AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i332_not_clear7_mjan_reg_100.orf -o332_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	RMJ03638	44	M_jannaschii_chromosome
#2	RMJ07698	216	M_jannaschii_chromosome

Motif number 1

    AGAATAATCCCAATTCATAAAAATAATTTTTA	1	7	1	ATCATTTAAA	    0.979736	-38
GAAAATCTATTTTTAAATTTATAATAAAGACAATTT	2	21	0	TTAATTTAAA	    0.984522	-196
TGAAGTGTAGTTAAAACATAATAAACAAAATAGTGG	2	68	1	TTAAATTAAC	    0.871094	-149
AAATAGTGGTATATAATTTACTACTATAAAAACCTT	2	95	1	ATAATTTACA	    0.979735	-122
ACCTTTGTATATTCAAATTAATAATAAGAGATAACT	2	126	1	ATAATTTAAA	    0.994535	-91
TAATAATAAGAGATAACTTTTTAACCCCCTACGATA	2	144	1	AGAATTTAAC	     0.96473	-73
CCCCTACGATATATAATTTCCTAAAAGCCTATCATA	2	169	1	ATAATTTAAA	    0.994502	-48
AAAGCCTATCATAAAATTTTATAAGAGGGATAGGG 	2	192	1	ATAATTTAAA	    0.994536	-25
          **  ** **  *** *

Masking position 6
Map Score:   12.984

Number of sites scoring better than the average of aligned sites = 271
Number in coding regions = 181
Number in noncoding regions = 90
Number of orfs with sites within 600 bp upstream = 85
Fraction of orfs with sites within 600 bp upstream = 0.0136524


Motif number 2

ATAAAAATTATTTTTATGAATTGGGATTAT	1	14	0	TTTTTATGAA	    0.949338	-31
ATAAAAATAATTTTTATGGAGGGAGATT  	1	27	1	TTTTTATGGA	    0.878645	-18
TAAATTGTCTTTATTATAAATTTAAAAATA	2	20	1	TTATTATAAA	    0.958326	-197
AATGGAAAATCTATTTTTAAATTTATAATA	2	31	0	CTATTTTTAA	    0.872955	-186
ATATAATTTACTACTATAAAAACCTTTGTA	2	105	1	CTACTATAAA	    0.946235	-112
AAGTTATCTCTTATTATTAATTTGAATATA	2	133	0	TTATTATTAA	    0.929086	-84
TTATGATAGGCTTTTAGGAAATTATATATC	2	176	0	CTTTTAGGAA	    0.930603	-41
TCCTAAAAGCCTATCATAAAATTTTATAAG	2	187	1	CTATCATAAA	    0.949995	-30
  CCCTATCCCTCTTATAAAATTTTATGAT	2	199	0	CTCTTATAAA	    0.966082	-18
          **********

Masking position 2
Map Score:   10.7569

Number of sites scoring better than the average of aligned sites = 725
Number in coding regions = 581
Number in noncoding regions = 144
Number of orfs with sites within 600 bp upstream = 138
Fraction of orfs with sites within 600 bp upstream = 0.0221651


Motif number 3

CTTTATTATAAATTTAAAAATAGATTTTCC	2	28	1	AATTTAAAAA	    0.959752	-189
GTTAAAACATAATAAACAAAATAGTGGTAT	2	77	1	AATAAACAAA	    0.974144	-140
ATAATTTACTACTATAAAAACCTTTGTATA	2	107	1	ACTATAAAAA	    0.972937	-110
TATTAATTTGAATATACAAAGGTTTTTATA	2	119	0	AATATACAAA	    0.989579	-98
          **********

Masking position 6
Map Score:   3.40175

Number of sites scoring better than the average of aligned sites = 201
Number in coding regions = 132
Number in noncoding regions = 69
Number of orfs with sites within 600 bp upstream = 85
Fraction of orfs with sites within 600 bp upstream = 0.0136524


Motif number 4

          **********

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 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