AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -igalR_rpxx_opreg_300.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	RP332	300	unknown
#2	RP333	32	CAPD PROTEIN (capD)

Motif number 1

GATTGTTGTACTTTTATTTTA          	1	1	0	CTTTTATTTA	    0.912534	-300
ATTAGTTATACTTATAGTATAACAATAATAC	1	37	1	CTTATATATA	    0.885311	-264
TTAAAATCTAATTTTTTTATATTTCAGTATT	1	63	0	ATTTTTTATA	      0.9834	-238
AAAAAATTAGATTTTAAAATATGCGATTAAG	1	77	1	ATTTTAAATA	    0.871977	-224
ATTAGATTTAATTATTACTTAATCGCATATT	1	94	0	ATTATTCTTA	     0.85459	-207
TACAGTATCAATTTTTATTCAAGTATAGAAA	1	136	1	ATTTTTTTCA	    0.898656	-165
ATATTTCTAGATTTTTCTATACTTGAATAAA	1	149	0	ATTTTTTATA	    0.983418	-152
TTTTATACAAATTTTAATATTTCTAGATTTT	1	165	0	ATTTTATATT	    0.839735	-136
ATCCTTATTACTTTTTATACAAATTTTAATA	1	177	0	CTTTTTTACA	    0.919446	-124
CCACTAATTAATTTATCCTTATTACTTTTTA	1	191	0	ATTTATCTTA	     0.72801	-110
TACAATAAGGTTTTTTACATAGCTCACAATA	1	231	0	TTTTTTCATA	    0.791832	-70
TGTAAAAAACCTTATTGTAAAGATATATTAT	1	243	1	CTTATTTAAA	    0.614594	-58
    GGTTATATTATTTTTTATCGCACCCTT	1	284	0	ATTATTTTTA	    0.920896	-17
TAAATACCTAATTTTACAATTAACTG     	2	6	0	ATTTTAAATT	    0.542888	-27
AAAATTAGGTATTTATATATA          	2	22	1	ATTTATTATA	    0.911349	-11
          ****** ****

Masking position 3
Map Score:   17.4094

Number of sites scoring better than the average of aligned sites = 2247
Number in coding regions = 1450
Number in noncoding regions = 797
Number of orfs with sites within 600 bp upstream = 313
Fraction of orfs with sites within 600 bp upstream = 0.050273


Motif number 2

 TAAAATAAAAGTACAACAATCATTGCATT	1	10	1	AGTACAACAA	    0.970247	-291
TTATACTATAAGTATAACTAATGCAATGAT	1	29	0	AGTATAACTA	    0.954711	-272
TTATACTTATAGTATAACAATAATACTGAA	1	42	1	AGTATAACAA	    0.988367	-259
ATAATACTGAAATATAAAAAAATTAGATTT	1	61	1	AATATAAAAA	    0.970866	-240
TGATACTGTAAGTTCTAAAACATTAGATTT	1	116	0	AGTTCTAAAA	    0.775084	-185
TTTCTATACTTGAATAAAAATTGATACTGT	1	137	0	TGAATAAAAA	    0.821359	-164
TTTTTATTCAAGTATAGAAAAATCTAGAAA	1	147	1	AGTATAGAAA	    0.944779	-154
AAAATCTAGAAATATTAAAATTTGTATAAA	1	165	1	AATATTAAAA	    0.930046	-136
TATTAAAATTTGTATAAAAAGTAATAAGGA	1	177	1	TGTATAAAAA	    0.972879	-124
ATAAATACCTAATTTTACAATTAACTG   	2	8	0	AATTTTACAA	    0.755208	-25
        TATATATAAATACCTAATTTTA	2	21	0	TATATAAATA	    0.749509	-12
          **********

Masking position 10
Map Score:   15.184

Number of sites scoring better than the average of aligned sites = 867
Number in coding regions = 542
Number in noncoding regions = 325
Number of orfs with sites within 600 bp upstream = 153
Fraction of orfs with sites within 600 bp upstream = 0.0245744


Motif number 3

CTAATTTTTTTATATTTCAGTATTATTGTTAT	1	55	0	TATATTCATA	    0.978619	-246
TAGATTTTAAAATATGCGATTAAGTAATAATT	1	84	1	AATATCGATA	    0.936853	-217
TAGATTTTTCTATACTTGAATAAAAATTGATA	1	141	0	TATACTGATA	    0.894467	-160
TACAAATTTTAATATTTCTAGATTTTTCTATA	1	159	0	AATATTCTGA	    0.962863	-142
TAGAAATATTAAAATTTGTATAAAAAGTAATA	1	171	1	AAAATTGTTA	    0.860084	-130
CATAGCTCACAATATGTCATGATCCACTAATT	1	213	0	AATATTCAGA	     0.97653	-88
TATCATAAATAATATATCTTTACAATAAGGTT	1	250	0	AATATTCTTA	    0.977121	-51
          TATATATAAATACCTAATTTTA	2	21	0	TATATTAATA	    0.769721	-12
          ***** *** **

Masking position 4
Map Score:   5.39224

Number of sites scoring better than the average of aligned sites = 325
Number in coding regions = 207
Number in noncoding regions = 118
Number of orfs with sites within 600 bp upstream = 67
Fraction of orfs with sites within 600 bp upstream = 0.0107613


Motif number 4

          **********

No masking
Map Score:   6.63809e-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 5

          **********

No masking
Map Score:   6.63809e-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:   6.63809e-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