AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i271_hypothetical16_pyro_reg_300.orf -o271_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	RPH00534	20	Pyrococcus_OT3
#2	RPH00533	119	Pyrococcus_OT3
#3	RPH00532	300	Pyrococcus_OT3

Motif number 1

TTGGAAGTTTAACTCTGGTAACCCCTCA        	2	3	0	ATTGGACCCT	    0.969867	-117
CATCTCCTGAGTTGCTGGATCCCACCTGGTGTGAGA	2	76	0	GGTGGTCCCC	    0.994677	-44
TTCAGAAAAGAGCAATGGTAGCCCCGCGGGGATTCG	3	66	1	AATGGACCCG	    0.994259	-235
TCCCGCGACCGGGGTTCGAATCCCCGCGGGGCTACC	3	82	0	GGTCGACCCG	    0.996748	-219
AAGCATGCGGGACTCTGGATCCCGCGACCGGGGTTC	3	101	0	GTTGGTCCCG	    0.996105	-200
TTGAGTGAAAATTGGACGTAGCCCCGTGGTGTAGCG	3	140	0	AGACGACCCG	    0.980131	-161
TAGAAATTTTAAAGGAGGAATCTGCCTAAACGGCTT	3	209	0	AGAGGACTCC	    0.918578	-92
TGTATATTAAGTTTTTGGCTTCCTCGCCTAGAAATT	3	237	0	GTTGGTCCCG	    0.996105	-64
TAATATACAGGGAAATGGTAACTTCGTTAAATCCGG	3	264	1	GATGGACTCG	    0.985293	-37
          *  * *** * ** **

Masking position 12
Map Score:   14.166

Number of sites scoring better than the average of aligned sites = 125
Number in coding regions = 107
Number in noncoding regions = 18
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 2

    TTTCAATACCTCCTACTAAT       	1	4	0	TACCTCTACT	    0.856847	-17
AGAGTTAAACTTCCAACTACCTATATACAAC	2	23	1	TTCCACTACC	    0.992786	-97
ACTACCTATATACAACTTCCCCTCCATTTTA	2	38	1	TACAATTCCC	    0.965474	-82
TATTCACTTTTTCCATCTCCTGAGTTGCTGG	2	94	0	TTCCACTCCT	    0.987267	-26
AAGTCCATGCTTTCATTTACCACTTGAAGTG	3	21	0	TTTCATTACC	    0.936635	-280
GCGACCGGGGTTCGAATCCCCGCGGGGCTAC	3	83	0	TTCGATCCCC	    0.943199	-218
TTAACGAAGTTACCATTTCCCTGTATATTAA	3	263	0	TACCATTCCC	    0.994498	-38
          ***** *****

Masking position 1
Map Score:   4.77551

Number of sites scoring better than the average of aligned sites = 673
Number in coding regions = 633
Number in noncoding regions = 40
Number of orfs with sites within 600 bp upstream = 36
Fraction of orfs with sites within 600 bp upstream = 0.0057822


Motif number 3

ATACAACTTCCCCTCCATTTTAGTTTGGGTCTC	2	47	1	CCTCCTTTAG	    0.938057	-73
CAGGTGGGATCCAGCAACTCAGGAGATGGAAAA	2	84	1	CCGCATCAGG	    0.986161	-36
    GCAACCCCCGCACTTCAAGTGGTAAATGA	3	7	1	CCGCATCAAG	     0.99278	-294
GATCCAGAGTCCCGCATGCTTGGCCGCTACACC	3	116	1	CCGCACTTGG	    0.972346	-185
ACTCAACGTTAATGCCTTTTAAGCTTTGCGGTT	3	170	1	AAGCCTTAAG	    0.904731	-131
CGGTTTTATTCAAGCCGTTTAGGCAGATTCCTC	3	198	1	CAGCCTTAGG	    0.988602	-103
TTACCATTTCCCTGTATATTAAGTTTTTGGCTT	3	252	0	CCGTATTAAG	    0.966453	-49
          ** ***  *****

Masking position 13
Map Score:   3.64195

Number of sites scoring better than the average of aligned sites = 185
Number in coding regions = 160
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 27
Fraction of orfs with sites within 600 bp upstream = 0.00433665


Motif number 4

TTTGGGTCTCACACCAGGTGGGATCCAGCA	2	70	1	ACACCAGGTG	    0.979166	-50
ATGCTTTCATTTACCACTTGAAGTGCGGGG	3	16	0	TTACCACTTG	    0.919749	-285
GGGGTTCGAATCCCCGCGGGGCTACCATTG	3	78	0	TCCCCGCGGG	    0.987072	-223
CTTGGCCGCTACACCACGGGGCTACGTCCA	3	134	1	ACACCACGGG	    0.997295	-167
     TTTATTCACCACCGGATTTAACGAA	3	286	0	TCACCACCGG	    0.995012	-15
          **********

Masking position 5
Map Score:   4.07064

Number of sites scoring better than the average of aligned sites = 50
Number in coding regions = 36
Number in noncoding regions = 14
Number of orfs with sites within 600 bp upstream = 19
Fraction of orfs with sites within 600 bp upstream = 0.00305172


Motif number 5

TAAAATGGAGGGGAAGTTGTATATAGGTAG	2	39	0	GGGAAGTTGT	    0.985938	-81
TTTCAGAAAAGAGCAATGGTAGCCCCGCGG	3	65	1	GAGCAATGGT	    0.985938	-236
TTAATATACAGGGAAATGGTAACTTCGTTA	3	263	1	GGGAAATGGT	    0.995624	-38
          **********

Masking position 5
Map Score:   0.131603

Number of sites scoring better than the average of aligned sites = 14
Number in coding regions = 14
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:   9.48026e-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:   9.48026e-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 8

          **********

No masking
Map Score:   9.48026e-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