AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00790_ctra_reg_100.orf -o00790_ctra_100.ace -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -g0.41 -x5 -e 
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 =  	0.41
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	gidA	293	FAD-dependent oxidoreductase
#2	uvrD	80	DNA Helicase
#3	rpoD	148	RNA Polymerase Sigma-66
#4	zntA	23	Metal Transport P-type ATPase
#5	CT728	36	hypothetical protein
#6	serS	41	Seryl tRNA Synthetase

Motif number 1

TACACTTTGAGAAGAAAACCTATGAGGATC	1	78	1	GAAGAAAACC	    0.945777	-216
GGTAAGTCTTTTGAAAAGACTCAGCTAATG	1	131	0	TTGAAAAGAC	    0.839235	-163
AAACCATTAAGAAGAAAACCATGTCATCTG	1	176	1	GAAGAAAACC	    0.945777	-118
GTCATCTGTTAAGAAAAAACGAAGACTTAA	1	198	1	AAGAAAAAAC	    0.950776	-96
GCATAAGCGTAAAAAAAGACGTCGAAGAGA	1	237	1	AAAAAAAGAC	    0.950776	-57
   GGATAAGTAGAAAAGACGGGAGGGGTT	3	8	1	TAGAAAAGAC	    0.954626	-141
GATTTAGGCCTAGAAAAACCCCTCCCGTCT	3	24	0	TAGAAAAACC	    0.954626	-125
TTTTTAGATAAAAAAAAGCCTGTTGATCAG	3	53	0	AAAAAAAGCC	    0.962854	-96
CAGTTTATCTTAAGAAAAACAAGAAATCTA	3	87	0	TAAGAAAAAC	     0.94004	-62
AATTAAAACTAAGGAAAAATCGGCCTAGAA	3	122	0	AAGGAAAAAT	    0.799733	-27
TTATAGTGAGATAGAAAGCTAGAGGAGCGG	5	13	1	ATAGAAAGCT	    0.570754	-24
          **********

Masking position 5
Map Score:   12.5902

Number of sites scoring better than the average of aligned sites = 488
Number in coding regions = 488
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 2

TGCCCGTTCTCATAGGCATTAGCTGAGTCT	1	115	1	CATAGGCATT	    0.895723	-179
ACTATCTATTTTTATGCCGATCTCTTCGAC	1	257	0	TTTATGCCGA	    0.891084	-37
ATGCATATACTCTATGCCTTAGATTAAGGA	2	17	0	TCTATGCCTT	    0.988041	-64
AGGCATAGAGTATATGCATTCTCGAAAATT	2	28	1	TATATGCATT	    0.931111	-53
GAGGGGTTTTTCTAGGCCTAAATCTGATCA	3	30	1	TCTAGGCCTA	    0.992426	-119
AAACAAGAAATCTAGGGATTTTTAGATAAA	3	71	0	TCTAGGGATT	    0.940767	-78
ACTGTCACTTTCTAGGCCGATTTTTCCTTA	3	113	1	TCTAGGCCGA	    0.988784	-36
          **********

Masking position 4
Map Score:   5.10704

Number of sites scoring better than the average of aligned sites = 80
Number in coding regions = 80
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 3

AATGGCTGTCAATTTTTGGGAATAAACTTG	1	12	0	AATTTTTGGG	    0.973422	-282
CTTCGACGTCTTTTTTTACGCTTATGCTTG	1	234	0	TTTTTTTACG	    0.841128	-60
TTTAACTATCTATTTTTATGCCGATCTCTT	1	261	0	TATTTTTATG	    0.781285	-33
AGATAGTTAAATTGTTTGGGTTCT      	1	280	1	ATTGTTTGGG	    0.906785	-14
GTTCGAAGAAAATTTTCGAGAATGCATATA	2	38	0	AATTTTCGAG	    0.847414	-43
ATGTAATATATATTTTCGGGTTCGAAGAAA	2	57	0	TATTTTCGGG	    0.972899	-24
ACGGGAGGGGTTTTTCTAGGCCTAAATCTG	3	26	1	TTTTTCTAGG	    0.859807	-123
TCGCTATCTGATTTTTCAGGTTGAGTAT  	6	9	0	ATTTTTCAGG	    0.957686	-33
          **********

Masking position 5
Map Score:   3.91962

Number of sites scoring better than the average of aligned sites = 254
Number in coding regions = 253
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 4

ACGGGCAAGCACCCGATCCTCATAGGTTTT	1	92	0	ACCCGATCCT	    0.958796	-202
TCGGGTGCTTGCCCGTTCTCATAGGCATTA	1	106	1	GCCCGTTCTC	    0.950719	-188
CGCTTATGCTTGGCGATCTTAAGTCTTCGT	1	216	0	TGGCGATCTT	    0.968858	-78
TCTATTTTTATGCCGATCTCTTCGACGTCT	1	253	0	TGCCGATCTC	    0.991189	-41
TCACTTTCTAGGCCGATTTTTCCTTAGTTT	3	117	1	GGCCGATTTT	    0.957735	-32
        CGTGCCGCTCCTCTAGCTTTCT	5	25	0	TGCCGCTCCT	    0.980631	-12
          **********

Masking position 7
Map Score:   3.11502

Number of sites scoring better than the average of aligned sites = 83
Number in coding regions = 83
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 5

          **********

No masking
Map Score:   1.21035e-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:   1.21035e-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:   1.21035e-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