AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i143_Cytochrome-ubiquinol_Oxidase__bsub_reg_300.orf -aORF_bsub.txt -zbsub.fna -g0.435 -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 =  	0.435
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	cydA	300	cytochrome bd ubiquinol oxidase (subunit I)

Motif number 1

TTTTGTCTATTTTGTTGCTTATTTATGTCGGC     	1	6	0	TTTCATTTTG	    0.989133	-295
AGTCCCGCACTATGTGACGGATTTTTGTCTATTTTGT	1	28	0	TTGCATTTTG	    0.998303	-273
TTTTAGGTATTTTAGGCTTTATTTTTGAAATGAATCG	1	65	1	TTGTATTTTG	    0.996502	-236
ATTGGATGACTTTTTGACACATTTGTGAAATATTGAG	1	170	1	TTGCATTTTG	    0.998303	-131
AGCAATATTTTTTTCGTCTATTTTGTGAATTACTGAT	1	205	1	TTGCTTTTTG	     0.99188	-96
CTGATCAAAGTCTCGGTTCTATTTGTGAAGTAGTGAG	1	237	1	TTGTATTTTG	    0.996502	-64
        GCTTTCTCCTCCATTTCCGGTTAAAACTG	1	282	0	TTCTATTTCG	    0.952602	-19
          * *  * *  **** **

Masking position 12
Map Score:   13.5403

Number of sites scoring better than the average of aligned sites = 43
Number in coding regions = 32
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 2

AATGACACAATCTCTGACTGGTTCATATTAAGTAC	1	109	0	TTTGATTTCA	    0.980185	-192
AGTCAGAGATTGTGTCATTTGGTCAGTCTGGCAAT	1	125	1	TTTCATGTCA	    0.994413	-176
ATTTGGTCAGTCTGGCAATCTTGCATCATATTGGA	1	141	1	TTGCATTGCA	    0.962142	-160
ATTTCACAAATGTGTCAAAAAGTCATCCAATATGA	1	166	0	TTTCAAGTCA	    0.973965	-135
GAAAAAAATATTGCTCAATATTTCACAAATGTGTC	1	185	0	TGTCATTTCA	      0.9969	-116
AACCGAGACTTTGATCAGTAATTCACAAAATAGAC	1	220	0	TGTCATTTCA	     0.99616	-81
AACTGTTAATTTGCTCACTACTTCACAAATAGAAC	1	252	0	TGTCATTTCA	    0.996767	-49
          * * *** *  ****

Masking position 7
Map Score:   10.9211

Number of sites scoring better than the average of aligned sites = 123
Number in coding regions = 105
Number in noncoding regions = 18
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 3

TACAACGATTCATTTCAAAAATAAAGCCTA	1	77	0	CATTTCAAAA	    0.919607	-224
TCATATTAAGTACTTTACAACGATTCATTT	1	92	0	TACTTTACAA	    0.971255	-209
TATTGCTCAATATTTCACAAATGTGTCAAA	1	182	0	TATTTCACAA	    0.994988	-119
ACGAAAAAAATATTGCTCAATATTTCACAA	1	192	0	TATTGCTCAA	     0.94794	-109
CTTTGATCAGTAATTCACAAAATAGACGAA	1	217	0	TAATTCACAA	    0.987645	-84
ATTTGCTCACTACTTCACAAATAGAACCGA	1	249	0	TACTTCACAA	    0.995421	-52
          **********

Masking position 4
Map Score:   9.36889

Number of sites scoring better than the average of aligned sites = 129
Number in coding regions = 85
Number in noncoding regions = 44
Number of orfs with sites within 600 bp upstream = 50
Fraction of orfs with sites within 600 bp upstream = 0.00803084


Motif number 4

AAGCAACAAAATAGACAAAAATCCGTCACA	1	23	1	ATAGACAAAA	     0.98502	-278
TTTCAAAAATAAAGCCTAAAATACCTAAAA	1	65	0	AAAGCCTAAA	    0.956282	-236
AGACTGACCAAATGACACAATCTCTGACTG	1	124	0	AATGACACAA	     0.93852	-177
AATTCACAAAATAGACGAAAAAAATATTGC	1	206	0	ATAGACGAAA	    0.982228	-95
          **********

Masking position 9
Map Score:   0.434325

Number of sites scoring better than the average of aligned sites = 268
Number in coding regions = 227
Number in noncoding regions = 41
Number of orfs with sites within 600 bp upstream = 46
Fraction of orfs with sites within 600 bp upstream = 0.00738837


Motif number 5

          **********

No masking
Map Score:   7.91135e-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:   7.91135e-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:   7.91135e-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