AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i323_mixed8_pyro_reg_300.orf -o323_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	RPH01199	158	Pyrococcus_OT3
#2	RPH01201	239	Pyrococcus_OT3

Motif number 1

GTGGGGAGTGGTTAGTGGTACGGCGGCCATAGCGGGGG	2	18	1	GTGTGGCGCC	    0.977686	-222
GGTTCGAAATGAGACCGGGTGTAACCCCCCCGCTATGG	2	44	0	GACCGGGCCC	    0.999488	-196
GTCTCATTTCGAACCCGGAAGTTAAGCCCCCCAGCGAT	2	67	1	GACCGGGGCC	    0.999737	-173
GCCCCCCAGCGATCCCGGTTGTACTGCCCTCCGAGAGG	2	92	1	GACCGGGGCC	    0.999728	-148
ACTGCCCTCCGAGAGGGGGCGGGAAGCCGGGGACGCCG	2	114	1	GAGGGGGGCC	    0.998186	-126
GAGAATTAGGGTGGCCGGCGGCGTCCCCGGCTTCCCGC	2	132	0	GTCCGGGCCC	    0.997668	-108
          **  ****  *    ***

Masking position 8
Map Score:   12.2864

Number of sites scoring better than the average of aligned sites = 20
Number in coding regions = 12
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 2

TTAAGTACTATTTGAAATTGTTAAATTTGGTGAC	1	16	0	TTTGATTTAA	     0.90362	-143
TTGATTTTTATTGGATAATGTTTTTAAGTACTAT	1	39	0	TTGGATTTTT	     0.98417	-120
TTAGATTAGTTTTGTCATTGTGTTTGATTTTTAT	1	62	0	TTTGATTGTT	    0.975509	-97
TATATTTATCTTTGACATTATTTTTATAAACATG	1	99	1	TTTGATTTTT	    0.979712	-60
CTGTAATATCTTTTTCCATGTTTATAAAAATAAT	1	115	0	TTTTCTTTTA	    0.936716	-44
CTTTCACCTCTTGTCGAATCTGTAATATCTTTTT	1	134	0	TTGTATTGTA	     0.96984	-25
TTTAAAGAATTTGGACATTTTGTTCAAGAGAATT	2	163	0	TTGGATTGTT	    0.980873	-77
TTCTTTAAATTTGTAAAGTTTTTATAGGGCAAAT	2	188	1	TTGTATTTTA	     0.97499	-52
      CACATTTTCACCTGTTTATGTGTTGAAT	2	222	0	TTTTCTTTTA	    0.936716	-18
          ****  * * ****

Masking position 9
Map Score:   10.3238

Number of sites scoring better than the average of aligned sites = 135
Number in coding regions = 112
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 3

GTGTTTGTGGGGAGTGGTTAGTGGTACGGC	2	12	1	GGAGTGGTTA	    0.937269	-228
TTAGTGGTACGGCGGCCATAGCGGGGGGGT	2	29	1	GGCGGCCATA	    0.981799	-211
CGGCCATAGCGGGGGGGTTACACCCGGTCT	2	41	1	GGGGGGGTTA	    0.996161	-199
CGGGATCGCTGGGGGGCTTAACTTCCGGGT	2	79	0	GGGGGGCTTA	    0.994948	-161
GCCCCCTCTCGGAGGGCAGTACAACCGGGA	2	104	0	GGAGGGCAGT	     0.90575	-136
CCCTCCGAGAGGGGGCGGGAAGCCGGGGAC	2	118	1	GGGGGCGGGA	    0.986608	-122
TAGGGTGGCCGGCGGCGTCCCCGGCTTCCC	2	134	0	GGCGGCGTCC	    0.858313	-106
          **********

Masking position 4
Map Score:   6.53502

Number of sites scoring better than the average of aligned sites = 190
Number in coding regions = 165
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 33
Fraction of orfs with sites within 600 bp upstream = 0.00530035


Motif number 4

ATTTGAAATTGTTAAATTTGGTGACTTAGA	1	11	0	GTTAAATTTG	    0.929359	-148
ATGTTTTTAAGTACTATTTGAAATTGTTAA	1	26	0	GTACTATTTG	    0.894688	-133
AGATTAGTTTTGTCATTGTGTTTGATTTTT	1	64	0	TGTCATTGTG	    0.902677	-95
TAAAAATATATTTATCTTTGACATTATTTT	1	93	1	TTTATCTTTG	    0.799339	-66
TAAAGAATTTGGACATTTTGTTCAAGAGAA	2	165	0	GGACATTTTG	    0.882743	-75
GTCCAAATTCTTTAAATTTGTAAAGTTTTT	2	181	1	TTTAAATTTG	    0.941002	-59
GTTTATGTGTTGAATATTTGCCCTATAAAA	2	207	0	TGAATATTTG	    0.953776	-33
CATTTTCACCTGTTTATGTGTTGAATATTT	2	218	0	TGTTTATGTG	    0.838081	-22
CATAAACAGGTGAAAATGTG          	2	230	1	TGAAAATGTG	    0.954504	-10
          **********

Masking position 7
Map Score:   5.3529

Number of sites scoring better than the average of aligned sites = 207
Number in coding regions = 165
Number in noncoding regions = 42
Number of orfs with sites within 600 bp upstream = 44
Fraction of orfs with sites within 600 bp upstream = 0.00706714


Motif number 5

          **********

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 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