AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i021_Succinyl-CoA_Synthetase_mjan_reg_100.orf -o021_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	RMJ05733	98	M_jannaschii_chromosome
#2	RMJ03497	300	M_jannaschii_chromosome

Motif number 1

TTAAACCTATAAATTTATCACCAAATTTTTT	1	22	1	AAATTTACAC	    0.928476	-77
ATTTATCACCAAATTTTTTATATGATAATTT	1	34	1	AAATTTTTAT	      0.9815	-65
GCAAAATTTTAAAATTATCATATAAAAAATT	1	45	0	AAAATTACAT	    0.966789	-54
GATAATTTTAAAATTTTGCATTAAAAAGAAA	1	57	1	AAATTTTCAT	    0.985602	-42
CATTAAAAAGAAATTTATCATTTAAGGTGAT	1	75	1	AAATTTACAT	    0.982281	-24
TCACAGGAATAAATCTACTATTGGAATGACG	2	156	1	AAATCTATAT	    0.909767	-145
TAGAACTTTCACAATTTATATATTTATAAGG	2	209	0	ACAATTTTAT	    0.931592	-92
ATCCCCTTTTACTTTTTATATGTGTCGTTGT	2	239	0	ACTTTTTTAT	    0.803803	-62
ATTAAACCGTAAAATTTATATATCCCCTTTT	2	260	0	AAAATTTTAT	    0.965314	-41
          ******* ***

Masking position 6
Map Score:   11.4936

Number of sites scoring better than the average of aligned sites = 515
Number in coding regions = 349
Number in noncoding regions = 166
Number of orfs with sites within 600 bp upstream = 157
Fraction of orfs with sites within 600 bp upstream = 0.0252168


Motif number 2

ATAAATTTATAGGTTTAATGTTGTCGGTG      	1	5	0	AGGTTGTGTC	    0.986335	-94
CCCAGGTCCAGGGATTTCTCCTGCCGTGGTCCAGC	2	51	1	GGGTTCTGCC	    0.997607	-250
TCTATCATCGGGGACTCCAGTTGCCTATAGGGCGC	2	84	0	GGGTAGTGCC	    0.995581	-217
ATTGATGCGGGGGTGTGGTGTAGCCAGGTCTATCA	2	112	0	GGGTTGAGCC	    0.996705	-189
GATGCCTAAAGGGTATCGTCATTCCAATAGTAGAT	2	168	0	GGGTTCTTCC	    0.991068	-133
TATATTTATAAGGCACTTTGATGCCTAAAGGGTAT	2	187	0	AGGCTGTGCC	    0.993926	-114
          ***  *  ** ****

Masking position 3
Map Score:   8.26033

Number of sites scoring better than the average of aligned sites = 22
Number in coding regions = 14
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 3

GGGTTCAAATCCCAGCACCCCCACCATTTT	2	24	0	CCCAGCACCC	    0.993505	-277
GGGATTTGAACCCAGGTCCAGGGATTTCTC	2	41	1	CCCAGGTCCA	    0.981863	-260
GCCTATAGGGCGCTGGACCACGGCAGGAGA	2	67	0	CGCTGGACCA	    0.990556	-234
TGATAGACCTGGCTACACCACACCCCCGCA	2	112	1	GGCTACACCA	    0.939573	-189
TACACCACACCCCCGCATCAATGTAGAATC	2	125	1	CCCCGCATCA	    0.974422	-176
   TTTATCCCTCAACACCATGTATTAAAC	2	284	0	CTCAACACCA	    0.972756	-17
          **********

Masking position 3
Map Score:   4.31058

Number of sites scoring better than the average of aligned sites = 100
Number in coding regions = 76
Number in noncoding regions = 24
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 4

GGTCCAGCGCCCTATAGGCAACTGGAGTCC	2	78	1	CCTATAGGCA	    0.995358	-223
GAATAAATCTACTATTGGAATGACGATACC	2	162	1	ACTATTGGAA	    0.942352	-139
ATGACGATACCCTTTAGGCATCAAAGTGCC	2	181	1	CCTTTAGGCA	    0.991844	-120
          **********

Masking position 10
Map Score:   0.379422

Number of sites scoring better than the average of aligned sites = 21
Number in coding regions = 9
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 5

          **********

No masking
Map Score:   2.43208e-15

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:   2.43208e-15

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:   2.43208e-15

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