AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i209_rpod_ecoli_hinf_reg_100.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 =  	0.46
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	dnaG	110	DNA biosynthesis; DNA primase
#2	rpoD	194	RNA polymerase, sigma(70) factor; regulation of proteins induced at high temperatures
#3	HI0532	133	DNA primase (dnaG)
#4	HI0533	69	RNA polymerase sigma-70 factor (rpoD)

Motif number 1

TGTAGTTGTAAGGCCGTGCTTCCGAAAGGA	1	46	1	AGGCCGTGCT	    0.988361	-65
AAACGAAAATAAGCCGCGCATTCCTTTCGG	1	67	0	AAGCCGCGCA	    0.991906	-44
          AGGCCCCGATTTTTAGCAAT	1	101	0	AGGCCCCGAT	    0.908872	-10
TTCGGCACTTAAGCCGTTAAA         	2	2	0	AAGCCGTTAA	    0.948886	-193
AAGCCCCCGACAGCCGCACTGAGAGGCAGC	2	43	1	CAGCCGCACT	    0.983141	-152
CACTGAGAGGCAGCGGCAAATATATAAGTA	2	59	1	CAGCGGCAAA	    0.835432	-136
GATAATTACGAGGGCGTACTTATATATTTG	2	75	0	AGGGCGTACT	    0.833922	-120
CGATGTCCTTCAGCCGTTAACGCTGAAATC	2	126	0	CAGCCGTTAA	    0.945538	-69
GAGTTAAGACAAACCGTGAATCCTTTGGAC	3	31	1	AAACCGTGAA	    0.943999	-103
TAAAGTAACAAAACCGTGAGTCCAAAGGAT	3	50	0	AAACCGTGAG	    0.860405	-84
ACGCCAAAAACGACCGCACTTTCACACCAC	3	96	1	CGACCGCACT	    0.930047	-38
          **********

Masking position 5
Map Score:   10.6346

Number of sites scoring better than the average of aligned sites = 4634
Number in coding regions = 4376
Number in noncoding regions = 258
Number of orfs with sites within 600 bp upstream = 255
Fraction of orfs with sites within 600 bp upstream = 0.0409573


Motif number 2

GGAGAGCAACGCTCTCGGGGAA        	1	3	0	GCTCTCGGGG	    0.997295	-108
CGAGAGCGTTGCTCTCCGATCAGACCGAGT	1	16	1	GCTCTCCGAT	    0.952154	-95
CTTCCCGATCGCTCTTCGGCACTTAAGCCG	2	16	0	GCTCTTCGGC	    0.956587	-179
TCTCAGTGCGGCTGTCGGGGGCTTCCCGAT	2	37	0	GCTGTCGGGG	    0.996564	-158
AGCGTTAACGGCTGAAGGACATCGGGTCAA	2	132	1	GCTGAAGGAC	     0.92036	-63
TCATGAGGTTGGTGTTGGGCGATTGACCCG	2	154	0	GGTGTTGGGC	    0.957373	-41
TTCACACCACGATCACGGAGGCTCGACA  	3	116	1	GATCACGGAG	    0.926532	-18
          **********

Masking position 3
Map Score:   6.28137

Number of sites scoring better than the average of aligned sites = 942
Number in coding regions = 895
Number in noncoding regions = 47
Number of orfs with sites within 600 bp upstream = 43
Fraction of orfs with sites within 600 bp upstream = 0.00690652


Motif number 3

AATGCGCGGCTTATTTTCGTTTATGAATTGCTAAAA	1	75	1	TTTTCGATGA	    0.850339	-36
TATCCACACTTATTTCATGAGGTTGGTGTTGGGCGA	2	162	0	TTTATGTTGG	    0.976741	-33
TTGGCGTAGATTTTTGTTGTGCTTAAAGTAACAAAA	3	67	0	TTTTTGTTAA	    0.946689	-67
GAAAGTGCGGTCGTTTTTGGCGTAGATTTTTGTTGT	3	83	0	TTTTTGTAGA	    0.965906	-51
GAAGATAAGATTTTTTATGAACTTGAGATTCTACCA	4	14	0	TTTATGTTGA	    0.991339	-56
ATACTCGTTTTGCTTGATGTGATTGAGAAGATAAGA	4	40	0	TTTATGTTGA	    0.991335	-30
          *  ** ***   ****

Masking position 5
Map Score:   0.817274

Number of sites scoring better than the average of aligned sites = 190
Number in coding regions = 162
Number in noncoding regions = 28
Number of orfs with sites within 600 bp upstream = 32
Fraction of orfs with sites within 600 bp upstream = 0.00513974


Motif number 4

TCGGTCTGATCGGAGAGCAACGCTCTCGGGGA	1	12	0	CGGGACAACG	    0.964893	-99
GAAGAGCGATCGGGAAGCCCCCGACAGCCGCA	2	29	1	CGGAACCCCC	    0.992881	-166
TTATCGTTGGCGGTAAACAACCGTTGGATTTC	2	100	1	CGGAACAACC	     0.99607	-95
GCCGTTAACGCTGAAATCCAACGGTTGTTTAC	2	112	0	CTGAACCAAC	    0.965044	-83
      AAGACGGTATCCACACTTATTTCATG	2	179	0	CGGATCACAC	    0.976934	-16
          *** ** *****

Masking position 8
Map Score:   1.07823

Number of sites scoring better than the average of aligned sites = 468
Number in coding regions = 436
Number in noncoding regions = 32
Number of orfs with sites within 600 bp upstream = 35
Fraction of orfs with sites within 600 bp upstream = 0.00562159


Motif number 5

          **********

No masking
Map Score:   4.64285e-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:   4.64285e-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:   4.64285e-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