AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i102_Ferric_Transport_ecoli_hinf_reg_100.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 =  	0.46
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	fecB	38	citrate-dependent iron transport, periplasmic protein
#2	fecA	86	outer membrane receptor; citrate-dependent iron transport, outer membrane receptor
#3	fecI	291	probable RNA polymerase sigma factor

Motif number 1

AACAAAAATGATGATGGGGAAGGT      	2	73	1	ATGATGGGGA	    0.998235	-14
GATTTAGTGTATGATGGTGATTTTAAGGTG	3	16	0	ATGATGGTGA	    0.993025	-276
ACTGCCCTAAAGGATGGGGATTTCGGTAAT	3	60	0	AGGATGGGGA	    0.996995	-232
AGAATGACTCATGATGTGGTCTGCTATTAT	3	100	0	ATGATGTGGT	    0.982559	-192
          **********

Masking position 5
Map Score:   7.13905

Number of sites scoring better than the average of aligned sites = 21
Number in coding regions = 17
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 2

GAACGAGAAGGGTAAAAAGGACAATCGAAATAAG	2	22	0	GGTAAGGCAA	    0.990337	-65
TGGGGATTTCGGTAATGCTGCCAACTTACTGATT	3	42	0	GGTACTGCAA	    0.990337	-250
CCTTTAGGGCAGTGAGGATGTCAATAATAGCAGA	3	77	1	AGTAATGCAA	    0.980963	-215
GGCATGTGTCGGTCAGAATGACTCATGATGTGGT	3	110	0	GGTAATGCTC	    0.987454	-182
AAAACAACATGTTAAAAATGTCTATTGGAAACAA	3	192	1	GTTAATGCTA	    0.975352	-100
ATATGAGAATGGTTATCATTACAATTGGAAATAA	3	228	0	GGTAATTCAA	    0.977377	-64
ACCATTCTCATATTAATATGACTACGTGATAATT	3	249	1	TATAATGCTA	    0.859557	-43
          *** *  *** ***

Masking position 5
Map Score:   4.87722

Number of sites scoring better than the average of aligned sites = 500
Number in coding regions = 456
Number in noncoding regions = 44
Number of orfs with sites within 600 bp upstream = 58
Fraction of orfs with sites within 600 bp upstream = 0.00931577


Motif number 3

ACATGTTGTTTTTCTAAGTGTTATAAGGTA	3	174	0	TTTCTAAGTG	    0.979472	-118
AATAAAATTGTTTCCAATAGACATTTTTAA	3	203	0	TTTCCAATAG	     0.98874	-89
AACAATTTTATTTCCAATTGTAATGATAAC	3	221	1	TTTCCAATTG	    0.993583	-71
          **********

Masking position 6
Map Score:   1.1008

Number of sites scoring better than the average of aligned sites = 4
Number in coding regions = 1
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 4

    TGTGTTAACGCCCGGCTTGCCGGGCT	1	7	1	AACGCCCGGC	    0.997984	-32
ATTCCAGCTAAAAGCCCGGCAAGCCGGGCG	1	19	0	AAAGCCCGGC	    0.998419	-20
          **********

Masking position 2
Map Score:   1.09855

Number of sites scoring better than the average of aligned sites = 27
Number in coding regions = 23
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 5

   GGAAAATAATTCTTATTTCGATTGTCC	2	8	1	AATTCTTATT	    0.862485	-79
TCCTTTTTACCCTTCTCGTTCGACTCATAG	2	35	1	CCTTCTCGTT	    0.958527	-52
TCCCCATCATCATTTTTGTTGTGTTCAGCT	2	63	0	CATTTTTGTT	    0.955328	-24
AGGCTCCATCCCATTTTATACCTACCTTAT	3	152	1	CCATTTTATA	    0.860004	-140
CTATTGGAAACAATTTTATTTCCAATTGTA	3	213	1	CAATTTTATT	    0.932548	-79
TAATGATAACCATTCTCATATTAATATGAC	3	241	1	CATTCTCATA	     0.94743	-51
          **********

Masking position 6
Map Score:   0.682866

Number of sites scoring better than the average of aligned sites = 506
Number in coding regions = 377
Number in noncoding regions = 129
Number of orfs with sites within 600 bp upstream = 152
Fraction of orfs with sites within 600 bp upstream = 0.0244137


Motif number 6

GTGTTCAGCTATGAGTCGAACGAGAAGGGTA	2	42	0	ATGAGTCGAC	    0.994476	-45
AGACCACATCATGAGTCATTCTGACCGACAC	3	108	1	ATGAGTCATC	    0.991556	-184
TGCTTCTGGCATGTGTCGGTCAGAATGACTC	3	120	0	ATGTGTCGTC	    0.994515	-172
          ******** **

Masking position 1
Map Score:   0.586733

Number of sites scoring better than the average of aligned sites = 11
Number in coding regions = 8
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 7

          **********

No masking
Map Score:   -3.17312e-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:   -3.17312e-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 9

          **********

No masking
Map Score:   -3.17312e-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