AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i289_mjan_pyro_300.orf -o289_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	RMJ01998	300	M_jannaschii_chromosome
#2	RPH00347	163	Pyrococcus_OT3

Motif number 1

TTTGCTATTGATGATACTTTTAGGCTTTCTTTATGA	1	42	0	ATGTTTTTGT	    0.921044	-259
CGCAGAGGCTATACTCTATTTGCTATTGATGATACT	1	60	0	ATATATTTTT	    0.894892	-241
ATTATATATGATGAATTTTGTTATATGGAGTATGCC	1	124	0	ATGATTGTTT	    0.924485	-177
AATTCATCATATATAATATTTTCGGTTTAATTTTTA	1	143	1	ATAAATTTGT	    0.967392	-158
TTAATTTTTAATATAAAATTTTATCTTAGATTAAAA	1	169	1	ATAAATTTTT	    0.656192	-132
ATATTATGTTATGAATATTTTAATCTAAGATAAAAT	1	186	0	ATGATTTTTT	    0.987277	-115
TAATTTAAATATACAAATATTATGTTATGAATATTT	1	202	0	ATAATATTGT	    0.877333	-99
ACGATGTTTTATAAAAATATTGCTATTAAAGATTAA	1	235	0	ATAATATTTT	    0.751197	-66
  GATATCACATGTAATATTTATTTTCTGGATAGTA	1	277	0	ATGAATTTTT	    0.985162	-24
CATGTAGACTATTCACCTTTTAGTATAGCTTAATGA	2	22	1	ATTATTTTTT	    0.909637	-142
GTATAGCTTAATGAACTATTTAAGGCTTTCCTGCTC	2	44	1	ATGAATTTGC	    0.939679	-120
TTTGAAATTTATGAAAGATTTTTTACATTATATAAA	2	84	1	ATGAATTTTC	    0.954203	-80
TTTACATTATATAAAGCTTTTAATCTGCTGAGCTAG	2	105	1	ATAATTTTTT	    0.979693	-59
          *** *  ****  * *

Masking position 1
Map Score:   18.6493

Number of sites scoring better than the average of aligned sites = 491
Number in coding regions = 339
Number in noncoding regions = 152
Number of orfs with sites within 600 bp upstream = 158
Fraction of orfs with sites within 600 bp upstream = 0.0253774


Motif number 2

AATTAAACCGAAAATATTATATATGATGAA	1	145	0	AAAATATTAT	    0.638515	-156
TTTTCGGTTTAATTTTTAATATAAAATTTT	1	161	1	AATTTTTAAT	    0.704208	-140
TTTTTAATATAAAATTTTATCTTAGATTAA	1	173	1	AAAATTTTAT	    0.937106	-128
TTATGTTATGAATATTTTAATCTAAGATAA	1	189	0	AATATTTTAA	    0.960352	-112
TTCATAACATAATATTTGTATATTTAAATT	1	207	1	AATATTTGTA	    0.889947	-94
TATTTAAATTAATCTTTAATAGCAATATTT	1	227	1	AATCTTTAAT	    0.866544	-74
CTTTAATAGCAATATTTTTATAAAACATCG	1	240	1	AATATTTTTA	    0.934164	-61
TATCACATGTAATATTTATTTTCTGGATAG	1	279	0	AATATTTATT	    0.872874	-22
TTTCCTGCTCAAAATTTGAAATTTATGAAA	2	70	1	AAAATTTGAA	    0.878006	-94
AAATTTATGAAAGATTTTTTACATTATATA	2	88	1	AAGATTTTTT	    0.904401	-76
ACATTATATAAAGCTTTTAATCTGCTGAGC	2	108	1	AAGCTTTTAA	    0.855063	-56
          **********

Masking position 2
Map Score:   9.37533

Number of sites scoring better than the average of aligned sites = 2087
Number in coding regions = 1500
Number in noncoding regions = 587
Number of orfs with sites within 600 bp upstream = 411
Fraction of orfs with sites within 600 bp upstream = 0.0660135


Motif number 3

TCATAAAGAAAGCCTAAAAGTATCATCAAT	1	42	1	AGCCTAAAAG	    0.975314	-259
ATAAAATTTTATATTAAAAATTAAACCGAA	1	163	0	ATATTAAAAA	    0.854273	-138
ATTTTATCTTAGATTAAAATATTCATAACA	1	186	1	AGATTAAAAT	    0.967158	-115
TAATATTTGTATATTTAAATTAATCTTTAA	1	216	1	ATATTTAAAT	     0.86555	-85
TCATTAAGCTATACTAAAAGGTGAATAGTC	2	28	0	ATACTAAAAG	    0.965958	-136
TGAGCAGGAAAGCCTTAAATAGTTCATTAA	2	51	0	AGCCTTAAAT	    0.916189	-113
CTAGCTCAGCAGATTAAAAGCTTTATATAA	2	111	0	AGATTAAAAG	    0.979784	-53
          **********

Masking position 7
Map Score:   7.3278

Number of sites scoring better than the average of aligned sites = 289
Number in coding regions = 235
Number in noncoding regions = 54
Number of orfs with sites within 600 bp upstream = 48
Fraction of orfs with sites within 600 bp upstream = 0.0077096


Motif number 4

CTATTCAATAGAACTTACGCATTTTTTTGA	1	11	1	GAACTTACGC	    0.997453	-290
TCCCACAATGGAACTTACGCAGAGGCTATA	1	83	0	GAACTTACGC	    0.997453	-218
          **********

Masking position 5
Map Score:   1.47308

Number of sites scoring better than the average of aligned sites = 2
Number in coding regions = 0
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 5

          **********

No masking
Map Score:   -4.16788e-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:   -4.16788e-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:   -4.16788e-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