AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i277_hypothetical21_mjan_reg_100.orf -o277_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	RMJ05553	32	M_jannaschii_chromosome
#2	RMJ08933	20	M_jannaschii_chromosome
#3	RMJ14466	42	M_jannaschii_chromosome
#4	RMJ13617	163	M_jannaschii_chromosome

Motif number 1

         TTTAATTTTTATAAATTTTTG	1	2	1	TTAATTTTTA	    0.870916	-31
TTAATTTTTATAAATTTTTGGAATATCTGA	1	12	1	TAAATTTTTG	    0.938259	-21
   ATTATTTTTAATTTTTAATTTTTCTTT	3	8	1	TTAATTTTTA	    0.870916	-35
ATTTTTAATTTTTCTTTTTAACTGAGGGTA	3	21	1	TTTCTTTTTA	    0.966604	-22
TTCGCAGGAATAAATTTTTATTGAACAATG	4	20	1	TAAATTTTTA	    0.756254	-144
TTTCGCAGTCTATATTATTAAATTTGGAAA	4	68	0	TATATTATTA	    0.952772	-96
ATTTAAAGATTATCTTTTAATAGGACTTTC	4	94	0	TATCTTTTAA	    0.945729	-70
ATTATATCATTATATTTAAAGATTATCTTT	4	107	0	TATATTTAAA	    0.752553	-57
GCATTGGCATTAACTAATTATATCATTATA	4	123	0	TAACTAATTA	    0.756657	-41
          **********

Masking position 5
Map Score:   13.2974

Number of sites scoring better than the average of aligned sites = 1593
Number in coding regions = 1064
Number in noncoding regions = 529
Number of orfs with sites within 600 bp upstream = 442
Fraction of orfs with sites within 600 bp upstream = 0.0709926


Motif number 2

     AATAGGACTTTCGCAGGAATAAATT	4	6	1	GACTTTCGCA	    0.998374	-158
CTTTTAATAGGACTTTCGCAGTCTATATTA	4	81	0	GACTTTCGCA	    0.998374	-83
TCATGGTTGTGGCATTGGCATTAACTAATT	4	134	0	GGCATTGGCA	    0.993525	-30
          **********

Masking position 10
Map Score:   4.49927

Number of sites scoring better than the average of aligned sites = 39
Number in coding regions = 5
Number in noncoding regions = 34
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 3

TTATAAATTTTTGGAATATCTGAG      	1	19	1	TTGGAATATC	    0.905328	-14
      TTATTTTCACCCTCTTATTA    	2	7	0	TTTCACCCTC	    0.960517	-14
        AATAGGACTTTCGCAGGAATAA	4	3	1	TAGGACTTTC	    0.994494	-161
TATCTTTTAATAGGACTTTCGCAGTCTATA	4	84	0	TAGGACTTTC	    0.994494	-80
        ATTATCACCTTCATGGTTGTGG	4	152	0	TATCACCTTC	     0.98345	-12
          **********

Masking position 5
Map Score:   4.07365

Number of sites scoring better than the average of aligned sites = 68
Number in coding regions = 34
Number in noncoding regions = 34
Number of orfs with sites within 600 bp upstream = 26
Fraction of orfs with sites within 600 bp upstream = 0.00417604


Motif number 4

          **********

No masking
Map Score:   -1.75204e-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:   -1.75204e-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:   -1.75204e-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