AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i021_Succinyl-CoA_Synthetase_mjan_reg_300.orf -o021_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	RMJ05733	98	M_jannaschii_chromosome
#2	RMJ03497	300	M_jannaschii_chromosome

Motif number 1

AAAAAATTTGGTGATAAATTTATAGGTTTAA	1	22	0	GTGTAAATTT	    0.922366	-77
AAATTATCATATAAAAAATTTGGTGATAAAT	1	34	0	ATAAAAATTT	    0.979828	-65
AATTTTTTATATGATAATTTTAAAATTTTGC	1	45	1	ATGTAATTTT	    0.963831	-54
TTTCTTTTTAATGCAAAATTTTAAAATTATC	1	57	0	ATGAAAATTT	    0.984289	-42
ATCACCTTAAATGATAAATTTCTTTTTAATG	1	75	0	ATGTAAATTT	    0.980679	-24
CGTCATTCCAATAGTAGATTTATTCCTGTGA	2	156	0	ATATAGATTT	    0.902228	-145
CCTTATAAATATATAAATTGTGAAAGTTCTA	2	209	1	ATAAAATTGT	    0.925738	-92
ACAACGACACATATAAAAAGTAAAAGGGGAT	2	239	1	ATAAAAAAGT	    0.789458	-62
AAAAGGGGATATATAAATTTTACGGTTTAAT	2	260	1	ATAAAATTTT	    0.962235	-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

      CACCGACAACATTAAACCTATAAATTTAT	1	5	1	GACACAACCT	    0.986691	-94
GCTGGACCACGGCAGGAGAAATCCCTGGACCTGGG	2	51	0	GGCAGAACCC	    0.997616	-250
GCGCCCTATAGGCAACTGGAGTCCCCGATGATAGA	2	84	1	GGCACTACCC	    0.995617	-217
TGATAGACCTGGCTACACCACACCCCCGCATCAAT	2	112	1	GGCTCAACCC	    0.996772	-189
ATCTACTATTGGAATGACGATACCCTTTAGGCATC	2	168	1	GGAAGAACCC	    0.991299	-133
ATACCCTTTAGGCATCAAAGTGCCTTATAAATATA	2	187	1	GGCACAGCCT	    0.994072	-114
          **** **  *  ***

Masking position 13
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

AAAATGGTGGGGGTGCTGGGATTTGAACCC	2	24	1	GGGTGCTGGG	     0.99327	-277
GAGAAATCCCTGGACCTGGGTTCAAATCCC	2	41	0	TGGACCTGGG	    0.981209	-260
TCTCCTGCCGTGGTCCAGCGCCCTATAGGC	2	67	1	TGGTCCAGCG	    0.990214	-234
TGCGGGGGTGTGGTGTAGCCAGGTCTATCA	2	112	0	TGGTGTAGCC	      0.9375	-189
GATTCTACATTGATGCGGGGGTGTGGTGTA	2	125	0	TGATGCGGGG	    0.973507	-176
GTTTAATACATGGTGTTGAGGGATAAA   	2	284	1	TGGTGTTGAG	    0.971783	-17
          **********

Masking position 8
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	    0.995579	-223
GAATAAATCTACTATTGGAATGACGATACC	2	162	1	ACTATTGGAA	     0.94496	-139
ATGACGATACCCTTTAGGCATCAAAGTGCC	2	181	1	CCTTTAGGCA	    0.992231	-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