AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -iglpR_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	RP053	300	ADP,ATP CARRIER PROTEIN (tlc1)
#2	RP054	72	GLYCEROL-3-PHOSPHATE TRANSPORTER (glpT)
#3	RP600	195	unknown

Motif number 1

ATGGGATGAAATTTTAATATTTTACCTTCAATA	1	24	1	ATTTAAATTT	    0.801003	-277
TTCTTATGACAATACAAAATATTGAAGGTAAAA	1	43	0	AATAAAATAT	    0.878204	-258
TTGTATTGTCATAAGAATATTGACCCCAAGAAA	1	59	1	ATAAAAATTA	    0.946499	-242
AAGCCTTTACAATTTAAAGTTCACTAAATTTTC	1	100	1	AATTAAGTTA	    0.920765	-201
TTAACTAACTAAATGAAAATTTAGTGAACTTTA	1	114	0	AAATAAATTA	    0.950633	-187
TAATATATAGAAATCAAAATTAAGTAAAAATTG	1	151	1	AAATAAATTA	    0.950633	-150
TGTGAAAAAGAAAACAATTTTTACTTAATTTTG	1	165	0	AAAAAATTTA	    0.872471	-136
TCCTATAGTTAATAAAATGTTTATTGAGTTCTT	1	198	1	AATAAAGTTA	    0.953683	-103
TTTTCTATTTATTTGAAGATAAACATTATACTA	1	271	0	ATTTAAATAA	    0.803078	-30
TCTTCAAATAAATAGAAAATTTAATT       	1	285	1	AATAAAATTA	      0.9653	-16
   AATTTGTAAAAAAATATAAAAAAGCTTCTA	2	8	1	AAAAAAATAA	    0.946097	-65
TCAACTATAAAAAGTAAGATTCAGGTTTTAGAA	2	36	0	AAAGAAATTA	      0.8556	-37
AAATTTTTTTATAATAATATTATTAAAATAATA	3	26	1	ATAAAAATTT	    0.796234	-170
TATTATTAAAATAATAAGGTTCTATGAACATCA	3	43	1	ATAAAAGTTT	    0.871512	-153
TATATCATTGAAAATGATGTTCATAGAACCTTA	3	57	0	AAAAGAGTTA	    0.743401	-139
TACCGAAATCATTTTAAAATACTTGAATAATTA	3	99	1	ATTTAAATAT	     0.67642	-97
TATTATTGATAATAAAAGTTAATAGAACTTTCC	3	158	0	AATAAATTAT	    0.598731	-38
TCAATAATAGAAAAAAACGTAAAT         	3	182	1	AAAAAAGTAA	    0.929762	-14
          **** ** *** *

Masking position 10
Map Score:   20.2705

Number of sites scoring better than the average of aligned sites = 1860
Number in coding regions = 1191
Number in noncoding regions = 669
Number of orfs with sites within 600 bp upstream = 285
Fraction of orfs with sites within 600 bp upstream = 0.0457758


Motif number 2

TATGGGATGAAATTTTAATATTTTACCTTC	1	23	1	AATTTTAATA	    0.968683	-278
ACTCAATAAACATTTTATTAACTATAGGAT	1	197	0	CATTTTATTA	    0.963479	-104
TTCTATCATATATTTTAGTATAATGTTTAT	1	256	1	TATTTTAGTA	    0.915968	-45
AGCTTTTTTATATTTTTTTACAAATT    	2	7	0	TATTTTTTTA	    0.927667	-66
CCTGAATCTTACTTTTTATAGTTGAGGAGA	2	44	1	ACTTTTTATA	    0.890903	-29
CATCTTGCAAAATTTTTTTATAATAATATT	3	17	1	AATTTTTTTA	    0.943523	-179
AGAACCTTATTATTTTAATAATATTATTAT	3	36	0	TATTTTAATA	    0.936034	-160
ATACCGAAATCATTTTAAAATACTTGAATA	3	98	1	CATTTTAAAA	    0.806257	-98
AGTTCTATTAACTTTTATTATCAATAATAG	3	162	1	ACTTTTATTA	     0.93964	-34
          **********

Masking position 5
Map Score:   9.9124

Number of sites scoring better than the average of aligned sites = 764
Number in coding regions = 479
Number in noncoding regions = 285
Number of orfs with sites within 600 bp upstream = 150
Fraction of orfs with sites within 600 bp upstream = 0.0240925


Motif number 3

AAAGGCTTATTTGATATTTCTTGGGGTCAAT	1	77	0	TTGATATTTT	    0.938908	-224
TTACTTAATTTTGATTTCTATATATTAACTG	1	147	0	TTGATTTCTT	    0.989643	-154
TAAGTAAAAATTGTTTTCTTTTTCACATCCT	1	171	1	TTGTTTTCTT	    0.967944	-130
AAAATGTTTATTGAGTTCTTTCTAGAAAAAA	1	211	1	TTGAGTTCTT	    0.967107	-90
GTCAAACAAATTGATTTTTTCTAGAAAGAAC	1	225	0	TTGATTTTTC	    0.919114	-76
ATCAATTTGTTTGACTTCTATCATATATTTT	1	241	1	TTGACTTCTT	    0.981854	-60
TAGAAGCTTTTTTATATTTTTTTACAAATT 	2	10	0	TTTATATTTT	    0.778526	-63
GAAAGTTCTATTAACTTTTATTATCAATAAT	3	159	1	TTAACTTTTT	    0.781284	-37
   ATTTACGTTTTTTTCTATTATTGATAAT	3	178	0	TTTTTTTCTT	    0.873519	-18
          ********* *

Masking position 7
Map Score:   8.96569

Number of sites scoring better than the average of aligned sites = 191
Number in coding regions = 130
Number in noncoding regions = 61
Number of orfs with sites within 600 bp upstream = 28
Fraction of orfs with sites within 600 bp upstream = 0.00449727


Motif number 4

          **********

No masking
Map Score:   8.40873e-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:   8.40873e-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:   8.40873e-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