AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i210_mjan_pyro_300.orf -o210_mjan_pyro_300.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.37 -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 =  	0.37
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RMJ05016	29	M_jannaschii_chromosome
#2	RPH01513	112	Pyrococcus_OT3

Motif number 1

    ACAGTCAAAGATTTATATAACAAATGT	1	7	1	AAAGATTATA	    0.988916	-23
TAGTGTGAGAAGGGGGTTATAGGAG      	2	5	0	AGGGGTTATA	    0.990019	-108
TTTATAAGTTAAGAGATTATCTCTCAGTTAA	2	38	0	AAGAGTTATC	    0.989076	-75
ATTCTTGTTGAAAAATTTATAAGTTAAGAGA	2	53	0	AAAAATTATA	    0.985505	-60
ATTTTTCAACAAGAATTTATAAAACTAGACG	2	68	1	AAGAATTATA	    0.992006	-45
          ***** *****

Masking position 7
Map Score:   7.13006

Number of sites scoring better than the average of aligned sites = 200
Number in coding regions = 185
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 19
Fraction of orfs with sites within 600 bp upstream = 0.00305172


Motif number 2

TTCTCACACTACATTAACTGAGAGATAATCTCT	2	25	1	ACTAACGAGA	    0.997299	-88
AATTTATAAAACTAGACGGGAGATTTTCTCTGG	2	81	1	ACAACGGAGA	    0.996744	-32
       ACCACCTCACCAGAGAAAATCTCCCG	2	97	0	ACTACCGAGA	    0.999005	-16
          ** * *** ****

Masking position 6
Map Score:   0.97235

Number of sites scoring better than the average of aligned sites = 3
Number in coding regions = 2
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 3

        ACAGTCAAAGATTTATATAACA	1	3	1	AGTCAAAGAT	     0.98594	-27
CAGTTAATGTAGTGTGAGAAGGGGGTTATA	2	15	0	AGTGTGAGAA	    0.991247	-98
CACTACATTAACTGAGAGATAATCTCTTAA	2	31	1	ACTGAGAGAT	      0.9948	-82
          **********

Masking position 7
Map Score:   0.634226

Number of sites scoring better than the average of aligned sites = 38
Number in coding regions = 36
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 4

    CTACATTTGTTATATAAATCTTTGAC	1	14	0	TTGTTATATA	    0.979143	-16
TTATAAATTCTTGTTGAAAAATTTATAAGT	2	60	0	TTGTTGAAAA	    0.959101	-53
ATCTCCCGTCTAGTTTTATAAATTCTTGTT	2	75	0	TAGTTTTATA	    0.973504	-38
          **********

Masking position 8
Map Score:   0.0210231

Number of sites scoring better than the average of aligned sites = 158
Number in coding regions = 131
Number in noncoding regions = 27
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


Motif number 5

          **********

No masking
Map Score:   5.21701e-14

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:   5.21701e-14

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:   5.21701e-14

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