AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i184_mjan_pyro_300.orf -o184_mjan_pyro_300.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	RMJ07723	300	M_jannaschii_chromosome
#2	RMJ03619	161	M_jannaschii_chromosome

Motif number 1

TTATTTTTAATATTTTTATTTTGTGTTTGT	1	15	1	TATTTTTATT	    0.712049	-286
TGTTTGTTGATATTAATAGTTTTGTTATCC	1	38	1	TATTAATAGT	    0.888636	-263
TTTGTTATCCTATCAAAATTTCAAAATTGA	1	58	1	TATCAAAATT	    0.958026	-243
GTGCCTTTGGTATCTAAATTCCAAATGTCC	1	137	1	TATCTAAATT	    0.962484	-164
CCAAATGTCCAATATAAAGTGCTTAAGTCC	1	157	1	AATATAAAGT	    0.802138	-144
TAGACACAAAAATCTAAGGTTTATTAAATA	1	187	0	AATCTAAGGT	    0.793607	-114
ATAGTGAGAGTATATAAAGTAGATATTACA	1	223	0	TATATAAAGT	    0.958284	-78
AATCAACACATATATATAGTGAGAGTATAT	1	238	0	TATATATAGT	    0.936168	-63
AATTTAGTGTTATTTAAATTTCTTCAATAT	1	276	1	TATTTAAATT	    0.871951	-25
TTATCATGTTTATAATTGTTGGGTGTTGTT	2	12	0	TATAATTGTT	    0.685438	-150
ATAGATAATTTATCATAATTAATAATGATA	2	69	1	TATCATAATT	    0.914489	-93
TTAAGCTAATTATCATTATTAATTATGATA	2	79	0	TATCATTATT	    0.872274	-83
AACAAAACTATATAAAAGGTTAAGCTAATT	2	98	0	TATAAAAGGT	    0.910648	-64
          **********

Masking position 2
Map Score:   14.6747

Number of sites scoring better than the average of aligned sites = 1070
Number in coding regions = 700
Number in noncoding regions = 370
Number of orfs with sites within 600 bp upstream = 360
Fraction of orfs with sites within 600 bp upstream = 0.057822


Motif number 2

ACAAACACAAAATAAAAATATTAAAAATAAA	1	14	0	AATAAAATAT	    0.935275	-287
TTGATAGGATAACAAAACTATTAATATCAAC	1	43	0	AACAAACTAT	    0.938576	-258
TGAGTGTTTTAATAGGTCTTACGCAGTAATA	1	85	1	AATAGGCTTA	    0.913168	-216
CTTACGCAGTAATAAATCTTTTCTATTGAAT	1	102	1	AATAAACTTT	    0.977742	-199
AGGTTTATTAAATAGGACTTAAGCACTTTAT	1	170	0	AATAGGCTTA	     0.91317	-131
AGTCCTATTTAATAAACCTTAGATTTTTGTG	1	182	1	AATAAACTTA	      0.9581	-119
GTTGATTGACAATAAAATTTAGTGTTATTTA	1	261	1	AATAAATTTA	    0.882274	-40
TAAACATGATAATAGGTATATGACTCACTAA	2	30	1	AATAGGATAT	    0.869204	-132
TAAGGTAATGAATAGATAATTTATCATAATT	2	58	1	AATAGAAATT	     0.72507	-104
ACTTTATTAAAACAAAACTATATAAAAGGTT	2	107	0	AACAAACTAT	    0.938576	-55
GTTTTGTTTTAATAAAGTTATCGAGATGCAT	2	120	1	AATAAATTAT	    0.935272	-42
 CAGATTTGTAATAAAATAATAATGCATCTC	2	142	0	AATAAATAAT	    0.763938	-20
          ****** ****

Masking position 4
Map Score:   12.7991

Number of sites scoring better than the average of aligned sites = 1330
Number in coding regions = 994
Number in noncoding regions = 336
Number of orfs with sites within 600 bp upstream = 297
Fraction of orfs with sites within 600 bp upstream = 0.0477032


Motif number 3

  TTTTTTATTTTTAATATTTTTATTTTGT	1	9	1	TTTTAATATT	    0.752478	-292
TAATATTTTTATTTTGTGTTTGTTGATATT	1	22	1	ATTTTGTGTT	    0.952209	-279
AAATTTCAAAATTGAGTGTTTTAATAGGTC	1	73	1	ATTGAGTGTT	    0.974844	-228
AATCTTTTCTATTGAATATTGGTGCCTTTG	1	116	1	ATTGAATATT	     0.91248	-185
TATATTGGACATTTGGAATTTAGATACCAA	1	143	0	ATTTGGAATT	    0.843769	-158
TGACAATAAAATTTAGTGTTATTTAAATTT	1	267	1	ATTTAGTGTT	    0.981958	-34
ATTTAGTGTTATTTAAATTTCTTCAATATT	1	277	1	ATTTAAATTT	    0.685695	-24
          CTTTAATATTGAAGAAATTT	1	291	0	CTTTAATATT	     0.81837	-10
GTTTATAATTGTTGGGTGTTGTTC      	2	5	0	GTTGGGTGTT	    0.925518	-157
CTTTTATATAGTTTTGTTTTAATAAAGTTA	2	110	1	GTTTTGTTTT	    0.792204	-52
          **********

Masking position 3
Map Score:   5.54728

Number of sites scoring better than the average of aligned sites = 854
Number in coding regions = 710
Number in noncoding regions = 144
Number of orfs with sites within 600 bp upstream = 127
Fraction of orfs with sites within 600 bp upstream = 0.0203983


Motif number 4

CTATTAATATCAACAAACACAAAATAAAAA	1	27	0	CAACAAACAC	    0.974471	-274
AATTTAGATACCAAAGGCACCAATATTCAA	1	127	0	CCAAAGGCAC	    0.973079	-174
TATTACAAACCCATAGACACAAAAATCTAA	1	200	0	CCATAGACAC	    0.990881	-101
ATTTTATTGTCAATCAACACATATATATAG	1	249	0	CAATCAACAC	    0.963819	-52
          **********

Masking position 3
Map Score:   0.21428

Number of sites scoring better than the average of aligned sites = 39
Number in coding regions = 33
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 5

          **********

No masking
Map Score:   7.55607e-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:   7.55607e-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:   7.55607e-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