AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i322_mixed7_pyro_reg_300.orf -o322_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	RPH01018	214	Pyrococcus_OT3
#2	RPH01015	36	Pyrococcus_OT3
#3	RPH01014	181	Pyrococcus_OT3

Motif number 1

AGCGAAAAGTTGAACAAAATATCAA       	1	4	0	TGACAAATAT	    0.996905	-211
ATCCGTCTTATGTACAAAATATAACTGCAATT	1	71	1	TGACAAATAT	    0.996905	-144
TTTTAGAATTTTGACTAAATATTATTGGATAT	1	102	1	TTACAAATAT	    0.988748	-113
GCTTGAGAATTGGATAAAATATCCAATAATAT	1	120	0	TGATAAATAT	    0.976626	-95
ATCTCCAAGTTGGACAAAATATCCAAGAGGTG	1	188	1	TGACAAATAT	    0.996905	-27
AGATCCCTTATGCCCTAAATCTTTATTTATTT	3	146	0	TGCCAAATCT	    0.968252	-36
    GGATGGTTCACCAAAGATCCCTTATGCC	3	164	0	TTACAAAGAT	    0.964335	-18
          ** ** ******

Masking position 7
Map Score:   14.7754

Number of sites scoring better than the average of aligned sites = 16
Number in coding regions = 13
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 2

TTATGGCATGAGGGCTTGAGAATTGGATAA	1	135	0	AGGGCTTGAG	     0.98792	-80
TCAAGCCCTCATGCCATAAATCCTAAAAGC	1	146	1	ATGCCATAAA	    0.898831	-69
TAAATCCTAAAAGCCTTGAATCTGCTATCT	1	162	1	AAGCCTTGAA	    0.934609	-53
TTTATCTGGGAGGGCGTTAAA         	2	26	1	AGGGCGTTAA	    0.969363	-11
CCCACCACAAAGGGCTTAAATTTACCAATT	3	15	1	AGGGCTTAAA	    0.990162	-167
TAATGTAAATTAGGCATTAGTTTTGTTTTC	3	100	1	TAGGCATTAG	    0.856599	-82
TTTGTTTTCAAAGGCAAAAACAGAAAAATA	3	121	1	AAGGCAAAAA	    0.919164	-61
ATAAAGATTTAGGGCATAAGGGATCTTTGG	3	152	1	AGGGCATAAG	    0.992275	-30
          **********

Masking position 9
Map Score:   7.70047

Number of sites scoring better than the average of aligned sites = 431
Number in coding regions = 396
Number in noncoding regions = 35
Number of orfs with sites within 600 bp upstream = 33
Fraction of orfs with sites within 600 bp upstream = 0.00530035


Motif number 3

AGATGAAAGTAAATCAATAAAGCGAAAAGT	1	26	0	AAATCAATAA	    0.867132	-189
CATTATTATCAAATAGATGAAAGTAAATCA	1	40	0	AAATAGATGA	    0.945162	-175
TCCAACTTGGAGATAGCAGATTCAAGGCTT	1	172	0	AGATAGCAGA	    0.933362	-43
GATAAAAAAGAAATAGAGAAA         	2	2	0	AAATAGAGAA	    0.937598	-35
ACGCCCTCCCAGATAAAAAAGAAATAGAGA	2	13	0	AGATAAAAAA	    0.962427	-24
CATTAAAAACAGATAACAAAGCTAACATAA	3	75	0	AGATAACAAA	    0.945165	-107
AAAAACAGAAAAATAAATAAAGATTTAGGG	3	136	1	AAATAAATAA	    0.954978	-46
          **********

Masking position 3
Map Score:   4.11662

Number of sites scoring better than the average of aligned sites = 385
Number in coding regions = 343
Number in noncoding regions = 42
Number of orfs with sites within 600 bp upstream = 45
Fraction of orfs with sites within 600 bp upstream = 0.00722775


Motif number 4

AAAATTCTAAAAATTGCAGTTATATTTTGTACAT	1	80	0	AATTCATTTA	    0.981655	-135
AATTGGATAAAATATCCAATAATATTTAGTCAAA	1	111	0	AAATCATATA	    0.981655	-104
GAATTTTAGGAAGATACATTTTTAATTGGTAAAT	3	34	0	AAATCATTTA	    0.987121	-148
GTATCTTCCTAAAATTCAAATCTATTATGTTAGC	3	51	1	AAATCAATTA	    0.958709	-131
ACTAATGCCTAATTTACATTAAAAACAGATAACA	3	87	0	AATTCATAAA	    0.919062	-95
          ** ** ** ** **

Masking position 8
Map Score:   0.673663

Number of sites scoring better than the average of aligned sites = 36
Number in coding regions = 27
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 5

          **********

No masking
Map Score:   7.76924e-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:   7.76924e-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:   7.76924e-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