AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i332_not_clear7_mjan_reg_300.orf -o332_mjan_300.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	RMJ03638	44	M_jannaschii_chromosome
#2	RMJ07698	216	M_jannaschii_chromosome

Motif number 1

AATCTCCCTCCATAAAAATTATTTTTATGAATTGGGA	1	18	0	CATAATTTTA	    0.989395	-27
GGAAAATCTATTTTTAAATTTATAATAAAGACAATTT	2	21	0	TTTAATTTTA	    0.978257	-196
AAAATAGTGGTATATAATTTACTACTATAAAAACCTT	2	94	1	TATAATTTTA	    0.996745	-123
AACCTTTGTATATTCAAATTAATAATAAGAGATAACT	2	125	1	TATAATTTTA	    0.994975	-92
CCCCCTACGATATATAATTTCCTAAAAGCCTATCATA	2	168	1	TATAATTTAA	    0.986932	-49
CTATCCCTCTTATAAAATTTTATGATAGGCTTTTAGG	2	188	0	TATAATTTTA	    0.962969	-29
          ***  ** **  *  **

Masking position 9
Map Score:   10.3152

Number of sites scoring better than the average of aligned sites = 83
Number in coding regions = 45
Number in noncoding regions = 38
Number of orfs with sites within 600 bp upstream = 40
Fraction of orfs with sites within 600 bp upstream = 0.00642467


Motif number 2

     AGAATAATCCCAATTCATAAAAATAATTTT	1	6	1	AATCCTATAA	    0.989415	-39
          AATCTCCCTCCATAAAAATTATTTT	1	30	0	AATCCTATAA	    0.989415	-15
TCTCAAATGGAAAATCTATTTTTAAATTTATAATA	2	31	0	AAAACTTTAA	     0.91965	-186
AGTGTAGTTAAAACATAATAAACAAAATAGTGGTA	2	71	1	AAACTTACAA	     0.87742	-146
TAATAAACAAAATAGTGGTATATAATTTACTACTA	2	86	1	AATATTATAA	    0.959671	-131
TACTACTATAAAAACCTTTGTATATTCAAATTAAT	2	113	1	AAAACTATAT	    0.958154	-104
TATTCAAATTAATAATAAGAGATAACTTTTTAACC	2	135	1	AATATGATAA	    0.879837	-82
ATAACTTTTTAACCCCCTACGATATATAATTTCCT	2	156	1	AACCCAATAT	    0.829684	-61
ATAATTTCCTAAAAGCCTATCATAAAATTTTATAA	2	181	1	AAAACAATAA	    0.963742	-36
          **** *  *  ****

Masking position 2
Map Score:   5.51553

Number of sites scoring better than the average of aligned sites = 861
Number in coding regions = 693
Number in noncoding regions = 168
Number of orfs with sites within 600 bp upstream = 170
Fraction of orfs with sites within 600 bp upstream = 0.0273049


Motif number 3

CTCCATAAAAATTATTTTTATGAATTGGGA	1	18	0	ATTATTTTTA	    0.778397	-27
GTAAATTGTCTTTATTATAAATTTAAAAAT	2	19	1	TTTATTATAA	    0.937752	-198
AAATGGAAAATCTATTTTTAAATTTATAAT	2	32	0	TCTATTTTTA	    0.948587	-185
TATATAATTTACTACTATAAAAACCTTTGT	2	104	1	ACTACTATAA	    0.922233	-113
TAAAAAGTTATCTCTTATTATTAATTTGAA	2	137	0	TCTCTTATTA	    0.966147	-80
TTCCTAAAAGCCTATCATAAAATTTTATAA	2	186	1	CCTATCATAA	    0.948304	-31
   CCCTATCCCTCTTATAAAATTTTATGA	2	200	0	CCTCTTATAA	    0.975679	-17
          **********

Masking position 10
Map Score:   4.9365

Number of sites scoring better than the average of aligned sites = 649
Number in coding regions = 536
Number in noncoding regions = 113
Number of orfs with sites within 600 bp upstream = 114
Fraction of orfs with sites within 600 bp upstream = 0.0183103


Motif number 4

TTTTAAATTTATAATAAAGACAATTTACGT	2	17	0	ATAATAAAGA	    0.976808	-200
TAGTTAAAACATAATAAACAAAATAGTGGT	2	75	1	ATAATAAACA	    0.958135	-142
CAAATTAATAATAAGAGATAACTTTTTAAC	2	139	1	ATAAGAGATA	    0.973647	-78
ATAAAATTTTATAAGAGGGATAGGG     	2	202	1	ATAAGAGGGA	    0.983364	-15
          **********

Masking position 6
Map Score:   1.61305

Number of sites scoring better than the average of aligned sites = 155
Number in coding regions = 138
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 5

          **********

No masking
Map Score:   -1.9652e-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:   -1.9652e-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:   -1.9652e-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