AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i122_Arsenical_Resistance_Pump_ecoli_reg_100.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

    CCCTCCGCCAGCTGAAGAAATCGCTA	1	7	1	GCCAGCTGAA	    0.988001	-294
GTTCTTATCTAACAGCTCAATACTATTAGC	1	59	0	AACAGCTCAA	    0.983317	-242
AGCCAGAGCCACCAACTCAGGGCTGGAAAG	1	100	1	ACCAACTCAG	    0.992294	-201
AAAGTAAAAAACCGACGCAAAGTCGGTTTT	1	126	1	ACCGACGCAA	    0.983058	-175
CAAATGAATAGCCAACTCAAAATTCACACC	1	182	1	GCCAACTCAA	    0.996769	-119
          **********

Masking position 9
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	    0.813099	-282
TTGCAATGTTAGCCACTGGCTAATAGTATTG	1	41	1	AGCACTGGCT	    0.674349	-260
CTCCAGCCAGAGCCACCAACTCAGGGCTGGA	1	96	1	AGCACCAACT	     0.97007	-205
CTGGAAAGTAAAAAACCGACGCAAAGTCGGT	1	122	1	AAAACCGACG	    0.954169	-179
CAGGACGTAAAAAAACCGACTTTGCGTCGGT	1	136	0	AAAACCGACT	    0.984799	-165
CTTTCAAATGAATAGCCAACTCAAAATTCAC	1	178	1	AAAGCCAACT	    0.973155	-123
CTTCGAAGAGAGACACTACCTGCAACAATCA	1	270	1	AGCACTACCT	    0.955739	-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	    0.991234	-297
CAATACTATTAGCCAGTGGCTAACATTGCA	1	42	0	AGCCAGTGGC	    0.991234	-259
AATAGTATTGAGCTGTTAGATAAGAACTCT	1	62	1	AGCTGTTAGA	    0.902125	-239
TCCAGCCCTGAGTTGGTGGCTCTGGCTGGA	1	97	0	AGTTGGTGGC	    0.993024	-204
TGATTGTTGCAGGTAGTGTCTCTCTTCGAA	1	271	0	AGGTAGTGTC	    0.947211	-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

CCACCAACTCAGGGCTGGAAAGTAAAAAAC	1	108	1	AGGGCTGGAA	    0.988184	-193
ATTTGAAAGGAGGTCTGAATCAGGACGTAA	1	157	0	AGGTCTGAAT	    0.995232	-144
GGAAGGTAATAGGTGTGAATTTTGAGTTGG	1	193	0	AGGTGTGAAT	    0.991261	-108
          **********

Masking position 9
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