AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i110_Amino_Acid_Transport_1_mjan_reg_100.orf -o110_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	RMJ06726	108	M_jannaschii_chromosome
#2	RMJ10646	245	M_jannaschii_chromosome
#3	RMJ07954	32	M_jannaschii_chromosome

Motif number 1

AAAAGAGTTATTTAAAGTTTTAGGAATTTT 	1	10	0	TTTAAGTTTT	    0.958826	-99
ATAACTCTTTTTTAAATTTTTAAGATATGCA	1	30	1	TTTAATTTTT	    0.988693	-79
GTTCTAAGATTATAAATTTTATTCTTTAAAC	1	62	1	TATAATTTTA	    0.950035	-47
AATTTTATTCTTTAAACTTTTTATCATTTTT	1	76	1	TTTAACTTTT	    0.958826	-33
TTAAACTTTTTATCATTTTTTTGAGGGATAC	1	87	1	TATCTTTTTT	     0.91657	-22
ATAACCAGCGTTTAGATTTTTTACTTTTATC	2	34	0	TTTAATTTTT	    0.988723	-212
AATTTTCCCTTTTCTATTTTTGCATTCACAT	2	87	0	TTTCATTTTT	    0.977221	-159
ATCTCTCCAGAATATATTTTTGTTAAACCAA	2	173	0	AATAATTTTT	    0.918079	-73
        GGTATAATTTTTATAAAACCTAA	3	3	1	TATATTTTTA	    0.855977	-30
          **** ******

Masking position 8
Map Score:   13.4011

Number of sites scoring better than the average of aligned sites = 974
Number in coding regions = 660
Number in noncoding regions = 314
Number of orfs with sites within 600 bp upstream = 280
Fraction of orfs with sites within 600 bp upstream = 0.0449727


Motif number 2

ATCTAAACGCTGGTTATGGAAAATTGCAGA	2	48	1	TGGTTATGGA	    0.983779	-198
CAGATACTATTTGATGTGAATGCAAAAATA	2	74	1	TTGATGTGAA	    0.973348	-172
TTGGACCTAATGGTAGTGGAAAATCCACAT	2	128	1	TGGTAGTGGA	    0.989652	-118
 CCTTGCTTTTTGATGTGGAGGGACTTTTG	2	227	0	TTGATGTGGA	    0.993386	-19
          **********

Masking position 7
Map Score:   3.07706

Number of sites scoring better than the average of aligned sites = 90
Number in coding regions = 84
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 3

TATTTAAAGTTTTAGGAATTTT        	1	3	0	TTTAGGAATT	    0.886739	-106
ATCTTAAAAATTTAAAAAAGAGTTATTTAA	1	26	0	TTTAAAAAAG	    0.952909	-83
TTTTTAAATTTTTAAGATATGCAAGTTCTA	1	38	1	TTTAAGATAT	    0.840828	-71
TGATAAAAAGTTTAAAGAATAAAATTTATA	1	72	0	TTTAAAGAAT	    0.932533	-37
AAACAACGTTTTTAAAAATGTGGATTTTCC	2	145	0	TTTAAAAATG	    0.952911	-101
CGTTGTTTGGTTTAACAAAAATATATTCTG	2	167	1	TTTAACAAAA	    0.854546	-79
AGAGATTATATTTAAGGATAAAGATATAGC	2	198	1	TTTAAGGATA	    0.899449	-48
CATTAGGTTTTATAAAAATTATACC     	3	6	0	TATAAAAATT	    0.813933	-27
          **********

Masking position 4
Map Score:   3.66342

Number of sites scoring better than the average of aligned sites = 1612
Number in coding regions = 1299
Number in noncoding regions = 313
Number of orfs with sites within 600 bp upstream = 252
Fraction of orfs with sites within 600 bp upstream = 0.0404754


Motif number 4

CGCTGGTTATGGAAAATTGCAGATACTATTT	2	55	1	GGAAAATTCA	    0.928609	-191
AATAGAAAAGGGAAAATTACCACAGTTGTTG	2	100	1	GGAAAATTCC	    0.626059	-146
TAATGGTAGTGGAAAATCCACATTTTTAAAA	2	135	1	GGAAAATCAC	    0.970488	-111
TAAAGATATAGCAAAAGTCCCTCCACATCAA	2	216	1	GCAAAAGTCC	    0.977962	-30
          ******** **

Masking position 6
Map Score:   1.20267

Number of sites scoring better than the average of aligned sites = 57
Number in coding regions = 54
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 5

          **********

No masking
Map Score:   8.26662e-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:   8.26662e-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 7

          **********

No masking
Map Score:   8.26662e-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