AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i175_biotin_biosynthesis1_mjan_reg_100.orf -o175_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

Purged sequences:
RMJ04314	50	M_jannaschii_chromosome

Input sequences:
#1	RMJ13159	50	M_jannaschii_chromosome
#2	RMJ01108	145	M_jannaschii_chromosome

Motif number 1

TATACAATAAATAAACATTAACTTTTAAAA	1	24	1	ATAAACATTA	    0.986911	-27
AACATTAACTTTTAAAATTTATTG      	1	37	1	TTTAAAATTT	    0.928982	-14
ATTTTATTTAATAAAAACTAAAAAAGAGAA	2	14	0	ATAAAAACTA	    0.939598	-132
ATTAAATAAAATAAGCATTTATTTGGTTTC	2	32	1	ATAAGCATTT	    0.957199	-114
AATTATTATAATTACAATTATCATTGATAT	2	64	0	ATTACAATTA	    0.918257	-82
AATTGTAATTATAATAATTACGATTATCAT	2	75	1	ATAATAATTA	    0.962221	-71
AATAATTACGATTATCATTTTGTGGTAAGT	2	87	1	ATTATCATTT	    0.933183	-59
GGTAAGTTATTTAAACAGTAGATTAAAAAT	2	110	1	TTAAACAGTA	    0.913086	-36
AAACAGTAGATTAAAAATTTTGATAGGTGA	2	122	1	TTAAAAATTT	    0.961443	-24
          **********

Masking position 4
Map Score:   11.9289

Number of sites scoring better than the average of aligned sites = 1294
Number in coding regions = 838
Number in noncoding regions = 456
Number of orfs with sites within 600 bp upstream = 393
Fraction of orfs with sites within 600 bp upstream = 0.0631224


Motif number 2

ACCCTATATACAATAAATAAACATTAACTT	1	18	1	CAATAAATAA	     0.75285	-33
AATAAATAAACATTAACTTTTAAAATTTAT	1	29	1	CATTAACTTT	    0.963399	-22
          CAATAAATTTTAAAAGTTAA	1	41	0	CAATAAATTT	    0.923239	-10
AGTTTTTATTAAATAAAATAAGCATTTATT	2	25	1	AAATAAAATA	     0.91272	-121
TTATAATTACAATTATCATTGATATAGGAA	2	59	0	AATTATCATT	    0.750977	-87
TGATAATTGTAATTATAATAATTACGATTA	2	71	1	AATTATAATA	    0.654963	-75
TAATAATTACGATTATCATTTTGTGGTAAG	2	86	1	GATTATCATT	    0.843141	-60
TCTACTGTTTAAATAACTTACCACAAAATG	2	102	0	AAATAACTTA	    0.956301	-44
          **********

Masking position 5
Map Score:   6.77131

Number of sites scoring better than the average of aligned sites = 2391
Number in coding regions = 1863
Number in noncoding regions = 528
Number of orfs with sites within 600 bp upstream = 417
Fraction of orfs with sites within 600 bp upstream = 0.0669772


Motif number 3

 AAAAATCACCCTATATACAATAAATAAAC	1	10	1	CCTATATACA	    0.968932	-41
TATTTGGTTTCCTATATCAATGATAATTGT	2	51	1	CCTATATCAA	    0.988068	-95
GTTTAAATAACTTACCACAAAATGATAATC	2	96	0	CTTACCACAA	    0.950988	-50
   TTTATCACCTATCAAAATTTTTAATCT	2	129	0	CCTATCAAAA	     0.98834	-17
          **********

Masking position 4
Map Score:   1.34148

Number of sites scoring better than the average of aligned sites = 166
Number in coding regions = 140
Number in noncoding regions = 26
Number of orfs with sites within 600 bp upstream = 31
Fraction of orfs with sites within 600 bp upstream = 0.00497912


Motif number 4

          **********

No masking
Map Score:   -1.60993e-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:   -1.60993e-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:   -1.60993e-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