AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i321_mixed6_hinf_reg_100.orf -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -g0.38 -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 =  	0.38
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	HI0454	54	conserved hypothetical protein
#2	HI0457	69	conserved hypothetical protein
#3	HI0458	70	stationary phase survival protein SurA, putative
#4	HI0459	131	pyrimidine operon regulatory protein (pyrR)

Motif number 1

GCCTTAGGCATAAGGAAAAATAATT        	1	40	1	TAAGAAAAAA	    0.963604	-15
         CAAAGTATCAAAAATAAAGGGGCT	2	2	1	AAAGACAAAA	    0.993143	-68
AAAAACAACAAAAGGGGCAATTAAGCCCCTTTA	2	25	0	AAAGGCAATA	    0.961613	-45
AAGCTATAAGAAAGAGAAAATAAAAAACAACAA	2	47	0	AAAGGAAAAA	    0.993143	-23
CTCATCCAAAAAAGAGTCAATAACGTTGGTTAG	3	48	0	AAAGGCAAAA	    0.992989	-23
ACATTCCATCAAAGGAAACCAAATT        	4	3	0	AAAGAACCAA	    0.956946	-129
AATGTTTTGGATAGTATAACGAACAAGAAAAAT	4	31	1	ATAGAAACAA	    0.937475	-101
TTCAATGCACAAAGTATAAAGAAAATACGCCTA	4	85	0	AAAGAAAAAA	    0.993279	-47
          **** * *** **

Masking position 3
Map Score:   12.7891

Number of sites scoring better than the average of aligned sites = 205
Number in coding regions = 148
Number in noncoding regions = 57
Number of orfs with sites within 600 bp upstream = 50
Fraction of orfs with sites within 600 bp upstream = 0.00803084


Motif number 2

CTAAGGCTTGAACGCCATAGACGATATATCT	1	16	0	AACGCCATGA	    0.992719	-39
TTAGAGTAACAATTCTATTGAAGGTTCACAA	3	21	0	AATTCTATGA	    0.974367	-50
TACTCTAACCAACGTTATTGACTCTTTTTTG	3	44	1	AACGTTATGA	    0.982323	-27
CCTTTGATGGAATGTTTTGGATAGTATAACG	4	21	1	AATGTTTTGA	    0.953213	-111
AAATGGTGCAAATGCCGTCGCTTTTTAGGCG	4	60	1	AATGCCGTGC	    0.964399	-72
TGTGCATTGAAATACTATTGATAAAGCTGGG	4	107	1	AATACTATGA	    0.974367	-25
          ******** **

Masking position 8
Map Score:   3.72554

Number of sites scoring better than the average of aligned sites = 214
Number in coding regions = 183
Number in noncoding regions = 31
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 3

TAGGCATAAGGAAAAATAATT         	1	44	1	GAAAAATAAT	    0.923497	-11
  CAAAGTATCAAAAATAAAGGGGCTTAAT	2	9	1	CAAAAATAAA	     0.94806	-61
AGAAAATAAAAAACAACAAAAGGGGCAATT	2	36	0	AAACAACAAA	    0.951065	-34
TATAAGAAAGAGAAAATAAAAAACAACAAA	2	46	0	AGAAAATAAA	    0.947379	-24
TTCCATCAAAGGAAACCAAATT        	4	3	0	GGAAACCAAA	    0.941217	-129
ATAGTATAACGAACAAGAAAAATGGTGCAA	4	41	1	GAACAAGAAA	    0.959669	-91
          **********

Masking position 5
Map Score:   1.62154

Number of sites scoring better than the average of aligned sites = 675
Number in coding regions = 490
Number in noncoding regions = 185
Number of orfs with sites within 600 bp upstream = 150
Fraction of orfs with sites within 600 bp upstream = 0.0240925


Motif number 4

TATCGTCTATGGCGTTCAAGCCTTAGGCATAA	1	21	1	GGCTTCAGCC	    0.576806	-34
CAACAAAAGGGGCAATTAAGCCCCTTTATTTT	2	21	0	GGCATTAGCC	    0.765263	-49
AAAAAGCGACGGCATTTGCACCATTTTTCTTG	4	54	0	GGCTTTCACC	    0.988418	-78
CAAATGCCGTCGCTTTTTAGGCGTATTTTCTT	4	68	1	CGCTTTAGGC	    0.985947	-64
          *** *** ****

Masking position 6
Map Score:   0.765375

Number of sites scoring better than the average of aligned sites = 62
Number in coding regions = 50
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 5

          **********

No masking
Map Score:   3.29282e-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:   3.29282e-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:   3.29282e-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