AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i214_Ribosomal_Operon_1_aquae_reg_300.orf -o214_aquae_300.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

CCACGACTCCTAAAAATTTTCCATCAGGTGAA	1	29	0	TAAAATTTCC	    0.987388	-272
AAAGTTTCCATCAAATTTTCCCGTTGTTTCAT	1	139	0	TAAATTTCCC	    0.934244	-162
TATCGTATCTTAAAAAGTTTCCATCAAATTTT	1	152	0	TAAAATTTCC	    0.989012	-149
ATCTTAAAGGTAAAAAGTTCCCTTATAAATTT	1	211	1	TAAAATTCCC	    0.990234	-90
AAAAGTTCCCTTATAAATTTACGGATATTGAA	1	223	1	TATAATTTAC	    0.893032	-78
AAAATCGTTCTTAAAATCTTCTATCAATTGTT	1	253	0	TAAAACTTCT	    0.978162	-48
AGAACGATTTTGAAAAATTAATTGAGGAGGTT	1	274	1	TAAAATTAAT	    0.742445	-27
         TTCACAACCTCCTCAATTAATTT	1	288	0	TACAACTCCT	    0.960631	-13
AGTTTTCTCTTTATAAATTTATTTAGTTAGGA	2	24	1	TATAATTTAT	    0.814504	-33
       GTTTTAAACTCTCCTAACTAAATAA	2	42	0	TAAACCTCCT	    0.912347	-15
  TGTTATAATTACAATCTTGCTTTAAACTCG	3	9	1	TACAACTTGC	    0.876373	-37
          * **** *****

Masking position 5
Map Score:   11.7534

Number of sites scoring better than the average of aligned sites = 818
Number in coding regions = 749
Number in noncoding regions = 69
Number of orfs with sites within 600 bp upstream = 71
Fraction of orfs with sites within 600 bp upstream = 0.0114038


Motif number 2

TATTTTCACCTGATGGAAAATTTTTAGGAG	1	25	1	TGATGGAAAA	    0.982512	-276
TTTCATTGTATAAGGCAAAAACAAGGGAGT	1	115	0	TAAGGCAAAA	     0.95615	-186
ACAATGAAACAACGGGAAAATTTGATGGAA	1	136	1	AACGGGAAAA	      0.8254	-165
CGGGAAAATTTGATGGAAACTTTTTAAGAT	1	148	1	TGATGGAAAC	    0.960253	-153
ATTATCAATGTGAAGGACACCATAAACATC	1	184	1	TGAAGGACAC	    0.867732	-117
ATAAACATCTTAAAGGTAAAAAGTTCCCTT	1	205	1	TAAAGGTAAA	    0.904778	-96
ATTGAACAATTGATAGAAGATTTTAAGAAC	1	249	1	TGATAGAAGA	    0.872067	-52
AAGAGAAAACTAAAAGAAAAGGGC      	2	5	0	TAAAAGAAAA	    0.950133	-52
ATAAATTTATAAAGAGAAAACTAAAAGAAA	2	16	0	AAAGAGAAAA	    0.864791	-41
CTTCCGAGTTTAAAGCAAGATTGTAATTAT	3	15	0	TAAAGCAAGA	    0.885895	-31
          **********

Masking position 7
Map Score:   6.38672

Number of sites scoring better than the average of aligned sites = 3423
Number in coding regions = 3207
Number in noncoding regions = 216
Number of orfs with sites within 600 bp upstream = 166
Fraction of orfs with sites within 600 bp upstream = 0.0266624


Motif number 3

TAAAACGGAGCGTATTTTCACCTGATGGAA	1	13	1	CGTATTTTCA	    0.987706	-288
TGGTACTTTCCATATCTTCATTTCCACGAC	1	54	0	CATATCTTCA	    0.982217	-247
CAAATTTTCCCGTTGTTTCATTGTATAAGG	1	130	0	CGTTGTTTCA	    0.940362	-171
AAGTTTCCATCAAATTTTCCCGTTGTTTCA	1	140	0	CAAATTTTCC	    0.909321	-161
TGATAATTATCGTATCTTAAAAAGTTTCCA	1	161	0	CGTATCTTAA	    0.930738	-140
AATCTTCTATCAATTGTTCAATATCCGTAA	1	241	0	CAATTGTTCA	    0.896088	-60
          **********

Masking position 7
Map Score:   2.34556

Number of sites scoring better than the average of aligned sites = 122
Number in coding regions = 116
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 4

GTACTTGTAGCCTTCAGGATGGCATTTATCT	1	86	0	CCTTCAGATG	    0.986452	-215
TTGTTTTTGCCTTATACAATGAAACAACGGG	1	121	1	CTTATAAATG	    0.914424	-180
TAAAAAGTTTCCATCAAATTTTCCCGTTGTT	1	143	0	CCATCAATTT	    0.885514	-158
TTTATGGTGTCCTTCACATTGATAATTATCG	1	179	0	CCTTCAATTG	    0.989194	-122
GAACTTTTTACCTTTAAGATGTTTATGGTGT	1	200	0	CCTTTAGATG	    0.979521	-101
AAAAAGTTCCCTTATAAATTTACGGATATTG	1	222	1	CTTATAATTT	    0.783194	-79
          ****** ****

Masking position 6
Map Score:   0.645407

Number of sites scoring better than the average of aligned sites = 232
Number in coding regions = 223
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


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