AlignACE version 2.2  July 7, 1998
alignACE -aORF_aful.txt -zaful.fna -icspA_aful_opreg_300.orf -g0.49 -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 =  	0.49
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	AF0465	274	DNA gyrase, subunit A (gyrA)
#2	AF0466	31	conserved hypothetical protein
#3	AF0471	125	2-ketoglutarate ferredoxin oxidoreductase, subunit gamma (korG)

Motif number 1

AATTGATGCTTTAAAATTTTGCT         	1	2	0	TTAAAATTTC	     0.93657	-273
AAAAAAAGCATTTTACCTTTTCAACCATGCCG	1	95	1	TTTTACCTTC	    0.898955	-180
CCAACTTGAATTAAAACTCTTTCGCTCAAAGC	1	211	1	TTAAAACTTT	    0.925813	-64
TGCTCAAAGTTTTAAACACTCCCTCAGACTGT	1	248	1	TTTAAACATC	    0.988942	-27
          TTTTAACAGTCTGAGGGAGTGT	1	263	0	TTTTAACATT	    0.938932	-12
       TTTTTTAAATTTTTTTATGGGGTGA	2	4	1	TTTAAATTTT	    0.902892	-28
TTTTGTTGTATTTAAACAATACGTATGCCTCA	3	26	1	TTTAAACATC	    0.988942	-100
TAGGAAAGATTTATAAAATTTCATGCGGAATA	3	97	1	TTATAAAATC	    0.791969	-29
         GTTTAAATATTCCGCATGAAATT	3	113	0	TTTAAATATC	    0.972189	-13
          ******** * *

Masking position 5
Map Score:   8.90191

Number of sites scoring better than the average of aligned sites = 220
Number in coding regions = 135
Number in noncoding regions = 85
Number of orfs with sites within 600 bp upstream = 100
Fraction of orfs with sites within 600 bp upstream = 0.0160617


Motif number 2

TGCACTCGTGGTTCGAACCTGCATAAAAAA	1	71	1	GTTCGAACCT	    0.973841	-204
GAGGTCGGGGGTTCGAATCCCCCCCTCGGC	1	123	0	GTTCGAATCC	    0.964432	-152
GGCTACCTCGGCTCAATGCCATTTAGCCCA	1	184	1	GCTCAATGCC	    0.985579	-91
AAACTCTTTCGCTCAAAGCTCAAGTGCTCA	1	224	1	GCTCAAAGCT	    0.995222	-51
AAGCTCAAGTGCTCAAAGTTTTAAACACTC	1	239	1	GCTCAAAGTT	    0.975558	-36
          **********

Masking position 6
Map Score:   3.6497

Number of sites scoring better than the average of aligned sites = 302
Number in coding regions = 291
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 3

TCAATTTTTTCCCATCAAACGCATTTAACA	1	28	1	CCCATCAAAC	      0.9364	-247
TTCGAATCCCCCCCTCGGCATGGTTGAAAA	1	112	0	CCCCTCGGCA	    0.967636	-163
GGGGATTCGAACCCCCGACCTCCTGATTAT	1	131	1	ACCCCCGACC	    0.993899	-144
ATGAGTCAGGCGCCCCAACCAGCTAGGCTA	1	159	1	CGCCCCAACC	    0.990247	-116
TTTTAAACACTCCCTCAGACTGTTAAAA  	1	257	1	TCCCTCAGAC	    0.952058	-18
CCTATATATTACTCCCAACCCTTCAGATGA	3	71	0	ACTCCCAACC	    0.968161	-55
          **********

Masking position 6
Map Score:   2.75101

Number of sites scoring better than the average of aligned sites = 1176
Number in coding regions = 1115
Number in noncoding regions = 61
Number of orfs with sites within 600 bp upstream = 43
Fraction of orfs with sites within 600 bp upstream = 0.00690652


Motif number 4

GCAAAATTTTAAAGCATCAATTTTTTCCCA	1	12	1	AAAGCATCAA	    0.975881	-263
TCGAACCACGAGTGCAGCAACCTTCTGGCT	1	57	0	AGTGCAGCAA	    0.972357	-218
GTATTGTTTAAATACAACAAAAACAAATAG	3	18	0	AATACAACAA	    0.958988	-108
AAACAATACGTATGCCTCAATAGTTGATGT	3	39	1	TATGCCTCAA	     0.94799	-87
CCTTCAGATGAATACATCAACTATTGAGGC	3	52	0	AATACATCAA	    0.983356	-74
          **********

Masking position 9
Map Score:   2.60462

Number of sites scoring better than the average of aligned sites = 75
Number in coding regions = 64
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 5

GTTAAATGCGTTTGATGGGAAAAAATTGAT	1	27	0	TTTGATGGGA	    0.970408	-248
AAAATGCTTTTTTTATGCAGGTTCGAACCA	1	79	0	TTTTATGCAG	    0.974984	-196
TTTTAAATTTTTTTATGGGGTGACCAATT 	2	13	1	TTTTATGGGG	    0.993614	-19
ATTTATAAAATTTCATGCGGAATATTTAAA	3	105	1	TTTCATGCGG	    0.992161	-21
          **********

Masking position 5
Map Score:   2.6307

Number of sites scoring better than the average of aligned sites = 38
Number in coding regions = 33
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 6

          **********

No masking
Map Score:   -7.57849e-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:   -7.57849e-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:   -7.57849e-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