AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i143_Cytochrome-ubiquinol_Oxidase__bsub_reg_100.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

     GCCGACATAAATAAGCAACAAAATAGACAAAA	1	6	1	CAAAATGAAA	    0.989608	-295
ACAAAATAGACAAAAATCCGTCACATAGTGCGGGACT	1	28	1	CAAAATGCAA	    0.998378	-273
CGATTCATTTCAAAAATAAAGCCTAAAATACCTAAAA	1	65	0	CAAAATACAA	    0.996656	-236
CTCAATATTTCACAAATGTGTCAAAAAGTCATCCAAT	1	170	0	CAAAATGCAA	    0.998378	-131
ATCAGTAATTCACAAAATAGACGAAAAAAATATTGCT	1	205	0	CAAAAAGCAA	    0.992235	-96
CTCACTACTTCACAAATAGAACCGAGACTTTGATCAG	1	237	0	CAAAATACAA	    0.996656	-64
CAGTTTTAACCGGAAATGGAGGAGAAAGC        	1	282	1	CGAAATAGAA	      0.9546	-19
          ** ****  * *  * *

Masking position 6
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	    0.979995	-192
AGTCAGAGATTGTGTCATTTGGTCAGTCTGGCAAT	1	125	1	TTTCATGTCA	    0.994356	-176
ATTTGGTCAGTCTGGCAATCTTGCATCATATTGGA	1	141	1	TTGCATTGCA	    0.961755	-160
ATTTCACAAATGTGTCAAAAAGTCATCCAATATGA	1	166	0	TTTCAAGTCA	    0.973696	-135
GAAAAAAATATTGCTCAATATTTCACAAATGTGTC	1	185	0	TGTCATTTCA	    0.996868	-116
AACCGAGACTTTGATCAGTAATTCACAAAATAGAC	1	220	0	TGTCATTTCA	    0.996135	-81
AACTGTTAATTTGCTCACTACTTCACAAATAGAAC	1	252	0	TGTCATTTCA	    0.996736	-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

TGTGACGGATTTTTGTCTATTTTGTTGCTT	1	23	0	TTTTGTCTAT	    0.932927	-278
GATTGTGTCATTTGGTCAGTCTGGCAATCT	1	132	1	TTTGGTCAGT	    0.992221	-169
CGAAAAAAATATTGCTCAATATTTCACAAA	1	191	0	ATTGCTCAAT	    0.743533	-110
GCAATATTTTTTTCGTCTATTTTGTGAATT	1	206	1	TTTCGTCTAT	    0.953726	-95
GAACCGAGACTTTGATCAGTAATTCACAAA	1	226	0	TTTGATCAGT	    0.954567	-75
AAACTGTTAATTTGCTCACTACTTCACAAA	1	258	0	TTTGCTCACT	    0.981024	-43
          **********

Masking position 6
Map Score:   6.05612

Number of sites scoring better than the average of aligned sites = 279
Number in coding regions = 246
Number in noncoding regions = 33
Number of orfs with sites within 600 bp upstream = 28
Fraction of orfs with sites within 600 bp upstream = 0.00449727


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