AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i322_mjan_pyro_100.orf -o322_mjan_pyro_100.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.37 -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 =  	0.37
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RPH01018	214	Pyrococcus_OT3

Motif number 1

       TTGATATTTTGTTCAACTTTTCGCT	1	4	1	ATATTTGTCA	      0.9986	-211
AATTGCAGTTATATTTTGTACATAAGACGGAT	1	71	0	ATATTTGTCA	      0.9986	-144
ATATCCAATAATATTTAGTCAAAATTCTAAAA	1	102	0	ATATTTGTAA	    0.992734	-113
ATATTATTGGATATTTTATCCAATTCTCAAGC	1	120	1	ATATTTATCA	    0.992735	-95
CACCTCTTGGATATTTTGTCCAACTTGGAGAT	1	188	0	ATATTTGTCA	      0.9986	-27
          ****** ** **

Masking position 6
Map Score:   14.4064

Number of sites scoring better than the average of aligned sites = 12
Number in coding regions = 12
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 2

AAATCAATAAAGCGAAAAGTTGAACAAAATATCA	1	12	0	AGCAAAGTGA	    0.995549	-203
ATACATTATTATCAAATAGATGAAAGTAAATCAA	1	39	0	ATCAAAGTGA	    0.983313	-176
TTAGTCAAAATTCTAAAAATTGCAGTTATATTTT	1	86	0	TTCAAAATGA	    0.971053	-129
TGAATCTGCTATCTCCAAGTTGGACAAAATATCC	1	178	1	ATCCCAGTGA	    0.990627	-37
TGGACAAAATATCCAAGAGGTGAAAGT       	1	198	1	ATCAAAGTGA	    0.997991	-17
          *** ** ** ** *

Masking position 8
Map Score:   6.36881

Number of sites scoring better than the average of aligned sites = 37
Number in coding regions = 34
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 3

GTACAAAATATAACTGCAATTTTTAGAATT	1	82	1	TAACTGCAAT	    0.924196	-133
ATATTTAGTCAAAATTCTAAAAATTGCAGT	1	94	0	AAAATTCTAA	    0.875319	-121
AATTGGATAAAATATCCAATAATATTTAGT	1	115	0	AATATCCAAT	     0.97559	-100
CCTCATGCCATAAATCCTAAAAGCCTTGAA	1	152	1	TAAATCCTAA	    0.937302	-63
AAAAGCCTTGAATCTGCTATCTCCAAGTTG	1	170	1	AATCTGCTAT	     0.95789	-45
AGTTGGACAAAATATCCAAGAGGTGAAAGT	1	195	1	AATATCCAAG	    0.959091	-20
          **********

Masking position 5
Map Score:   2.453

Number of sites scoring better than the average of aligned sites = 855
Number in coding regions = 761
Number in noncoding regions = 94
Number of orfs with sites within 600 bp upstream = 78
Fraction of orfs with sites within 600 bp upstream = 0.0125281


Motif number 4

          **********

No masking
Map Score:   -1.32571e-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:   -1.32571e-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:   -1.32571e-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