AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i122_Arsenical_Resistance_Pump_ecoli_reg_300.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.5 -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 =  	0.5
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	arsR	300	transcriptional repressor of chromosomal ars operon

Motif number 1

TAGCGATTTCTTCAGCTGGCGGAGGG    	1	7	0	TTCAGCTGGC	     0.98675	-294
GCTAATAGTATTGAGCTGTTAGATAAGAAC	1	59	1	TTGAGCTGTT	    0.981049	-242
CTTTCCAGCCCTGAGTTGGTGGCTCTGGCT	1	100	0	CTGAGTTGGT	    0.991229	-201
AAAACCGACTTTGCGTCGGTTTTTTACTTT	1	126	0	TTGCGTCGGT	    0.980739	-175
GGTGTGAATTTTGAGTTGGCTATTCATTTG	1	182	0	TTGAGTTGGC	     0.99632	-119
          **********

Masking position 2
Map Score:   5.60578

Number of sites scoring better than the average of aligned sites = 368
Number in coding regions = 345
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 26
Fraction of orfs with sites within 600 bp upstream = 0.00417604


Motif number 2

CAGCTGAAGAAATCGCTAATTCTTGCAATGT	1	19	1	AACGCTAATT	    0.819235	-282
TTGCAATGTTAGCCACTGGCTAATAGTATTG	1	41	1	AGCACTGGCT	    0.669499	-260
CTCCAGCCAGAGCCACCAACTCAGGGCTGGA	1	96	1	AGCACCAACT	    0.969263	-205
CTGGAAAGTAAAAAACCGACGCAAAGTCGGT	1	122	1	AAAACCGACG	    0.956377	-179
CAGGACGTAAAAAAACCGACTTTGCGTCGGT	1	136	0	AAAACCGACT	    0.985488	-165
CTTTCAAATGAATAGCCAACTCAAAATTCAC	1	178	1	AAAGCCAACT	     0.97437	-123
CTTCGAAGAGAGACACTACCTGCAACAATCA	1	270	1	AGCACTACCT	    0.957328	-31
          ** ********

Masking position 1
Map Score:   4.24078

Number of sites scoring better than the average of aligned sites = 859
Number in coding regions = 795
Number in noncoding regions = 64
Number of orfs with sites within 600 bp upstream = 53
Fraction of orfs with sites within 600 bp upstream = 0.00851269


Motif number 3

CGATTTCTTCAGCTGGCGGAGGG       	1	4	0	AGCTGGCGGA	    0.991798	-297
CAATACTATTAGCCAGTGGCTAACATTGCA	1	42	0	AGCCAGTGGC	    0.991798	-259
AATAGTATTGAGCTGTTAGATAAGAACTCT	1	62	1	AGCTGTTAGA	    0.907895	-239
TCCAGCCCTGAGTTGGTGGCTCTGGCTGGA	1	97	0	AGTTGGTGGC	    0.993474	-204
TGATTGTTGCAGGTAGTGTCTCTCTTCGAA	1	271	0	AGGTAGTGTC	    0.950469	-30
          **********

Masking position 1
Map Score:   1.8463

Number of sites scoring better than the average of aligned sites = 2171
Number in coding regions = 2097
Number in noncoding regions = 74
Number of orfs with sites within 600 bp upstream = 83
Fraction of orfs with sites within 600 bp upstream = 0.0133312


Motif number 4

ACCGACTTTGCGTCGGTTTTTTACTTTCCA	1	123	0	CGTCGGTTTT	    0.994075	-178
ACCGACGCAAAGTCGGTTTTTTTACGTCCT	1	136	1	AGTCGGTTTT	    0.995015	-165
GTGAATTTTGAGTTGGCTATTCATTTGAAA	1	179	0	AGTTGGCTAT	     0.97213	-122
          **********

Masking position 3
Map Score:   0.807304

Number of sites scoring better than the average of aligned sites = 101
Number in coding regions = 84
Number in noncoding regions = 17
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 5

GTTTTTTACTTTCCAGCCCTGAGTTGGTGG	1	108	0	TTCCAGCCCT	    0.987109	-193
TTACGTCCTGATTCAGACCTCCTTTCAAAT	1	157	1	ATTCAGACCT	    0.994795	-144
CCAACTCAAAATTCACACCTATTACCTTCC	1	193	1	ATTCACACCT	    0.990463	-108
          **********

Masking position 5
Map Score:   0.807304

Number of sites scoring better than the average of aligned sites = 83
Number in coding regions = 77
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 6

          **********

No masking
Map Score:   7.91135e-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 7

          **********

No masking
Map Score:   7.91135e-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 8

          **********

No masking
Map Score:   7.91135e-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