AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i231_mjan_pyro_100.orf -o231_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	RMJ00617	135	M_jannaschii_chromosome
#2	RPH00628	66	Pyrococcus_OT3

Motif number 1

TAATCTTATATTTATAATTTTTAGTTATGGT	1	17	0	TTTATAATTT	    0.974685	-119
AGGAAGATGCCTTATCATAATATCATAATCT	1	42	0	CTTATCATAT	    0.975985	-94
AGGCATCTTCCTTTTAATAGTAACTAAAAAT	1	61	1	CTTTTAATAT	    0.972786	-75
ATATATAAATCTTTTAAATTTTTAGTTACTA	1	78	0	CTTTTAAATT	    0.973023	-58
ATTTAAAAGATTTATATATGTCAATATATTT	1	90	1	TTTATATATT	    0.873457	-46
  ATTAACACCTTATAAAAATCTCTGTAAAT	1	117	0	CTTATAAAAT	    0.987569	-19
GTAGGTGAAGTTTATAAAACTGGAATAAAAA	2	11	1	TTTATAAAAT	    0.974606	-56
GCTCTCGCCACTTAACATTTTTATTCCAGTT	2	28	0	CTTAACATTT	    0.909085	-39
          ********* *

Masking position 3
Map Score:   11.6403

Number of sites scoring better than the average of aligned sites = 592
Number in coding regions = 503
Number in noncoding regions = 89
Number of orfs with sites within 600 bp upstream = 97
Fraction of orfs with sites within 600 bp upstream = 0.0155798


Motif number 2

CTTATATTTATAATTTTTAGTTATGGTGAT	1	14	0	TAATTTTTAG	    0.902514	-122
TATAAATATAAGATTATGATATTATGATAA	1	32	1	AGATTATGAT	    0.889191	-104
TAAATCTTTTAAATTTTTAGTTACTATTAA	1	74	0	AAATTTTTAG	    0.974034	-62
AAAATTTAAAAGATTTATATATGTCAATAT	1	87	1	AGATTTATAT	    0.962522	-49
ATATTTACAGAGATTTTTATAAGGTGTTAA	1	115	1	AGATTTTTAT	    0.992076	-21
CATTTTTATTCCAGTTTTATAAACTTCACC	2	14	0	CCAGTTTTAT	    0.906583	-53
TCGCCACTTAACATTTTTATTCCAGTTTTA	2	25	0	ACATTTTTAT	    0.988512	-42
          **********

Masking position 3
Map Score:   8.04604

Number of sites scoring better than the average of aligned sites = 857
Number in coding regions = 602
Number in noncoding regions = 255
Number of orfs with sites within 600 bp upstream = 249
Fraction of orfs with sites within 600 bp upstream = 0.0399936


Motif number 3

ATATTTATAATTTTTAGTTATGGTGATATG	1	11	0	TTTTTAGTTA	    0.989766	-125
ATATCATAATCTTATATTTATAATTTTTAG	1	24	0	CTTATATTTA	    0.935633	-112
ATCTTTTAAATTTTTAGTTACTATTAAAAG	1	71	0	TTTTTAGTTA	    0.989766	-65
CCACTTAACATTTTTATTCCAGTTTTATAA	2	22	0	TTTTTATTCC	    0.955685	-45
          **********

Masking position 5
Map Score:   2.19865

Number of sites scoring better than the average of aligned sites = 264
Number in coding regions = 190
Number in noncoding regions = 74
Number of orfs with sites within 600 bp upstream = 66
Fraction of orfs with sites within 600 bp upstream = 0.0106007


Motif number 4

AATTTTTAGTTATGGTGATATG         	1	2	0	TATGTGATAT	    0.984839	-134
AATATAAGATTATGATATTATGATAAGGCAT	1	36	1	TATGTATTAT	    0.983653	-100
TTTTAAATTTTTAGTTACTATTAAAAGGAAG	1	67	0	TTAGTACTAT	     0.90256	-69
AAGATTTATATATGTCAATATATTTACAGAG	1	96	1	TATGCAATAT	    0.964421	-40
GAGATTTTTATAAGGTGTTAAT         	1	124	1	TAAGTGTTAA	    0.932292	-12
          **** ******

Masking position 9
Map Score:   0.87119

Number of sites scoring better than the average of aligned sites = 173
Number in coding regions = 139
Number in noncoding regions = 34
Number of orfs with sites within 600 bp upstream = 41
Fraction of orfs with sites within 600 bp upstream = 0.00658529


Motif number 5

          **********

No masking
Map Score:   -7.57276e-14

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:   -7.57276e-14

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:   -7.57276e-14

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