AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -imetR_aquae_opreg_100.orf -g0.435 -x5 
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 =  	0.435
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	oppB	300	transporter (OppBC family)
#2	metF	80	5,10-methylenetetrahydrofolate reductase
#3	metE	44	tetrahydropteroyltriglutamate methyltransferase

Motif number 1

TCAGGTTTCTGACGTACTCCATGGTGGGAGGGAC	1	30	0	GACGTACAGG	     0.99421	-271
TTTCTTCTATGAAGTACCAAAGAGCTGCTGTAAA	1	138	0	GAAGTACAAG	    0.997166	-163
GTACTTCATAGAAGAAAAGGACAGGATACCCGAC	1	155	1	GAAGAAAAAG	    0.891045	-146
ACAAGGTAATCAAGTACGTGAAGGAAAAACACAA	1	220	1	CAAGTACAGG	     0.99496	-81
AGGAGATAGACAGGTACTTTAAGGAAACGAAGTT	1	256	1	CAGGTACAGG	    0.983805	-45
TTAAGGAAACGAAGTTCTTTATAGCTAATTACTT	1	274	1	GAAGTTCAAG	    0.992296	-27
       AAGGAAGTATTTTAAAGGTGGACTAAG	2	64	0	GAAGTATAAG	    0.978557	-17
TTTAAAATAAGAAGTTCTAAAAGGAGGAGAAATC	3	20	1	GAAGTTCAGG	    0.995129	-25
          *******   * **

Masking position 11
Map Score:   13.852

Number of sites scoring better than the average of aligned sites = 226
Number in coding regions = 212
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 2

GGGACTTTTGCGAGTTTCCTTCTA      	1	5	0	CGAGTTTCCT	    0.995455	-296
TTAGGGTCGGAGAGTATCCTGAAGAGGAGT	1	77	0	AGAGTATCCT	    0.981094	-224
GGAACCCAGTCGGGTATCCTGTCCTTTTCT	1	167	0	CGGGTATCCT	    0.978319	-134
TGTAGTCGTCCCAGTATCCTAACATGGGAA	1	193	0	CCAGTATCCT	    0.995207	-108
          **********

Masking position 5
Map Score:   7.0453

Number of sites scoring better than the average of aligned sites = 27
Number in coding regions = 25
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 3

GGAGGCAAGGGAAGATTTTACAGCAGCTCT	1	122	1	GAAGATTTTA	    0.929208	-179
TTAAGGAAACGAAGTTCTTTATAGCTAATT	1	274	1	GAAGTTCTTT	    0.770037	-27
        TAAAAGTAATTAGCTATAAAGA	1	289	0	AAAGTAATTA	    0.844608	-12
ACCTCCCTTGAAAGTTTTTTACACTTTTTA	2	16	1	AAAGTTTTTT	    0.702082	-65
TTATTTCTTAAAAATTCTTAGTCCACCTTT	2	48	1	AAAATTCTTA	    0.687712	-33
       AAGGAAGTATTTTAAAGGTGGAC	2	68	0	GAAGTATTTT	     0.84784	-13
         AAAAGATATTTTAAAATAAGA	3	2	1	AAAGATATTT	    0.683623	-43
TTTAAAATAAGAAGTTCTAAAAGGAGGAGA	3	20	1	GAAGTTCTAA	    0.918785	-25
          **********

Masking position 3
Map Score:   6.4285

Number of sites scoring better than the average of aligned sites = 935
Number in coding regions = 869
Number in noncoding regions = 66
Number of orfs with sites within 600 bp upstream = 66
Fraction of orfs with sites within 600 bp upstream = 0.0106007


Motif number 4

AAGGAAACTCGCAAAAGTCCCTCCCACCATG	1	14	1	GCAAAGTCCC	    0.986294	-287
GATTCTGGACGCCAAACTCCTCTTCAGGATA	1	62	1	GCCAACTCCT	    0.986422	-239
TGATTACCTTGTAGTCGTCCCAGTATCCTAA	1	201	0	GTATCGTCCC	    0.963636	-100
TAAAGTACCTGTCTATCTCCTCTTTGTGTTT	1	246	0	GTCATCTCCT	    0.969919	-55
         GGCACACCTCCCTTGAAAGTTT	2	2	1	GCAACCTCCC	     0.99533	-79
          GGATTTCTCCTCCTTTTAGAA	3	34	0	GGATTCTCCT	    0.946005	-11
          *** *******

Masking position 8
Map Score:   2.92803

Number of sites scoring better than the average of aligned sites = 319
Number in coding regions = 294
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 5

AAAAGTCCCTCCCACCATGGAGTACGTCAG	1	26	1	CCCACCATGG	    0.922275	-275
ACGTCAGAAACCTGATTCTGGACGCCAAAC	1	49	1	CCTGATTCTG	    0.894605	-252
ACTCTCCGACCCTAACTTTGACCTGAGTGA	1	92	1	CCTAACTTTG	    0.976378	-209
TCCCTTGCCTCCTCACTCAGGTCAAAGTTA	1	104	0	CCTCACTCAG	    0.955372	-197
GGACAGGATACCCGACTGGGTTCCCATGTT	1	173	1	CCCGACTGGG	    0.953002	-128
GTCCCAGTATCCTAACATGGGAACCCAGTC	1	186	0	CCTAACATGG	    0.968746	-115
CTGTCTATCTCCTCTTTGTGTTTTTCCTTC	1	239	0	CCTCTTTGTG	    0.753148	-62
    GGCACACCTCCCTTGAAAGTTTTTTA	2	7	1	CCTCCCTTGA	    0.910128	-74
          **********

Masking position 2
Map Score:   2.46455

Number of sites scoring better than the average of aligned sites = 566
Number in coding regions = 518
Number in noncoding regions = 48
Number of orfs with sites within 600 bp upstream = 43
Fraction of orfs with sites within 600 bp upstream = 0.00690652


Motif number 6

          **********

No masking
Map Score:   -8.99957e-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:   -8.99957e-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 8

          **********

No masking
Map Score:   -8.99957e-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