AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i323_mixed8_pyro_reg_100.orf -o323_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	RPH01201	239	Pyrococcus_OT3

Motif number 1

CCCCCGCTATGGCCGCCGTACCACTAACCACTCCCCAC	1	18	0	GGCGCCACAC	    0.985011	-222
CCATAGCGGGGGGGTTACACCCGGTCTCATTTCGAACC	1	44	1	GGGCCCGGTC	    0.999683	-196
ATCGCTGGGGGGCTTAACTTCCGGGTTCGAAATGAGAC	1	67	0	GGCCCCGGTC	    0.999841	-173
CCTCTCGGAGGGCAGTACAACCGGGATCGCTGGGGGGC	1	92	0	GGCCCCGGTC	    0.999828	-148
CGGCGTCCCCGGCTTCCCGCCCCCTCTCGGAGGGCAGT	1	114	0	GGCCCCCCTC	    0.998863	-126
GCGGGAAGCCGGGGACGCCGCCGGCCACCCTAATTCTC	1	132	1	GGGCCCGGAC	    0.997122	-108
          ***    *  ****  **

Masking position 11
Map Score:   15.3311

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

      AGTGTTTGTGGGGAGTGGTTAGTGG	1	5	1	TTTGGGGGAG	    0.961952	-235
ACGGCGGCCATAGCGGGGGGGTTACACCCGG	1	37	1	TAGCGGGGGG	    0.998698	-203
ACAACCGGGATCGCTGGGGGGCTTAACTTCC	1	83	0	TCGCGGGGGG	    0.998419	-157
CCGCCCCCTCTCGGAGGGCAGTACAACCGGG	1	105	0	TCGGGGGCAG	    0.995535	-135
TGCCCTCCGAGAGGGGGCGGGAAGCCGGGGA	1	116	1	GAGGGGCGGG	    0.986087	-124
AGGGGGCGGGAAGCCGGGGACGCCGCCGGCC	1	127	1	AAGCGGGGAC	    0.958543	-113
TCAAGAGAATTAGGGTGGCCGGCGGCGTCCC	1	143	0	TAGGTGGCCG	    0.953679	-97
          **** ******

Masking position 7
Map Score:   8.07155

Number of sites scoring better than the average of aligned sites = 277
Number in coding regions = 238
Number in noncoding regions = 39
Number of orfs with sites within 600 bp upstream = 35
Fraction of orfs with sites within 600 bp upstream = 0.00562159


Motif number 3

AAAAACTTTACAAATTTAAAGAATTTGGAC	1	181	0	CAAATTTAAA	    0.938568	-59
TTTTATAGGGCAAATATTCAACACATAAAC	1	207	1	CAAATATTCA	    0.982962	-33
AAATATTCAACACATAAACAGGTGAAAATG	1	218	1	CACATAAACA	    0.973797	-22
          CACATTTTCACCTGTTTATG	1	230	0	CACATTTTCA	    0.989455	-10
          **********

Masking position 5
Map Score:   2.22219

Number of sites scoring better than the average of aligned sites = 65
Number in coding regions = 52
Number in noncoding regions = 13
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 4

GTTAGTGGTACGGCGGCCATAGCGGGGGGG	1	28	1	CGGCGGCCAT	    0.993506	-212
GCGGCCATAGCGGGGGGGTTACACCCGGTC	1	40	1	CGGGGGGGTT	    0.964067	-200
GCTTAACTTCCGGGTTCGAAATGAGACCGG	1	64	0	CGGGTTCGAA	     0.93225	-176
GCAGTACAACCGGGATCGCTGGGGGGCTTA	1	89	0	CGGGATCGCT	    0.947607	-151
CGCCCCCTCTCGGAGGGCAGTACAACCGGG	1	105	0	CGGAGGGCAG	    0.943517	-135
GCGGCGTCCCCGGCTTCCCGCCCCCTCTCG	1	123	0	CGGCTTCCCG	    0.527762	-117
GGGACGCCGCCGGCCACCCTAATTCTCTTG	1	143	1	CGGCCACCCT	    0.618449	-97
          **********

Masking position 3
Map Score:   3.76068

Number of sites scoring better than the average of aligned sites = 228
Number in coding regions = 184
Number in noncoding regions = 44
Number of orfs with sites within 600 bp upstream = 31
Fraction of orfs with sites within 600 bp upstream = 0.00497912


Motif number 5

          **********

No masking
Map Score:   -2.7468e-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:   -2.7468e-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:   -2.7468e-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