AlignACE version 2.2  July 7, 1998
alignACE -aORF_aful.txt -zaful.fna -icspA_aful_opreg_100.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)

Motif number 1

TTTTATGCAGGTTCGAACCACGAGTGCAGCAACCTTC	1	62	0	GTTCAACCGC	     0.99893	-213
GAGGTCGGGGGTTCGAATCCCCCCCTCGGCATGGTTG	1	116	0	GTTCAACCTC	    0.996887	-159
TGAGTCAGGCGCCCCAACCAGCTAGGCTACCTCGGCT	1	160	1	GCCCAACGGC	    0.993246	-115
GGCTACCTCGGCTCAATGCCATTTAGCCCAACTTGAA	1	184	1	GCTCATCAGC	    0.918683	-91
AAACTCTTTCGCTCAAAGCTCAAGTGCTCAAAGTTTT	1	224	1	GCTCAACCGC	    0.998983	-51
AGTGCTCAAAGTTTTAAACACTCCCTCAGACTGTTAA	1	246	1	GTTTAACCTC	    0.980214	-29
          **** ** * *    **

Masking position 6
Map Score:   7.41875

Number of sites scoring better than the average of aligned sites = 121
Number in coding regions = 104
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 2

CAATTTTTTCCCATCAAACGCATTTAACAGCCA	1	29	1	CCTCAACGCT	    0.983845	-246
AGTGCAGCAACCTTCTGGCTGTTAAATGCGTTT	1	44	0	CCTCGGCTGT	    0.996553	-231
TCGAATCCCCCCCTCGGCATGGTTGAAAAGGTA	1	108	0	CCTCGCATGT	    0.987998	-167
GGGATTCGAACCCCCGACCTCCTGATTATGAGT	1	132	1	CCCCACCTCT	    0.993336	-143
GCTGGTTGGGGCGCCTGACTCATAATCAGGAGG	1	149	0	GCCCGACTCT	     0.98944	-126
TTTAAACACTCCCTCAGACTGTTAAAA      	1	258	1	CCTCGACTGT	    0.997975	-17
          ** ** ***** *

Masking position 13
Map Score:   5.89584

Number of sites scoring better than the average of aligned sites = 254
Number in coding regions = 242
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 3

GTTCGAACCACGAGTGCAGCAACCTTCTGG	1	59	0	CGAGTGCAGC	    0.964905	-216
TCAACCATGCCGAGGGGGGGATTCGAACCC	1	115	1	CGAGGGGGGG	    0.997008	-160
CTCATAATCAGGAGGTCGGGGGTTCGAATC	1	134	0	GGAGGTCGGG	    0.983595	-141
CTCCTGATTATGAGTCAGGCGCCCCAACCA	1	150	1	TGAGTCAGGC	    0.961169	-125
GGCATTGAGCCGAGGTAGCCTAGCTGGTTG	1	174	0	CGAGGTAGCC	     0.98336	-101
AGTTTTAATTCAAGTTGGGCTAAATGGCAT	1	199	0	CAAGTTGGGC	    0.945906	-76
TTTAACAGTCTGAGGGAGTGTTTAAAACTT	1	254	0	TGAGGGAGTG	     0.94166	-21
          **********

Masking position 3
Map Score:   4.78383

Number of sites scoring better than the average of aligned sites = 1585
Number in coding regions = 1515
Number in noncoding regions = 70
Number of orfs with sites within 600 bp upstream = 44
Fraction of orfs with sites within 600 bp upstream = 0.00706714


Motif number 4

AAAAAATTGATGCTTTAAAATTTTGCT   	1	8	0	TGCTTTAAAA	    0.985995	-267
GGTTCGAACCTGCATAAAAAAAGCATTTTA	1	80	1	TGCATAAAAA	    0.980132	-195
CCCCTCGGCATGGTTGAAAAGGTAAAATGC	1	102	0	TGGTTGAAAA	    0.970051	-173
TAGCCCAACTTGAATTAAAACTCTTTCGCT	1	207	1	TGAATTAAAA	    0.948073	-68
TCTGAGGGAGTGTTTAAAACTTTGAGCACT	1	246	0	TGTTTAAAAC	    0.918812	-29
          **********

Masking position 5
Map Score:   2.89841

Number of sites scoring better than the average of aligned sites = 134
Number in coding regions = 105
Number in noncoding regions = 29
Number of orfs with sites within 600 bp upstream = 30
Fraction of orfs with sites within 600 bp upstream = 0.0048185


Motif number 5

ATTGATGCTTTAAAATTTTGCT          	1	1	0	TAAATTTGCT	    0.821364	-274
CGAGTGCAGCAACCTTCTGGCTGTTAAATGCG	1	47	0	AACCTCTGCT	    0.986895	-228
AGAAGGTTGCTGCACTCGTGGTTCGAACCTGC	1	61	1	TGCATCGGGT	    0.911723	-214
GCATAAAAAAAGCATTTTACCTTTTCAACCAT	1	91	1	AGCATTTCCT	    0.973614	-184
GGGGGATTCGAACCCCCGACCTCCTGATTATG	1	130	1	AACCCCGCCT	    0.878028	-145
CTCGGCTCAATGCCATTTAGCCCAACTTGAAT	1	190	1	TGCCTTTGCC	    0.954253	-85
CTTGAATTAAAACTCTTTCGCTCAAAGCTCAA	1	215	1	AACTTTTGCT	    0.952097	-60
TAAAACTTTGAGCACTTGAGCTTTGAGCGAAA	1	230	0	AGCATTGGCT	     0.92411	-45
          **** *** ***

Masking position 6
Map Score:   1.42673

Number of sites scoring better than the average of aligned sites = 1284
Number in coding regions = 1201
Number in noncoding regions = 83
Number of orfs with sites within 600 bp upstream = 74
Fraction of orfs with sites within 600 bp upstream = 0.0118856


Motif number 6

          **********

No masking
Map Score:   -1.17788e-14

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:   -1.17788e-14

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:   -1.17788e-14

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