AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i143_Cytochrome-ubiquinol_Oxidase__hinf_reg_300.orf -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -g0.38 -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 =  	0.38
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	HI1076	300	cytochrome D ubiquinol oxidase, subunit I (cydA)

Motif number 1

       GTCAATTTGATCTAAGTCAATTAAATA	1	4	1	AATTGCTAAT	    0.965016	-297
TTATTTGTTATATTTTATTTAATTGACTTAGATC	1	19	0	TATTTTTAAT	    0.729032	-282
AAATATAACAAATAAGCCCTATTTTTGTATTTAT	1	38	1	AATAGCTATT	     0.80853	-263
TTATATCAAAAATGTGATCTATATAGCATTTTTT	1	68	1	AATTGCTATT	    0.988323	-233
TCTATATAGCATTTTTTACTATTTTTTATCCTTA	1	85	1	ATTTTCTATT	    0.890319	-216
AATAGCCGCCAATTTGGATTATCTCTATAATAAC	1	132	1	AATTGTTATT	    0.979421	-169
TTTAACCTTTAAAAATAATTATGTAGATAAGTCA	1	175	1	AAAATTTATT	    0.850695	-126
AGCTAAGTTTAAATTGACTTATCTACATAATTAT	1	189	0	AAATGTTATT	    0.950074	-112
AAGTCAATTTAAACTTAGCTGATTGGAGTTGAGT	1	203	1	AAATTCTGAT	    0.747027	-98
CGATGCCTTAAATAATCCCTAATTACTCAACTCC	1	227	0	AATATCTAAT	    0.923356	-74
TGTTGGAACTAATGTTGTTTATACAAAGGAGTTG	1	274	1	AATTTTTATC	    0.871195	-27
          *** **  **** *

Masking position 10
Map Score:   10.6845

Number of sites scoring better than the average of aligned sites = 628
Number in coding regions = 482
Number in noncoding regions = 146
Number of orfs with sites within 600 bp upstream = 133
Fraction of orfs with sites within 600 bp upstream = 0.021362


Motif number 2

          GTCAATTTGATCTAAGTCAA	1	1	1	GTCAATTTGA	    0.979974	-300
TTTGATCTAAGTCAATTAAATAAAATATAA	1	16	1	GTCAATTAAA	    0.899097	-285
CAAAAATAGGGCTTATTTGTTATATTTTAT	1	35	0	GCTTATTTGT	    0.828202	-266
TAGAATAGCCGCCAATTTGGATTATCTCTA	1	129	1	GCCAATTTGG	    0.948035	-172
AATAACTGGTGTTTTTTTAACCTTTAAAAA	1	160	1	GTTTTTTTAA	    0.877788	-141
ATGTAGATAAGTCAATTTAAACTTAGCTGA	1	195	1	GTCAATTTAA	    0.980379	-106
AGTAATTAGGGATTATTTAAGGCATCGCCT	1	234	1	GATTATTTAA	    0.856389	-67
TTAAGGCATCGCCTTGTTAATCATTGTTGG	1	250	1	GCCTTGTTAA	    0.854938	-51
          **********

Masking position 7
Map Score:   4.92932

Number of sites scoring better than the average of aligned sites = 751
Number in coding regions = 622
Number in noncoding regions = 129
Number of orfs with sites within 600 bp upstream = 84
Fraction of orfs with sites within 600 bp upstream = 0.0134918


Motif number 3

CCTTATGTTTAGTAGTAGAATAGCCGCCAA	1	114	1	AGTAGTAGAA	    0.925583	-187
AAAATAATTATGTAGATAAGTCAATTTAAA	1	186	1	TGTAGATAAG	     0.92557	-115
CTTAGCTGATTGGAGTTGAGTAATTAGGGA	1	216	1	TGGAGTTGAG	    0.994849	-85
GTTTATACAAAGGAGTTGAGA         	1	290	1	AGGAGTTGAG	    0.994849	-11
          **********

Masking position 4
Map Score:   1.56023

Number of sites scoring better than the average of aligned sites = 44
Number in coding regions = 35
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 4

          **********

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 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