AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i347_mjan_pyro_300.orf -o347_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	RMJ12183	300	M_jannaschii_chromosome
#2	RPH00141	201	Pyrococcus_OT3

Motif number 1

TTAATATTAATAATGGATATTTGAACGCTC	1	24	0	TAATGGATAT	     0.97164	-277
ATTTCTTTTATTATGATTATCCTCCAAATT	1	87	1	TTATGATTAT	    0.980148	-214
ATAAAAGGAAATATGATTATAAAACTGACT	1	123	0	ATATGATTAT	    0.911843	-178
ATATTTCCTTTTATGGATATTATAGAGCGG	1	139	1	TTATGGATAT	    0.979239	-162
GAGCGGTAGCTTATGGTTATTTAAATTTTA	1	163	1	TTATGGTTAT	    0.990104	-138
AATAAATTTTTAATGATTAATGCTAAATAG	1	240	0	TAATGATTAA	    0.904871	-61
TAAATAACGTTTATGGAAAAGATTCAATAG	1	278	1	TTATGGAAAA	    0.876592	-23
          **********

Masking position 3
Map Score:   8.74899

Number of sites scoring better than the average of aligned sites = 273
Number in coding regions = 243
Number in noncoding regions = 30
Number of orfs with sites within 600 bp upstream = 32
Fraction of orfs with sites within 600 bp upstream = 0.00513974


Motif number 2

ATTACCTGTAGGGTCCCGCGGTAGCCTAGCC	2	88	1	GGGTCCGCGG	      0.9995	-114
AGCCTAGCCTGGGAGTGGCGGCGGACTGTAG	2	110	1	GGGAGTGCGG	     0.99471	-92
ATTTGAACCGGGGACCTGCGGATCTACAGTC	2	133	0	GGGACCGCGG	    0.999501	-69
AGAATTCTGGTGGTCCCGCGGCCCGGATTTG	2	159	0	TGGTCCGCGG	     0.99802	-43
          ****** ****

Masking position 8
Map Score:   8.17444

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 3

TATAGTGTCTTTCAAAGTTGTTAAAATTAAT	1	49	0	TTCAAAGTTT	    0.981834	-252
ACACTATATTTTAAAATTTCTTTTATTATGA	1	72	1	TTAAAATTTT	    0.977777	-229
ATGATTATCCTCCAAATTTATTGAAGTCAGT	1	99	1	TCCAAATTTT	    0.960907	-202
GTGAAATCATTTAAAATTTAAATAACCATAA	1	173	0	TTAAAATTTA	    0.726016	-128
TATCCAAGATTACAAATCTATTTAGCATTAA	1	223	1	TACAAATCTT	    0.918367	-78
CATTAATCATTAAAAATTTATTTCCCAGTAT	1	248	1	TAAAAATTTT	    0.961459	-53
AATGTGGGTTTATAAAGTTTTCGCGAGGAGT	2	39	0	TATAAAGTTT	    0.912664	-163
ATTAATCGCCTTAAAAGTTGTGAGAATTCTG	2	181	0	TTAAAAGTTT	    0.977967	-21
          ********* *

Masking position 6
Map Score:   7.81843

Number of sites scoring better than the average of aligned sites = 558
Number in coding regions = 399
Number in noncoding regions = 159
Number of orfs with sites within 600 bp upstream = 152
Fraction of orfs with sites within 600 bp upstream = 0.0244137


Motif number 4

ATATTAATAATGGATATTTGAACGCTCTCCT	1	20	0	TGGATATTTA	    0.994999	-281
TTTCCTTTTATGGATATTATAGAGCGGTAGC	1	142	1	TGGATATTAA	     0.98748	-159
CGGTAGCTTATGGTTATTTAAATTTTAAATG	1	166	1	TGGTTATTTA	    0.987493	-135
TTTGTAATCTTGGATATTTAATATTGGGTAA	1	208	0	TGGATATTTA	    0.994999	-93
          ********* *

Masking position 6
Map Score:   5.85971

Number of sites scoring better than the average of aligned sites = 37
Number in coding regions = 34
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

TTGAACGCTCTCCTATAGGGAGG        	1	3	0	TCTATAGGGA	    0.969767	-298
AGAAATTTTAAAATATAGTGTCTTTCAAAGT	1	62	0	AATATAGTGT	    0.887167	-239
CTTGGATATTTAATATTGGGTAAACTGGTGA	1	200	0	TATATTGGGT	    0.966462	-101
TAAACGTTATTTATACTGGGAAATAAATTTT	1	260	0	TATACTGGGA	      0.9203	-41
TTATAAACCCACATTTAGTGAGATGATTTTG	2	55	1	AATTTAGTGA	    0.845601	-147
TTTAGTGAGATGATTTTGGGATTACCTGTAG	2	68	1	TATTTTGGGA	    0.952629	-134
TTTTGGGATTACCTGTAGGGTCCCGCGGTAG	2	81	1	ACTGTAGGGT	    0.897267	-121
          * *********

Masking position 4
Map Score:   1.04852

Number of sites scoring better than the average of aligned sites = 441
Number in coding regions = 385
Number in noncoding regions = 56
Number of orfs with sites within 600 bp upstream = 61
Fraction of orfs with sites within 600 bp upstream = 0.00979762


Motif number 6

          **********

No masking
Map Score:   -5.09159e-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:   -5.09159e-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 8

          **********

No masking
Map Score:   -5.09159e-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