AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i171_mjan_pyro_100.orf -o171_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	RMJ05650	213	M_jannaschii_chromosome

Motif number 1

TATGTAGGTGTTTATAGATTTTAAGTAATCTC	1	40	0	TTTATATTTT	    0.988291	-174
ATATTTGGATTTTATCCATTTACAACCACCGT	1	79	0	TTTATATTTA	    0.973311	-135
AAAATAATGTTTGAGAGATTTTCCTCAATATT	1	106	0	TTGAGATTTT	    0.988312	-108
AACATTATTTTTTATTTATTTTGTATTTTTGA	1	127	1	TTTATATTTT	    0.988291	-87
TTTTGTATTTTTGACAAGTTTTTGTTTATGTT	1	145	1	TTGACGTTTT	    0.974418	-69
CAAGTTTTTGTTTATGTTTTTTTGGGATAATT	1	159	1	TTTATTTTTT	    0.962509	-55
TTTGGGATAATTGAGAAGTTTATTTTAAAGGG	1	179	1	TTGAGGTTTA	    0.968246	-35
          *****  *****

Masking position 4
Map Score:   10.2674

Number of sites scoring better than the average of aligned sites = 470
Number in coding regions = 337
Number in noncoding regions = 133
Number of orfs with sites within 600 bp upstream = 120
Fraction of orfs with sites within 600 bp upstream = 0.019274


Motif number 2

AGAACGGGAGAACCAATACAAGAGATTACT	1	19	1	AACCAATACA	     0.94353	-195
CAAAATAAATAAAAAATAATGTTTGAGAGA	1	120	0	AAAAAATAAT	    0.895032	-94
AAAAACTTGTCAAAAATACAAAATAAATAA	1	138	0	CAAAAATACA	    0.978585	-76
AAAAAACATAAACAAAAACTTGTCAAAAAT	1	151	0	AACAAAAACT	    0.978585	-63
TCAATTATCCCAAAAAAACATAAACAAAAA	1	163	0	CAAAAAAACA	    0.978585	-51
ACTTCCCTTTAAAATAAACTTCTCAATTAT	1	185	0	AAAATAAACT	    0.931494	-29
          **********

Masking position 6
Map Score:   5.46459

Number of sites scoring better than the average of aligned sites = 355
Number in coding regions = 318
Number in noncoding regions = 37
Number of orfs with sites within 600 bp upstream = 33
Fraction of orfs with sites within 600 bp upstream = 0.00530035


Motif number 3

          AAGAGGACAGAACGGGAGAA	1	1	1	AAGAGGACAG	    0.969367	-213
ACCTACATAGTGGAGGACGGTGGTTGTAAA	1	63	1	TGGAGGACGG	    0.994661	-151
TAAAAAATAATGTTTGAGAGATTTTCCTCA	1	111	0	TGTTTGAGAG	    0.950699	-103
TAAAGGGAAGTGTTGGACAG          	1	204	1	TGTTGGACAG	    0.995153	-10
          **********

Masking position 7
Map Score:   1.49425

Number of sites scoring better than the average of aligned sites = 115
Number in coding regions = 109
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 4

          **********

No masking
Map Score:   -1.68098e-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:   -1.68098e-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:   -1.68098e-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