0.988897	-14
ATTTAAAACTTACACCTAAAAATAATAGAT	2	27	0	TACACCTAAA	    0.928192	-130
CATAATGATGTTATGCTAAAATAATTGTTA	2	62	0	TTATGCTAAA	    0.588904	-95
CAAAAACAAAAAATCCATAATGATGTTATG	2	77	0	AAATCCATAA	    0.913842	-80
AATTAATAAAAAAAGCAAAAACAAAAAATC	2	92	0	AAAAGCAAAA	    0.976136	-65
     TATGCATCACCATTAATGTGTTTTT	3	12	0	ATCACCATTA	    0.889415	-15
          ATAAGCAAAAACTTTATAAG	4	1	1	ATAAGCAAAA	    0.976572	-29
          **********

Masking position 10
Map Score:   4.70992

Number of sites scoring better than the average of aligned sites = 1166
Number in coding regions = 975
Number in noncoding regions = 191
Number of orfs with sites within 600 bp upstream = 189
Fraction of orfs with sites within 600 bp upstream = 0.0303566


Motif number 3

TAAATCACCAAAAAATAAAATT        	1	3	0	AAAAATAAAA	    0.890612	-21
ACTTACACCTAAAAATAATAGATAGTAAAT	2	20	0	AAAAATAATA	    0.913797	-137
ATTGTTAGTCATATTTAAAACTTACACCTA	2	39	0	ATATTTAAAA	     0.89062	-118
CATTACTCAATGAATTAATAAAAAAAGCAA	2	104	0	TGAATTAATA	    0.967145	-53
CACCTTTTTAAGATTTAAAAAATAATATCA	2	132	0	AGATTTAAAA	    0.948321	-25
GGAATTATTATTAATTAATAATACTTTTCG	5	23	0	TTAATTAATA	    0.928878	-25
     TAAAAGGAATTATTATTAATTAATA	5	33	0	GGAATTATTA	    0.837053	-15
          **********

Masking position 7
Map Score:   3.79928

Number of sites scoring better than the average of aligned sites = 1373
Number in coding regions = 1037
Number in noncoding regions = 336
Number of orfs with sites within 600 bp upstream = 279
Fraction of orfs with sites within 600 bp upstream = 0.0448121


Motif number 4

          **********

No masking
Map Score:   -2.39152e-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 5

          **********

No masking
Map Score:   -2.39152e-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:   -2.39152e-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