AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i179_mjan_pyro_100.orf -o179_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	RMJ02668	101	M_jannaschii_chromosome
#2	RPH00764	148	Pyrococcus_OT3

Motif number 1

AATACATATTTGTAAATTTATAAATC    	1	7	0	TGTAAATTTA	    0.971361	-95
ATAGTTGAGGTTTAAATAAATAACTCTCTA	1	36	0	TTTAAATAAA	     0.68315	-66
TTGAAGAGTTTTTAATTTAATAAAAATAGT	1	61	0	TTTAATTTAA	    0.705059	-41
AAAAGCTTTATGTAAAATAAGGAAGAGGGA	2	13	0	TGTAAAATAA	    0.971553	-136
AAAAGAAGGGTGTAATTTAAGTCCTTTCTA	2	97	0	TGTAATTTAA	    0.947012	-52
          **********

Masking position 5
Map Score:   6.05518

Number of sites scoring better than the average of aligned sites = 209
Number in coding regions = 117
Number in noncoding regions = 92
Number of orfs with sites within 600 bp upstream = 82
Fraction of orfs with sites within 600 bp upstream = 0.0131706


Motif number 2

GGTTTAAATAAATAACTCTCTAATACATATTTG	1	25	0	AAACTTCTAA	    0.947445	-77
TTATTTATTTAAACCTCAACTATTTTTATTAAA	1	43	1	AACTCACTAT	    0.913326	-59
TATTAAATTAAAAACTCTTCAAAAGATTTGACG	1	69	1	AACTCTCAAA	    0.966388	-33
      TATGAATCACCGTCAAATCTTTTGAAG	1	85	0	AAACCTCAAA	    0.966223	-17
CATTAGAACTTATTCCCGTCTTAAAAGCTTTAT	2	32	0	TACCCTCTTA	    0.978403	-117
GGTGTAATTTAAGTCCTTTCTATGTGAAGCGAA	2	86	0	AACCTTCTAT	    0.980679	-63
GGACTTAAATTACACCCTTCTTTTCTTGGCTAG	2	103	1	TACCCTCTTT	    0.972383	-46
          **  *** *****

Masking position 2
Map Score:   3.48792

Number of sites scoring better than the average of aligned sites = 543
Number in coding regions = 488
Number in noncoding regions = 55
Number of orfs with sites within 600 bp upstream = 48
Fraction of orfs with sites within 600 bp upstream = 0.0077096


Motif number 3

CGTCAAATCTTTTGAAGAGTTTTTAATTTA	1	72	0	TTTGAAGAGT	    0.840147	-30
CTTCAAAAGATTTGACGGTGATTCATA   	1	85	1	TTTGACGGTG	    0.823406	-17
TATGTAAAATAAGGAAGAGGGAAA      	2	5	0	AAGGAAGAGG	    0.967089	-144
ATAAAGCTTTTAAGACGGGAATAAGTTCTA	2	32	1	TAAGACGGGA	    0.972402	-117
ATGTGAAGCGAAGGACGATATGCACCACCA	2	68	0	AAGGACGATA	    0.888222	-81
TTCGCTTCACATAGAAAGGACTTAAATTAC	2	86	1	ATAGAAAGGA	    0.865586	-63
CTAGCCAAGAAAAGAAGGGTGTAATTTAAG	2	106	0	AAAGAAGGGT	    0.968659	-43
AGTTTAGATTATGGGAGGGATGTCT     	2	134	1	ATGGGAGGGA	    0.960135	-15
          **********

Masking position 4
Map Score:   3.04454

Number of sites scoring better than the average of aligned sites = 1456
Number in coding regions = 1342
Number in noncoding regions = 114
Number of orfs with sites within 600 bp upstream = 92
Fraction of orfs with sites within 600 bp upstream = 0.0147767


Motif number 4

          **********

No masking
Map Score:   -3.95472e-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:   -3.95472e-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:   -3.95472e-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