AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i214_Ribosomal_Operon_1_aquae_reg_100.orf -o214_aquae_100.ace -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -g0.44 -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 =  	0.44
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RAA00786	300	Aquifex_aeolicus
#2	RAA00789	56	Aquifex_aeolicus
#3	RAA01712	45	Aquifex_aeolicus

Motif number 1

TTCACCTGATGGAAAATTTTTAGGAGTCGTGG	1	29	1	GGAAATTTTA	    0.980159	-272
ATGAAACAACGGGAAAATTTGATGGAAACTTT	1	139	1	GGGAAATTGA	    0.914442	-162
AAAATTTGATGGAAACTTTTTAAGATACGATA	1	152	1	GGAAATTTTA	    0.980219	-149
GAAGGACACCATAAACATCTTAAAGGTAAAAA	1	195	1	ATAAAATTTA	    0.671626	-106
AAATTTATAAGGGAACTTTTTACCTTTAAGAT	1	211	0	GGGAATTTTA	    0.978896	-90
TTCAATATCCGTAAATTTATAAGGGAACTTTT	1	223	0	GTAAATTTAA	    0.945076	-78
AACAATTGATAGAAGATTTTAAGAACGATTTT	1	253	1	AGAAGTTTAA	    0.967768	-48
AAATTAATTGAGGAGGTTGTGAA         	1	288	1	AGGAGTTTGA	     0.94977	-13
TCCTAACTAAATAAATTTATAAAGAGAAAACT	2	24	0	ATAAATTTAA	    0.900548	-33
TTATTTAGTTAGGAGAGTTTAAAAC       	2	42	1	AGGAGGTTAA	    0.867815	-15
CGAGTTTAAAGCAAGATTGTAATTATAACA  	3	9	0	GCAAGTTTAA	    0.904375	-37
          ***** ** ***

Masking position 4
Map Score:   11.4418

Number of sites scoring better than the average of aligned sites = 883
Number in coding regions = 808
Number in noncoding regions = 75
Number of orfs with sites within 600 bp upstream = 74
Fraction of orfs with sites within 600 bp upstream = 0.0118856


Motif number 2

CTTTTGGTACTTTCCATATCTTCATTTCCA	1	58	0	TTTCCATATC	    0.937233	-243
TCTATCAATTGTTCAATATCCGTAAATTTA	1	236	0	GTTCAATATC	    0.948443	-65
TCAAAATCGTTCTTAAAATCTTCTATCAAT	1	257	0	TCTTAAAATC	     0.94657	-44
TCAATTAATTTTTCAAAATCGTTCTTAAAA	1	269	0	TTTCAAAATC	    0.987045	-32
         GTTTTAAACTCTCCTAACTAA	2	46	0	TTTTAAACTC	    0.975712	-11
TACAATCTTGCTTTAAACTCGGAAGAGGTG	3	20	1	CTTTAAACTC	    0.947635	-26
          **********

Masking position 6
Map Score:   4.36964

Number of sites scoring better than the average of aligned sites = 244
Number in coding regions = 230
Number in noncoding regions = 14
Number of orfs with sites within 600 bp upstream = 15
Fraction of orfs with sites within 600 bp upstream = 0.00240925


Motif number 3

ACGGAGCGTATTTTCACCTGATGGAAAATTTTTAG	1	17	1	TTTTCCTGGA	    0.988726	-284
TCAGGATGGCATTTATCTTTTGGTACTTTCCATAT	1	69	0	ATTTCTTTGA	    0.952372	-232
AAGGGAGTACTTGTAGCCTTCAGGATGGCATTTAT	1	88	0	TTGTCCTTGA	    0.988727	-213
TACTCCCTTGTTTTTGCCTTATACAATGAAACAAC	1	114	1	TTTTCCTTAA	    0.993486	-187
ATAAGGGAACTTTTTACCTTTAAGATGTTTATGGT	1	202	0	TTTTCCTTAA	    0.992979	-99
TTTCTTTTAGTTTTCTCTTTATAAATTTATTTAGT	2	16	1	TTTTCTTTAA	     0.98094	-41
          ****  ****  * *

Masking position 9
Map Score:   5.01378

Number of sites scoring better than the average of aligned sites = 103
Number in coding regions = 94
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 4

GAGCGTATTTTCACCTGATGGAAAATTTTTAG	1	20	1	TCACTGATGA	    0.912667	-281
AACAACGGGAAAATTTGATGGAAACTTTTTAA	1	143	1	AAATTGATGA	    0.980136	-158
CGATAATTATCAATGTGAAGGACACCATAAAC	1	179	1	CAATTGAAGA	    0.922603	-122
CGGATATTGAACAATTGATAGAAGATTTTAAG	1	244	1	ACAATGATGA	    0.982534	-57
ACGATTTTGAAAAATTAATTGAGGAGGTTGTG	1	277	1	AAAATAATGA	    0.951287	-24
TTATAAAGAGAAAACTAAAAGAAAAGGGC   	2	8	0	AAAATAAAGA	    0.927585	-49
          **** **** **

Masking position 6
Map Score:   0.756404

Number of sites scoring better than the average of aligned sites = 117
Number in coding regions = 109
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 5

          **********

No masking
Map Score:   4.92707e-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:   4.92707e-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:   4.92707e-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