AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -imelR_rpxx_opreg_100.orf -g0.290 -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 =  	0.29
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	RP500	215	ADP,ATP CARRIER PROTEIN (tlc4)

Motif number 1

GAATATATGATATAAAATGCAAAATTGATA	1	11	1	TATAAAATGC	    0.988457	-205
GAGCAAAAAGTTTATAATGCAAGGAGCATT	1	62	1	TTTATAATGC	    0.994344	-154
TACTCATGCATTAATAATGCTCCTTGCATT	1	77	0	TTAATAATGC	     0.98162	-139
CTTAGCCAATTTTAAAATTAAACGAGTATA	1	128	1	TTTAAAATTA	     0.91255	-88
AAATCTTTAATATATAATTCTAGCCAATAG	1	177	1	TATATAATTC	    0.981933	-39
          **********

Masking position 6
Map Score:   7.00678

Number of sites scoring better than the average of aligned sites = 155
Number in coding regions = 95
Number in noncoding regions = 60
Number of orfs with sites within 600 bp upstream = 27
Fraction of orfs with sites within 600 bp upstream = 0.00433665


Motif number 2

AAATTGATAGACACAGTTTAATTTCAACAA	1	32	1	ACACAGTTTA	    0.993103	-184
CAACAAGAGCAAAAAGTTTATAATGCAAGG	1	56	1	AAAAAGTTTA	    0.929946	-160
CATGAGTACTACAGAGCTTATTAAGACAAC	1	99	1	ACAGAGCTTA	    0.991795	-117
GAGCTTATTAAGACAACTTAGCCAATTTTA	1	112	1	AGACAACTTA	    0.940939	-104
TAGCCAATAGACATAGGTTAGACTCAATA 	1	197	1	ACATAGGTTA	    0.977974	-19
          **********

Masking position 5
Map Score:   3.52657

Number of sites scoring better than the average of aligned sites = 54
Number in coding regions = 39
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 3

AATGCAAAATTGATAGACACAGTTTAATTT	1	26	1	TGATAGACAC	    0.981521	-190
TAATAAGCTCTGTAGTACTCATGCATTAAT	1	92	0	TGTAGTACTC	    0.952736	-124
TTTAAGTCAAGGATATACTCGTTTAATTTT	1	141	0	GGATATACTC	    0.989188	-75
AATAGACATAGGTTAGACTCAATA      	1	202	1	GGTTAGACTC	    0.994886	-14
          **********

Masking position 7
Map Score:   2.44119

Number of sites scoring better than the average of aligned sites = 17
Number in coding regions = 7
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 4

        GAATATATGATATAAAATGCAA	1	3	1	ATATATGATA	    0.888282	-213
TATAAAATGCAAAATTGATAGACACAGTTT	1	21	1	AAAATTGATA	    0.933495	-195
ACAAGAGCAAAAAGTTTATAATGCAAGGAG	1	58	1	AAAGTTTATA	    0.875462	-158
TTTAATTTTAAAATTGGCTAAGTTGTCTTA	1	120	0	AAATTGGCTA	    0.983661	-96
TATATATTAAAGATTTTCTACATTTAAGTC	1	163	0	AGATTTTCTA	    0.935036	-53
TAACCTATGTCTATTGGCTAGAATTATATA	1	187	0	CTATTGGCTA	    0.938884	-29
          **********

Masking position 3
Map Score:   0.737794

Number of sites scoring better than the average of aligned sites = 744
Number in coding regions = 532
Number in noncoding regions = 212
Number of orfs with sites within 600 bp upstream = 117
Fraction of orfs with sites within 600 bp upstream = 0.0187922


Motif number 5

          **********

No masking
Map Score:   3.08538e-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 6

          **********

No masking
Map Score:   3.08538e-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:   3.08538e-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