AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i301_mixed16_mjan_reg_100.orf -o301_mjan_100.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.31 -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 =  	0.31
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RMJ12630	135	M_jannaschii_chromosome

Motif number 1

TTTAGTTTTTTGCAAAAGTTATTAAAATTC	1	26	1	TGCAAAAGTT	    0.992156	-110
TGGGAAGGCGTTCAATTTTTCATTATGAAT	1	52	0	TTCAATTTTT	    0.953362	-84
AAGGAAGGCGTTCATAAGTTCCTTATGTAC	1	82	1	TTCATAAGTT	    0.985059	-54
CCTTATGTACTTCAAATGTTTTGCAAAAAA	1	102	1	TTCAAATGTT	    0.990422	-34
    AATATCACCAATAGTTTTTTGCAAAA	1	120	0	ACCAATAGTT	    0.955025	-16
          **********

Masking position 4
Map Score:   6.44562

Number of sites scoring better than the average of aligned sites = 378
Number in coding regions = 343
Number in noncoding regions = 35
Number of orfs with sites within 600 bp upstream = 40
Fraction of orfs with sites within 600 bp upstream = 0.00642467


Motif number 2

ATGAAAAATTGAACGCCTTCCCAAAGGAAG	1	59	1	GAACGCCTTC	    0.516002	-77
AGGAACTTATGAACGCCTTCCTTTGGGAAG	1	75	0	GAACGCCTTC	    0.516002	-61
          **********

Masking position 3
Map Score:   4.48877

Number of sites scoring better than the average of aligned sites = 32
Number in coding regions = 4
Number in noncoding regions = 28
Number of orfs with sites within 600 bp upstream = 29
Fraction of orfs with sites within 600 bp upstream = 0.00465789


Motif number 3

ACCTTAATTTAGTTTTTTGCAAAAGTTATT	1	19	1	AGTTTTTTGC	    0.998377	-117
TATCACCAATAGTTTTTTGCAAAACATTTG	1	114	0	AGTTTTTTGC	    0.998377	-22
          **********

Masking position 5
Map Score:   3.30835

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 4

TGAATTTTAATAACTTTTGCAAAAAACTAAA	1	26	0	TAACTTTTGA	    0.973814	-110
CGTTCAATTTTTCATTATGAATTTTAATAAC	1	43	0	TTCATTATGA	    0.529718	-93
TATGAACGCCTTCCTTTGGGAAGGCGTTCAA	1	67	0	TTCCTTTGGA	     0.90493	-69
CGTTCATAAGTTCCTTATGTACTTCAAATGT	1	90	1	TTCCTTATGA	    0.615144	-46
          ********* *

Masking position 6
Map Score:   4.16574

Number of sites scoring better than the average of aligned sites = 94
Number in coding regions = 82
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 5

          **********

No masking
Map Score:   -1.11255e-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:   -1.11255e-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:   -1.11255e-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