AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i122_mjan_pyro_100.orf -o122_mjan_pyro_100.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	RMJ03685	139	M_jannaschii_chromosome
#2	RPH00245	138	Pyrococcus_OT3
#3	RPH00244	40	Pyrococcus_OT3
#4	RPH00243	43	Pyrococcus_OT3

Motif number 1

TTACTAGTATTTAAATATTTTGGTTTTGT  	1	9	0	TTAAAATTTT	    0.909082	-131
TGCAATCAACTTTACTATAATACATTACTAG	1	33	0	TTTACATAAT	    0.830231	-107
AGACATATATTTTTCCATATTGATGTTTAAA	1	65	0	TTTTCATATT	    0.979682	-75
AAATATATACTTAAACATTTTAATAGAAATA	1	96	1	TTAAAATTTT	    0.909082	-44
TGATTATTTTTTATTTCTATTAAAATGTTTA	1	107	0	TTATTCTATT	    0.839194	-33
ATAGGTAATTTTATAAATTTTGGAAGGGTAC	2	29	0	TTATAATTTT	    0.956677	-110
ATTTATAAAATTACCTATTTTGGTTCAGCTT	2	42	1	TTACCATTTT	    0.902942	-97
ATTTATAAAGTTTTCTATAATATTCGAGTTA	2	72	0	TTTTCATAAT	    0.915279	-67
ATAGAAAACTTTATAAATATTTTTGTGATAT	2	85	1	TTATAATATT	    0.968153	-54
TATAAATATTTTTGTGATATTACAAATTGGG	2	96	1	TTTGTATATT	    0.889798	-43
       GCCTTTTTTATTTTTTGGACTATA	4	4	1	TTTTTATTTT	    0.956676	-40
  ATGTTAAATTTTTTATATTTATAGTCCAA	4	25	0	TTTTTATATT	    0.968151	-19
          ***** *****

Masking position 8
Map Score:   15.6359

Number of sites scoring better than the average of aligned sites = 1892
Number in coding regions = 1336
Number in noncoding regions = 556
Number of orfs with sites within 600 bp upstream = 427
Fraction of orfs with sites within 600 bp upstream = 0.0685834


Motif number 2

ACATTACTAGTATTTAAATATTTTGGTTTTGT 	1	10	0	TATAATATTT	    0.936641	-130
TAATGTATTATAGTAAAGTTGATTGCAATTTAA	1	37	1	TAGAATTGAT	    0.965659	-103
AACATCAATATGGAAAAATATATGTCTAAATAT	1	69	1	TGGAATATAT	    0.988339	-71
TCTATTAAAATGTTTAAGTATATATTTAGACAT	1	90	0	TGTAATATAT	    0.976211	-50
TGAACCAAAATAGGTAATTTTATAAATTTTGGA	2	36	0	TAGAATTTAT	    0.989176	-103
TCGAATATTATAGAAAACTTTATAAATATTTTT	2	76	1	TAGAATTTAT	    0.989176	-63
         ATGTTAAATTTTTTATATTTATAG	4	30	0	TGTAATTTTT	    0.958754	-14
          ***  ** *****

Masking position 7
Map Score:   7.31236

Number of sites scoring better than the average of aligned sites = 264
Number in coding regions = 204
Number in noncoding regions = 60
Number of orfs with sites within 600 bp upstream = 72
Fraction of orfs with sites within 600 bp upstream = 0.0115644


Motif number 3

       CTTCTATCACCATATTATGTACC	2	4	1	CTATCACCAT	    0.975884	-135
ATTATGTACCCTTCCAAAATTTATAAAATT	2	24	1	CTTCCAAAAT	    0.962244	-115
ACCCCTATTGCTTTCCCAATTTGTAATATC	2	111	0	CTTTCCCAAT	    0.982304	-28
          CTTTCACCACCCCTATTGCT	2	129	0	CTTTCACCAC	    0.983599	-10
  CTTAACCACCTCCACAATATCTCCTCAA	3	23	0	CCTCCACAAT	      0.9836	-18
          **********

Masking position 9
Map Score:   3.7709

Number of sites scoring better than the average of aligned sites = 87
Number in coding regions = 81
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 4

          **********

No masking
Map Score:   1.3033e-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:   1.3033e-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:   1.3033e-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