AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i231_mjan_pyro_300.orf -o231_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	RMJ00617	135	M_jannaschii_chromosome
#2	RPH00628	66	Pyrococcus_OT3

Motif number 1

 CATATCACCATAACTAAAAATTATAAATAT	1	10	1	AAACTAAAAA	    0.851415	-126
ACTAAAAATTATAAATATAAGATTATGATAT	1	23	1	AAAATATAAG	    0.975384	-113
AGATTATGATATTATGATAAGGCATCTTCCT	1	42	1	ATATGATAAG	    0.973565	-94
ATTTTTAGTTACTATTAAAAGGAAGATGCCT	1	61	0	ATATTAAAAG	    0.978678	-75
TAGTAACTAAAAATTTAAAAGATTTATATAT	1	78	1	AATTTAAAAG	    0.978777	-58
AAATATATTGACATATATAAATCTTTTAAAT	1	90	0	AATATATAAA	    0.913413	-46
ATTTACAGAGATTTTTATAAGGTGTTAAT  	1	117	1	ATTTTATAAG	    0.984218	-19
TTTTTATTCCAGTTTTATAAACTTCACCTAC	2	11	0	ATTTTATAAA	    0.958935	-56
AACTGGAATAAAAATGTTAAGTGGCGAGAGC	2	28	1	AAATGTTAAG	    0.893012	-39
          * *********

Masking position 9
Map Score:   11.8347

Number of sites scoring better than the average of aligned sites = 1176
Number in coding regions = 944
Number in noncoding regions = 232
Number of orfs with sites within 600 bp upstream = 237
Fraction of orfs with sites within 600 bp upstream = 0.0380662


Motif number 2

CTTATATTTATAATTTTTAGTTATGGTGAT	1	14	0	TAATTTTTAG	    0.906402	-122
TATAAATATAAGATTATGATATTATGATAA	1	32	1	AGATTATGAT	    0.893546	-104
TAAATCTTTTAAATTTTTAGTTACTATTAA	1	74	0	AAATTTTTAG	    0.975147	-62
AAAATTTAAAAGATTTATATATGTCAATAT	1	87	1	AGATTTATAT	    0.964063	-49
ATATTTACAGAGATTTTTATAAGGTGTTAA	1	115	1	AGATTTTTAT	     0.99242	-21
CATTTTTATTCCAGTTTTATAAACTTCACC	2	14	0	CCAGTTTTAT	    0.910325	-53
TCGCCACTTAACATTTTTATTCCAGTTTTA	2	25	0	ACATTTTTAT	     0.98901	-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

         CATATCACCATAACTAAAAATT	1	2	1	ATATCACATA	    0.985684	-134
ATGCCTTATCATAATATCATAATCTTATATT	1	36	0	ATAATACATA	    0.984563	-100
CTTCCTTTTAATAGTAACTAAAAATTTAAAA	1	67	1	ATAGTACTAA	     0.90622	-69
CTCTGTAAATATATTGACATATATAAATCTT	1	96	0	ATATTGCATA	    0.966364	-40
         ATTAACACCTTATAAAAATCTC	1	124	0	TTAACACTTA	    0.935869	-12
          ****** ****

Masking position 3
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 4

          **********

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 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