AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i340_weak11_pyro_reg_100.orf -o340_pyro_100.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	RPH01548	300	Pyrococcus_OT3

Motif number 1

ATCTCAGCCCTCATCGTTAATTCATTGTAAA	1	76	0	TCATCGTTAT	    0.926783	-225
TAGGTCTCTCCCATTCCTGATCTCAGCCCTC	1	95	0	CCATTCCTAT	     0.96963	-206
CCTTCACTCTTACTTCCTTAGGTCTCTCCCA	1	113	0	TACTTCCTAG	    0.837555	-188
GAGAATGGTTCAATCCTTCACTCTTACTTCC	1	127	0	CAATCCTTAC	    0.983005	-174
AAGGATTGAACCATTCTCCATGTAATCACCT	1	140	1	CCATTCTCAT	    0.825523	-161
CTCCTTTATTAAATCCTTTAGGTGATTACAT	1	159	0	AAATCCTTAG	    0.929724	-142
GTATTTTTGACTCTCCTTTATTAAATCCTTT	1	171	0	CTCTCCTTAT	    0.916151	-130
AAACCGGTCATCATTCCTAAGTATTTTTGAC	1	191	0	TCATTCCTAG	    0.955774	-110
GCTGGTGTCATCATCGTTCAGTCCCGAAACC	1	217	0	TCATCGTTAG	    0.952556	-84
ATGACACCAGCTATCGCTGACCTTGTCTAAA	1	237	1	CTATCGCTAC	    0.925735	-64
AAATCTTTATCAATCCTTAACACCTGCAAGG	1	265	1	CAATCCTTAC	    0.983005	-36
          ACCTCCCTCACCACTCCTTGC	1	290	0	ACCTCCCTAC	    0.952553	-11
          ******** **

Masking position 10
Map Score:   13.0849

Number of sites scoring better than the average of aligned sites = 1941
Number in coding regions = 1820
Number in noncoding regions = 121
Number of orfs with sites within 600 bp upstream = 127
Fraction of orfs with sites within 600 bp upstream = 0.0203983


Motif number 2

TTCATTTTACAATGAATTAACGATGAGGGC	1	71	1	AATGAATTAA	    0.849071	-230
GGGCTGAGATCAGGAATGGGAGAGACCTAA	1	97	1	CAGGAATGGG	    0.914187	-204
GGAGAGACCTAAGGAAGTAAGAGTGAAGGA	1	115	1	AAGGAAGTAA	    0.921694	-186
AGTAAGAGTGAAGGATTGAACCATTCTCCA	1	130	1	AAGGATTGAA	    0.989998	-171
TAATCACCTAAAGGATTTAATAAAGGAGAG	1	162	1	AAGGATTTAA	    0.980536	-139
CAAAAATACTTAGGAATGATGACCGGTTTC	1	193	1	TAGGAATGAT	     0.93161	-108
AAGGATTGATAAAGATTTAGACAAGGTCAG	1	253	0	AAAGATTTAG	    0.823441	-48
TGCAGGTGTTAAGGATTGATAAAGATTTAG	1	263	0	AAGGATTGAT	    0.987015	-38
TAACACCTGCAAGGAGTGGTGAGGGAGGT 	1	282	1	AAGGAGTGGT	    0.943623	-19
          **********

Masking position 5
Map Score:   10.2902

Number of sites scoring better than the average of aligned sites = 598
Number in coding regions = 553
Number in noncoding regions = 45
Number of orfs with sites within 600 bp upstream = 42
Fraction of orfs with sites within 600 bp upstream = 0.0067459


Motif number 3

TGATCTCAGCCCTCATCGTTAATTCATTGT	1	79	0	CCTCATCGTT	    0.996334	-222
TCCCGAAACCGGTCATCATTCCTAAGTATT	1	197	0	GGTCATCATT	    0.972395	-104
TAGCTGGTGTCATCATCGTTCAGTCCCGAA	1	220	0	CATCATCGTT	    0.990034	-81
     ACCTCCCTCACCACTCCTTGCAGGT	1	286	0	CCTCACCACT	     0.98374	-15
          **********

Masking position 5
Map Score:   2.05095

Number of sites scoring better than the average of aligned sites = 111
Number in coding regions = 98
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 4

          **********

No masking
Map Score:   7.91135e-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 5

          **********

No masking
Map Score:   7.91135e-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:   7.91135e-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