AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -inagC_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	RP456	171	RIBOSOMAL PROTEIN L36 (rpmJ)
#2	RP581	114	unknown

Motif number 1

      TTAAGAATTTATAAATTAATTTTAAT	1	5	1	GATTTATAAT	    0.939318	-167
TTATAAATTAATTTTAATTAATAGTTTAATAC	1	19	1	ATTTAATTAT	     0.97142	-153
AATACATTAAAACGTTATTAATTCCGAGCTTT	1	46	1	AAGTTATTAT	    0.963355	-126
AGTTTTAATAGAATTAATAATTAATGCTATTT	1	78	0	GATTAATAAT	    0.928836	-94
AACTATACAGAACTTAATTGACTGATTAGATA	1	106	1	AATTAATTGC	    0.871854	-66
TTAGATAAAAATGTTTATTATTAATCCCAATT	1	131	1	ATTTTATTAT	    0.975818	-41
AATCCCAATTAATGTAATAAGTATATTGT   	1	153	1	AAGTAATAAT	     0.92884	-19
ATACATATTGAACTTTATTACTTGTTGCTAGA	2	18	1	AATTTATTAT	    0.985595	-97
CGTTATAGTCATTTTTATTGTTTCTAGCAACA	2	40	0	ATTTTATTGT	    0.961026	-75
AAACTTTACTATTTTAATAAGTTACGTTATAG	2	64	0	ATTTAATAAT	    0.952464	-51
TAAAATAGTAAAGTTTCTTGATTTAAAATTAG	2	80	1	AATTTCTTGT	    0.889929	-35
          ** ******* *

Masking position 5
Map Score:   14.9437

Number of sites scoring better than the average of aligned sites = 1222
Number in coding regions = 793
Number in noncoding regions = 429
Number of orfs with sites within 600 bp upstream = 207
Fraction of orfs with sites within 600 bp upstream = 0.0332477


Motif number 2

AAAATTAATTTATAAATTCTTAA         	1	2	0	TATAAATTTA	    0.681259	-170
TGTATTAAACTATTAATTAAAATTAATTTATA	1	20	0	TATTAATAAA	    0.494609	-152
ATTAATAACGTTTTAATGTATTAAACTATTAA	1	36	0	TTTTAATATT	    0.957341	-136
ATTAAAACGTTATTAATTCCGAGCTTTAAATA	1	51	1	TATTAATCGA	    0.911728	-121
AATTCCGAGCTTTAAATAGCATTAATTATTAA	1	65	1	TTTAAATCAT	    0.925507	-107
TTCTGTATAGTTTTAATAGAATTAATAATTAA	1	86	0	TTTTAATAAT	    0.963093	-86
ATAATAAACATTTTTATCTAATCAGTCAATTA	1	120	0	TTTTTATAAT	    0.879348	-52
AAATGTTTATTATTAATCCCAATTAATGTAAT	1	139	1	TATTAATCAA	    0.938753	-33
GTTATAGTCATTTTTATTGTTTCTAGCAACAA	2	39	0	TTTTTATTTT	    0.736169	-76
AACTTTACTATTTTAATAAGTTACGTTATAGT	2	63	0	TTTTAATGTT	    0.901819	-52
TCCCGCTAATTTTAAATCAAGAAACTTTACTA	2	85	0	TTTAAATAGA	    0.847197	-30
          *******  ***

Masking position 6
Map Score:   8.29237

Number of sites scoring better than the average of aligned sites = 1696
Number in coding regions = 1093
Number in noncoding regions = 603
Number of orfs with sites within 600 bp upstream = 274
Fraction of orfs with sites within 600 bp upstream = 0.044009


Motif number 3

         TTAAGAATTTATAAATTAATT	1	2	1	TAAGAATTTA	    0.817547	-170
TATTAATTAAAATTAATTTATAAATTCTTA	1	12	0	AATTAATTTA	     0.84687	-160
TAATTTTAATTAATAGTTTAATACATTAAA	1	27	1	TAATAGTTTA	    0.933496	-145
TTAATAGAATTAATAATTAATGCTATTTAA	1	76	0	TAATAATTAA	    0.606009	-96
TTAATTCTATTAAAACTATACAGAACTTAA	1	93	1	TAAAACTATA	    0.845634	-79
TGATTAGATAAAAATGTTTATTATTAATCC	1	128	1	AAAATGTTTA	    0.846913	-44
CAATTAATGTAATAAGTATATTGT      	1	158	1	AATAAGTATA	    0.933668	-14
AATAAAGTTCAATATGTATATGTATT    	2	7	0	AATATGTATA	    0.794068	-108
AAACAATAAAAATGACTATAACGTAACTTA	2	49	1	AATGACTATA	    0.832025	-66
TAACTTATTAAAATAGTAAAGTTTCTTGAT	2	72	1	AAATAGTAAA	    0.852132	-43
          **********

Masking position 7
Map Score:   5.61173

Number of sites scoring better than the average of aligned sites = 1509
Number in coding regions = 969
Number in noncoding regions = 540
Number of orfs with sites within 600 bp upstream = 231
Fraction of orfs with sites within 600 bp upstream = 0.0371025


Motif number 4

          **********

No masking
Map Score:   1.09013e-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:   1.09013e-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:   1.09013e-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