AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -itorR_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	RP071	196	TRANSCRIPTIONAL ACTIVATOR PROTEIN CZCR (czcR)
#2	RP427	121	PETR PROTEIN (ompR)

Motif number 1

AACAACAATATTATTGGATAATTAGGTAATTTT 	1	10	0	TTATTGATTA	    0.803714	-187
AATAATATTGTTGTTTTTCAATTAAAGGTAGAAT	1	29	1	TTGTTTTTTA	    0.979079	-168
AGTAAAAATTTTATAATTTGATTAAATATTCTTT	1	68	1	TTATATTTTA	    0.993593	-129
ATTTGATTAAATATTCTTTACTTATATTATTAAT	1	83	1	ATATTTTTTA	     0.93892	-114
ATCTAGTGCTTTATACGTTCATTAATAATATAAG	1	103	0	TTATAGTTTA	    0.985385	-94
AGATAAAAAATTATAATTTAGTTAATAATTATTA	1	133	1	TTATATTTTA	    0.993706	-64
TCAATTTTGATAATAATTTAGTTAATAATTATTA	1	155	0	TAATATTTTA	    0.954875	-42
      TAAGTTATATTTATATTAGATTAGAAAC	2	5	1	TTATATTTTA	    0.989864	-117
AATATCATAGTTGTTTTTGGCTTTCGTGGTCAAA	2	50	0	TTGTTTTTTT	     0.86861	-72
          TTATACTCATTTTACATCTCGTGG	2	108	0	TTATATCTTA	    0.972602	-14
          ***** **   ***

Masking position 4
Map Score:   16.0716

Number of sites scoring better than the average of aligned sites = 292
Number in coding regions = 168
Number in noncoding regions = 124
Number of orfs with sites within 600 bp upstream = 83
Fraction of orfs with sites within 600 bp upstream = 0.0133312


Motif number 2

ATTACCTAATTATCCAATAATATTGTTGTTTTT	1	14	1	TACAATATAT	    0.746012	-183
ATATTGTTGTTTTTCAATTAAAGGTAGAATTTA	1	33	1	TTCAATAAAG	    0.981291	-164
TTATAAAATTTTTACTATTAAATTCTACCTTTA	1	51	0	TTCTATAAAT	    0.929884	-146
AAGTAAAGAATATTTAATCAAATTATAAAATTT	1	73	0	TATAATAAAT	    0.939593	-124
TATACGTTCATTAATAATATAAGTAAAGAATAT	1	93	0	TTTAATTAAG	    0.939811	-104
TAGTTAATAATTATTAACTAAATTATAATTTTT	1	138	0	TTTAACAAAT	    0.975164	-59
TAGTTAATAATTATTAACTAAATTATTATCAAA	1	151	1	TTTAACAAAT	    0.975164	-46
     TATTTTTCTCCATAAAATTCAATTTTGA	1	179	0	TTCCATAAAT	    0.973098	-18
ACGGGATGAGTTTCTAATCTAATATAAATATAA	2	15	0	TTTAATTAAT	    0.961492	-107
ATCCCGTGGTTTGACCACGAAAGCCAAAAACAA	2	41	1	TTCCACAAAG	    0.934169	-81
GGGTTCAAAATTATTAATATCATAGTTGTTTTT	2	66	0	TTTAATTCAT	      0.8387	-56
          **  **** ****

Masking position 7
Map Score:   12.9932

Number of sites scoring better than the average of aligned sites = 787
Number in coding regions = 511
Number in noncoding regions = 276
Number of orfs with sites within 600 bp upstream = 154
Fraction of orfs with sites within 600 bp upstream = 0.024735


Motif number 3

ATAATTTTTTATCTAGTGCTTTATACGTTC	1	117	0	ATCTAGTGCT	    0.970879	-80
TTAGAAACTCATCCCGTGGTTTGACCACGA	2	31	1	ATCCCGTGGT	    0.987689	-91
TTGTTTTTGGCTTTCGTGGTCAAACCACGG	2	44	0	CTTTCGTGGT	    0.981671	-78
AATAATTTTGAACCCGTGGTCAAACCACGA	2	84	1	AACCCGTGGT	    0.984333	-38
CTCATTTTACATCTCGTGGTTTGACCACGG	2	97	0	ATCTCGTGGT	    0.987572	-25
          **********

Masking position 7
Map Score:   9.91397

Number of sites scoring better than the average of aligned sites = 14
Number in coding regions = 7
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 4

ATTGAAAAACAACAATATTATTGGATAATT	1	21	0	AACAATATTA	    0.923288	-176
ATCAAATTATAAAATTTTTACTATTAAATT	1	60	0	AAAATTTTTA	    0.947074	-137
ATTCTTTACTTATATTATTAATGAACGTAT	1	95	1	TATATTATTA	     0.89041	-102
CACTAGATAAAAAATTATAATTTAGTTAAT	1	129	1	AAAATTATAA	    0.975067	-68
AATTTAGTTAATAATTATTAACTAAATTAT	1	145	0	ATAATTATTA	    0.975067	-52
AATTATTAACTAAATTATTATCAAAATTGA	1	159	1	TAAATTATTA	    0.971651	-38
CTAATCTAATATAAATATAACTTA      	2	5	0	ATAAATATAA	    0.839632	-117
CCACGGGTTCAAAATTATTAATATCATAGT	2	73	0	AAAATTATTA	    0.990611	-49
          **********

Masking position 4
Map Score:   12.2674

Number of sites scoring better than the average of aligned sites = 745
Number in coding regions = 474
Number in noncoding regions = 271
Number of orfs with sites within 600 bp upstream = 143
Fraction of orfs with sites within 600 bp upstream = 0.0229682


Motif number 5

          **********

No masking
Map Score:   -8.2833e-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:   -8.2833e-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:   -8.2833e-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