AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -icynR_aquae_opreg_300.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	nirB	120	nitrite reductase (NAD(P)H) large subunit
#2	fhp	133	flavohemoprotein
#3	lysR1	300	transcriptional regulator (LysR family)

Motif number 1

ATAACTTTCATTTTACAACCTCTGTAAGGACTTA	1	31	1	TTTCACTCTG	    0.966491	-90
GGTAGTTATGTTTTGTAAGTCCTTACAGAGGTTG	1	46	0	TTTTAGCCTT	    0.765292	-75
CCCGGAACTTTTTGGCACGTTTTTTGCAAGAGTT	1	78	1	TTTCCGTTTT	    0.960718	-43
         CTTTCACTCCTCCTGAGGAAACTCT	1	106	0	TTTCCCCCTG	    0.982816	-15
CGTACAATTTTGTAGCTACATTTTTGTT      	2	5	0	TGTCACTTTT	    0.865656	-129
TTTCTCTGATTGTGGAGACGCTTTGCGTACAATT	2	30	0	TGTAACCTTT	    0.558938	-104
CCCCGTTCTGTTTTAACAGTTCTTGGAAACTTTT	2	61	0	TTTAAGTCTT	    0.883648	-73
GCGTGCCAAATTCTCCCCGTTCTGTTTTAACAGT	2	75	0	TTCCCGTCTG	    0.925517	-59
ACGGGGAGAATTTGGCACGCTTTTTGCAATTAGT	2	89	1	TTTCCGTTTT	    0.960718	-45
          CTTTTCACCTCCTTCACTCAAACT	2	120	0	CTTCCCCCTT	    0.962124	-14
GACGTATGCTTTCCGCAACGCCTTTCTTGAGAAG	3	13	0	TTCCACCCTT	    0.932869	-288
GTTCGTCGGATGTCTCCAGTCCTTAGAACTCAAC	3	108	1	TGTCAGCCTT	    0.950528	-193
CAGGCACTTCCTTCGCTCGGTCAGGCGGGAAGAG	3	193	1	CTTCCGTCAG	    0.683187	-108
CCTGGTAATCTTTCTCTCCATTTTTCTTTTTTAT	3	233	1	TTTCCCTTTT	    0.965348	-68
ATTTTTCTTTTTTATAACCCTCATAAACATTTCT	3	252	1	TTTACCTCAT	    0.732945	-49
          ***  * ** ****

Masking position 13
Map Score:   14.4009

Number of sites scoring better than the average of aligned sites = 2043
Number in coding regions = 1882
Number in noncoding regions = 161
Number of orfs with sites within 600 bp upstream = 114
Fraction of orfs with sites within 600 bp upstream = 0.0183103


Motif number 2

TGCAAAAAACGTGCCAAAAAGTTCCGGGTAGTTAT	1	71	0	GTGCCAATCC	    0.992939	-50
TCTCCACAATCAGAGAAAAGTTTCCAAGAACTGTT	2	46	1	CAGAGAATCC	    0.988246	-88
TGCAAAAAGCGTGCCAAATTCTCCCCGTTCTGTTT	2	82	0	GTGCCAATCC	    0.977492	-52
AGGCGTTGCGGAAAGCATACGTCCCATGGAAGAAG	3	24	1	GAAAGCATCC	    0.887692	-277
TTTTAACACCCAGCCAGGCACTTCCTTCGCTCGGT	3	179	1	CAGCCAGTCC	    0.959656	-122
AGATTACCAGGTGAGAACTCTTCCCGCCTGACCGA	3	209	0	GTGAGAATCC	    0.992671	-92
AAGAAAAATGGAGAGAAAGATTACCAGGTGAGAAC	3	226	0	GAGAGAATCC	    0.995006	-75
          *******    * **

Masking position 12
Map Score:   6.23771

Number of sites scoring better than the average of aligned sites = 93
Number in coding regions = 85
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 3

ATAACTTTCATTTTACAACCTCTGTAAGGAC	1	31	1	TTTTAAACCT	    0.935585	-90
GGTAGTTATGTTTTGTAAGTCCTTACAGAGG	1	49	0	TTTTGAAGTC	    0.935026	-72
ACCCGGAACTTTTTGGCACGTTTTTTGCAAG	1	77	1	TTTTGCACGT	    0.942946	-44
CCCCGTTCTGTTTTAACAGTTCTTGGAAACT	2	64	0	TTTTACAGTT	    0.825067	-70
AACGGGGAGAATTTGGCACGCTTTTTGCAAT	2	88	1	ATTTGCACGC	    0.888262	-46
ATCAAGGACTTTATGGAACTCGCATTGGACA	3	67	1	TTATGAACTC	    0.881629	-234
GACGTACCGCTTTTAACACCCAGCCAGGCAC	3	169	1	TTTTACACCC	    0.982775	-132
CATTTTTCTTTTTTATAACCCTCATAAACAT	3	251	1	TTTTAAACCC	    0.977933	-50
 CCTTATTAATTTTATACCTCGGATAAGAAA	3	281	0	TTTTAACCTC	    0.895554	-20
          ***** *****

Masking position 4
Map Score:   5.86269

Number of sites scoring better than the average of aligned sites = 357
Number in coding regions = 326
Number in noncoding regions = 31
Number of orfs with sites within 600 bp upstream = 38
Fraction of orfs with sites within 600 bp upstream = 0.00610344


Motif number 4

 CTTTTCACCTCCTTCACTCAAACTAATTG	2	115	0	TCCTTCACTC	     0.99247	-19
          TCCTTCTCAAGAAAGGCGTT	3	1	1	TCCTTCTCAA	    0.961913	-300
TGATGGTATTTCCTTCTTCCATGGGACGTA	3	41	0	TCCTTCTTCC	     0.97398	-260
GCCAGGCACTTCCTTCGCTCGGTCAGGCGG	3	191	1	TCCTTCGCTC	    0.994907	-110
CACCTGGTAATCTTTCTCTCCATTTTTCTT	3	231	1	TCTTTCTCTC	    0.984571	-70
          **********

Masking position 5
Map Score:   5.45549

Number of sites scoring better than the average of aligned sites = 114
Number in coding regions = 109
Number in noncoding regions = 5
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:   1.51589e-12

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:   1.51589e-12

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:   1.51589e-12

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