AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -imelR_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	RP500	215	ADP,ATP CARRIER PROTEIN (tlc4)

Motif number 1

GAATATATGATATAAAATGCAAAATTGATA	1	11	1	TATAAAATGC	    0.988093	-205
GAGCAAAAAGTTTATAATGCAAGGAGCATT	1	62	1	TTTATAATGC	    0.994165	-154
TACTCATGCATTAATAATGCTCCTTGCATT	1	77	0	TTAATAATGC	    0.981053	-139
CTCGTTTAATTTTAAAATTGGCTAAGTTGT	1	124	0	TTTAAAATTG	    0.937454	-92
AAATCTTTAATATATAATTCTAGCCAATAG	1	177	1	TATATAATTC	    0.981395	-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

TTGTTGAAATTAAACTGTGTCTATCAATTT	1	32	0	TAAACTGTGT	    0.992774	-184
CCTTGCATTATAAACTTTTTGCTCTTGTTG	1	56	0	TAAACTTTTT	    0.926831	-160
GTTGTCTTAATAAGCTCTGTAGTACTCATG	1	99	0	TAAGCTCTGT	    0.991405	-117
TAAAATTGGCTAAGTTGTCTTAATAAGCTC	1	112	0	TAAGTTGTCT	    0.938272	-104
 TATTGAGTCTAACCTATGTCTATTGGCTA	1	197	0	TAACCTATGT	    0.976938	-19
          **********

Masking position 6
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

AAATTAAACTGTGTCTATCAATTTTGCATT	1	26	0	GTGTCTATCA	     0.97978	-190
ATTAATGCATGAGTACTACAGAGCTTATTA	1	92	1	GAGTACTACA	    0.948419	-124
AAAATTAAACGAGTATATCCTTGACTTAAA	1	141	1	GAGTATATCC	    0.988783	-75
      TATTGAGTCTAACCTATGTCTATT	1	202	0	GAGTCTAACC	    0.994456	-14
          **********

Masking position 4
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

TGCTCTTGTTGAAATTAAACTGTGTCTATC	1	37	0	GAAATTAAAC	     0.97876	-179
AGCCAATTTTAAAATTAAACGAGTATATCC	1	131	1	AAAATTAAAC	    0.968841	-85
AAAGATTTTCTACATTTAAGTCAAGGATAT	1	155	0	TACATTTAAG	    0.948021	-61
GCTAGAATTATATATTAAAGATTTTCTACA	1	171	0	TATATTAAAG	     0.96884	-45
          **********

Masking position 5
Map Score:   0.44814

Number of sites scoring better than the average of aligned sites = 224
Number in coding regions = 146
Number in noncoding regions = 78
Number of orfs with sites within 600 bp upstream = 41
Fraction of orfs with sites within 600 bp upstream = 0.00658529


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