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

Motif number 1

AATGCAATGATTGTTGTACTTTTATTTTA 	1	10	0	TTGTTGTACT	    0.953402	-291
ATCATTGCATTAGTTATACTTATAGTATAA	1	29	1	TAGTTATACT	    0.929708	-272
TTCAGTATTATTGTTATACTATAAGTATAA	1	42	0	TTGTTATACT	    0.984793	-259
AAATCTAATTTTTTTATATTTCAGTATTAT	1	61	0	TTTTTATATT	    0.979294	-240
AAAAATTAGATTTTAAAATATGCGATTAAG	1	78	1	TTTTAAAATA	    0.830583	-223
AAATCTAATGTTTTAGAACTTACAGTATCA	1	116	1	TTTTAGAACT	    0.820984	-185
ACAGTATCAATTTTTATTCAAGTATAGAAA	1	137	1	TTTTTATTCA	    0.857077	-164
TTTCTAGATTTTTCTATACTTGAATAAAAA	1	147	0	TTTCTATACT	    0.932933	-154
TTTATACAAATTTTAATATTTCTAGATTTT	1	165	0	TTTTAATATT	    0.956448	-136
TCCTTATTACTTTTTATACAAATTTTAATA	1	177	0	TTTTTATACA	    0.982206	-124
ACAATAAGGTTTTTTACATAGCTCACAATA	1	231	0	TTTTTACATA	    0.861084	-70
   CAGTTAATTGTAAAATTAGGTATTTAT	2	8	1	TTGTAAAATT	    0.851487	-25
TAAAATTAGGTATTTATATATA        	2	21	1	TATTTATATA	    0.818326	-12
          **********

Masking position 1
Map Score:   17.8003

Number of sites scoring better than the average of aligned sites = 1310
Number in coding regions = 813
Number in noncoding regions = 497
Number of orfs with sites within 600 bp upstream = 225
Fraction of orfs with sites within 600 bp upstream = 0.0361388


Motif number 2

          TAAAATAAAAGTACAACAAT	1	1	1	TAAAATAAAA	    0.873648	-300
GTTATACTATAAGTATAACTAATGCAATGA	1	30	0	AAGTATAACT	     0.74244	-271
GTTATACTTATAGTATAACAATAATACTGA	1	41	1	TAGTATAACA	     0.74244	-260
AATAATACTGAAATATAAAAAAATTAGATT	1	60	1	AAATATAAAA	    0.955519	-241
ACTTAATCGCATATTTTAAAATCTAATTTT	1	79	0	ATATTTTAAA	    0.612621	-222
CGATTAAGTAATAATTAAATCTAATGTTTT	1	100	1	ATAATTAAAT	     0.63172	-201
TTTTCTATACTTGAATAAAAATTGATACTG	1	138	0	TTGAATAAAA	    0.890443	-163
AAAAATCTAGAAATATTAAAATTTGTATAA	1	164	1	AAATATTAAA	    0.864399	-137
ATATTAAAATTTGTATAAAAAGTAATAAGG	1	176	1	TTGTATAAAA	    0.908545	-125
AGTAATAAGGATAAATTAATTAGTGGATCA	1	196	1	ATAAATTAAT	    0.726642	-105
ATTGTGAGCTATGTAAAAAACCTTATTGTA	1	232	1	ATGTAAAAAA	    0.720152	-69
CCTTTCTATCATAAATAATATATCTTTACA	1	258	0	ATAAATAATA	    0.829912	-43
GGGTGCGATAAAAAATAATATAACC     	1	286	1	AAAAATAATA	    0.788111	-15
         TATATATAAATACCTAATTTT	2	22	0	ATATATAAAT	     0.91547	-11
          **********

Masking position 8
Map Score:   12.4707

Number of sites scoring better than the average of aligned sites = 3244
Number in coding regions = 2063
Number in noncoding regions = 1181
Number of orfs with sites within 600 bp upstream = 371
Fraction of orfs with sites within 600 bp upstream = 0.0595888


Motif number 3

ATTAGTTATACTTATAGTATAACAATAATA	1	37	1	CTTATAGTAT	     0.96216	-264
ATTTTTTTATATTTCAGTATTATTGTTATA	1	54	0	ATTTCAGTAT	    0.973096	-247
AAAATTAGATTTTAAAATATGCGATTAAGT	1	79	1	TTTAAAATAT	      0.8166	-222
AAAACATTAGATTTAATTATTACTTAATCG	1	100	0	ATTTAATTAT	    0.816114	-201
TGTTTTAGAACTTACAGTATCAATTTTTAT	1	124	1	CTTACAGTAT	    0.982889	-177
ATCAATTTTTATTCAAGTATAGAAAAATCT	1	142	1	ATTCAAGTAT	    0.931126	-159
TTTTATACAAATTTTAATATTTCTAGATTT	1	166	0	ATTTTAATAT	    0.876294	-135
TTTTACATAGCTCACAATATGTCATGATCC	1	220	0	CTCACAATAT	    0.880785	-81
          **********

Masking position 6
Map Score:   6.19475

Number of sites scoring better than the average of aligned sites = 366
Number in coding regions = 224
Number in noncoding regions = 142
Number of orfs with sites within 600 bp upstream = 68
Fraction of orfs with sites within 600 bp upstream = 0.0109219


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