AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i283_hypothetical8_pyro_reg_300.orf -o283_pyro_300.ace -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -g0.42 -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 =  	0.42
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RPH00500	97	Pyrococcus_OT3
#2	RPH00499	300	Pyrococcus_OT3

Motif number 1

TCAAATCCCGGCCGGGGCACCAGGAATTTT	2	128	0	GCCGGGGCAC	    0.999475	-173
GGGATTTGAACCCGGGGCGCGGGCTCGAAA	2	149	1	CCCGGGGCGC	    0.998329	-152
CGCATGTTTGGCCGGGCTACACCACCGGGG	2	183	1	GCCGGGCTAC	    0.994377	-118
GGGCTACACCACCGGGGCAGACCCATTAGC	2	196	1	ACCGGGGCAG	    0.996206	-105
          **********

Masking position 5
Map Score:   6.64624

Number of sites scoring better than the average of aligned sites = 13
Number in coding regions = 4
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 2

AAGAAAGGTTAATAAAAGTTTCG        	1	3	0	AAAAAAGTTT	    0.938408	-95
AGATTTTAGTAAAGAAAGGTTAATAAAAGTT	1	14	0	AAGAAAGGTT	    0.952377	-84
TGTTGATCCTCACAAGATTTTAGTAAAGAAA	1	28	0	CAAAGATTTT	    0.871362	-70
TCTTGTGAGGATCAACAGGTTTAAATTCCAA	1	42	1	ATAACAGGTT	    0.865029	-56
GGGAGAGTAAAATAAATTGTTTGGAGGTGAT	1	73	1	AAAAATTGTT	    0.780722	-25
CATGTTCTGCAAGAACAGGCTTAGGGCATAA	2	20	0	AAAACAGGCT	    0.970112	-281
CCTGTTCTTGCAGAACATGTTAGGGAATATC	2	32	1	CAAACATGTT	    0.968651	-269
ACCCCTTTCTCAAAAGAGACTGTGAAGATTG	2	90	0	CAAAGAGACT	    0.757973	-211
ATCGAAAATTAAGGAAATGCTAATGGGTCTG	2	213	0	AAGAAATGCT	    0.899292	-88
AGCTTCACCTCAGAAAATTTTCATTCATTGA	2	278	0	CAAAAATTTT	    0.911941	-23
          ** ********

Masking position 5
Map Score:   5.76795

Number of sites scoring better than the average of aligned sites = 447
Number in coding regions = 383
Number in noncoding regions = 64
Number of orfs with sites within 600 bp upstream = 63
Fraction of orfs with sites within 600 bp upstream = 0.0101189


Motif number 3

TTAGTAAAGAAAGGTTAATAAAAGTTTCG 	1	10	0	AAGGTTAATA	    0.931777	-88
CTTAGGGCATAAGTTTTATGC         	2	2	0	AAGTTTTATG	    0.936336	-299
GGGCACCAGGAATTTTCATGCTTACCCCTT	2	114	0	AATTTTCATG	    0.978466	-187
AAATTAAGGAAATGCTAATGGGTCTGCCCC	2	209	0	AATGCTAATG	    0.929863	-92
GAACTGACGCAATTTTAATATTCAATGAAT	2	257	1	AATTTTAATA	    0.950636	-44
CACCTCAGAAAATTTTCATTCATTGAATAT	2	274	0	AATTTTCATT	    0.900647	-27
          **********

Masking position 6
Map Score:   2.77015

Number of sites scoring better than the average of aligned sites = 122
Number in coding regions = 101
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 4

TGAGGATCAACAGGTTTAAATTCCAAGGGA	1	47	1	CAGGTTTAAA	      0.9669	-51
GCCCGCGCCCCGGGTTCAAATCCCGGCCGG	2	143	0	CGGGTTCAAA	    0.995419	-158
ACCCGGGGCGCGGGCTCGAAAGGCCCGCAT	2	158	1	CGGGCTCGAA	    0.993528	-143
          **********

Masking position 9
Map Score:   0.387506

Number of sites scoring better than the average of aligned sites = 37
Number in coding regions = 13
Number in noncoding regions = 24
Number of orfs with sites within 600 bp upstream = 27
Fraction of orfs with sites within 600 bp upstream = 0.00433665


Motif number 5

TCTGCAAGAACAGGCTTAGGGCATAAGTTT	2	16	0	CAGGCTTAGG	    0.984326	-285
TCTTGCAGAACATGTTAGGGAATATCTAGA	2	37	1	CATGTTAGGG	    0.976945	-264
CAGGAATTTTCATGCTTACCCCTTTCTCAA	2	108	0	CATGCTTACC	    0.975575	-193
GAAAGGCCCGCATGTTTGGCCGGGCTACAC	2	175	1	CATGTTTGGC	    0.990747	-126
          **********

Masking position 6
Map Score:   0.259057

Number of sites scoring better than the average of aligned sites = 58
Number in coding regions = 52
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 6

          **********

No masking
Map Score:   -8.92852e-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:   -8.92852e-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:   -8.92852e-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