AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i130_Transmembrane_Transport_4_aquae_reg_100.orf -o130_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	RAA00044	263	Aquifex_aeolicus

Motif number 1

AGCTGTTCTTTTTGGTTTATAATGCTAAATTTT	1	51	1	TTGGTTAAAT	    0.944678	-213
TTACCCTAAATATGCTTGAAAATTTAGCATTAT	1	69	0	TTGCTTAAAT	    0.975884	-195
TTTTATTTGCTGTTGTTATAATTACCCTAAATA	1	90	0	TTTGTTTATT	    0.977284	-174
TATAAACACGTATTCTTTTAATTTATCCCTTAA	1	131	0	TTTCTTTATT	    0.990287	-133
GGAAAAGCTTTTTTCTTTTCCTTTCCAAGTTTT	1	173	0	TTTCTTTCTT	    0.985635	-91
GTAGATTATTTCTTCTTCTAAATCAAGATTACC	1	221	0	TTTCTTTAAT	    0.987391	-43
      TTTATGTTCTTAAGCTTTGAGTAGATT	1	247	0	TTTCTTACTT	    0.981376	-17
          * ***** * ***

Masking position 7
Map Score:   8.92095

Number of sites scoring better than the average of aligned sites = 223
Number in coding regions = 201
Number in noncoding regions = 22
Number of orfs with sites within 600 bp upstream = 25
Fraction of orfs with sites within 600 bp upstream = 0.00401542


Motif number 2

ATTAGGTTATTTTAAGCTATAATTTTTCAATTATG	1	12	1	TTTAGATATT	    0.926608	-252
TAATTTTTCAATTATGGGCAAGCTGTTCTTTTTGG	1	31	1	ATTAGCAATG	    0.967957	-233
TTTTTGGTTTATAATGCTAAATTTTCAAGCATATT	1	59	1	ATAAGAAATT	    0.978849	-205
TGTTGTTATAATTACCCTAAATATGCTTGAAAATT	1	78	0	ATTACAAATG	    0.969557	-186
AAATTCCCTTATTAAGGGATAAATTAAAAGAATAC	1	120	1	ATTAGATATT	    0.975581	-144
GTGTTTATATATTTAGTAAAAACTTGGAAAGGAAA	1	155	1	ATTTGAAATT	    0.975582	-109
TTCAAGATTCTTAATGGAAAAGCTTTTTTCTTTTC	1	186	0	TTAAGAAATT	    0.936005	-78
CTAAATCAAGATTACCTTCAAGATTCTTAATGGAA	1	202	0	ATTACCAATT	    0.969557	-62
AGAAGAAATAATCTACTCAAAGCTTAAGAACATAA	1	238	1	ATCTCAAATT	    0.863676	-26
          **** *  ***  **

Masking position 11
Map Score:   7.3374

Number of sites scoring better than the average of aligned sites = 294
Number in coding regions = 267
Number in noncoding regions = 27
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 3

TTATAGCTTAAAATAACCTAATT       	1	4	0	AAATAACCTA	    0.989959	-260
CTGTTGTTATAATTACCCTAAATATGCTTG	1	84	0	AATTACCCTA	    0.970018	-180
ACAGCAAATAAAATTCCCTTATTAAGGGAT	1	110	1	AAATTCCCTT	    0.981032	-154
TTCTAAATCAAGATTACCTTCAAGATTCTT	1	209	0	AGATTACCTT	    0.955802	-55
TTAGAAGAAGAAATAATCTACTCAAAGCTT	1	233	1	AAATAATCTA	    0.949736	-31
          **********

Masking position 4
Map Score:   4.59378

Number of sites scoring better than the average of aligned sites = 118
Number in coding regions = 108
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 4

AACAGCTTGCCCATAATTGAAAAATTATAG	1	28	0	CCATAATTGA	    0.911624	-236
GCATTATAAACCAAAAAGAACAGCTTGCCC	1	46	0	CCAAAAAGAA	    0.961548	-218
GTTATAATTACCCTAAATATGCTTGAAAAT	1	79	0	CCCTAAATAT	    0.961451	-185
TTTAATTTATCCCTTAATAAGGGAATTTTA	1	118	0	CCCTTAATAA	     0.98046	-146
AAAAGCTTTTCCATTAAGAATCTTGAAGGT	1	194	1	CCATTAAGAA	     0.98046	-70
          **********

Masking position 6
Map Score:   2.81644

Number of sites scoring better than the average of aligned sites = 92
Number in coding regions = 81
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 5

          **********

No masking
Map Score:   -2.81785e-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:   -2.81785e-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:   -2.81785e-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