AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i102_Ferric_Transport_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	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	    0.998506	-14
GATTTAGTGTATGATGGTGATTTTAAGGTG	3	16	0	ATGATGGTGA	     0.99409	-276
ACTGCCCTAAAGGATGGGGATTTCGGTAAT	3	60	0	AGGATGGGGA	    0.997456	-232
AGAATGACTCATGATGTGGTCTGCTATTAT	3	100	0	ATGATGTGGT	    0.985199	-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

CTTATTTCGATTGTCCTTTTTACCCTTCTCGTTC	2	22	1	TTGCCTTACC	    0.989747	-65
AATCAGTAAGTTGGCAGCATTACCGAAATCCCCA	3	42	1	TTGCAGTACC	    0.989747	-250
TCTGCTATTATTGACATCCTCACTGCCCTAAAGG	3	77	0	TTGCATTACT	    0.979811	-215
ACCACATCATGAGTCATTCTGACCGACACATGCC	3	110	1	GAGCATTACC	     0.98669	-182
TTGTTTCCAATAGACATTTTTAACATGTTGTTTT	3	192	0	TAGCATTAAC	     0.97387	-100
TTATTTCCAATTGTAATGATAACCATTCTCATAT	3	228	1	TTGAATTACC	    0.976014	-64
AATTATCACGTAGTCATATTAATATGAGAATGGT	3	249	0	TAGCATTATA	    0.852172	-43
          *** ***  * ***

Masking position 12
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

TACCTTATAACACTTAGAAAAACAACATGT	3	174	1	CACTTAGAAA	    0.975818	-118
TTAAAAATGTCTATTGGAAACAATTTTATT	3	203	1	CTATTGGAAA	    0.986713	-89
GTTATCATTACAATTGGAAATAAAATTGTT	3	221	0	CAATTGGAAA	    0.992422	-71
          **********

Masking position 8
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

AGCCCGGCAAGCCGGGCGTTAACACA    	1	7	0	GCCGGGCGTT	     0.99797	-32
CGCCCGGCTTGCCGGGCTTTTAGCTGGAAT	1	19	1	GCCGGGCTTT	    0.998241	-20
          **********

Masking position 9
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	    0.857801	-79
TCCTTTTTACCCTTCTCGTTCGACTCATAG	2	35	1	CCTTCTCGTT	    0.956949	-52
TCCCCATCATCATTTTTGTTGTGTTCAGCT	2	63	0	CATTTTTGTT	    0.953634	-24
AGGCTCCATCCCATTTTATACCTACCTTAT	3	152	1	CCATTTTATA	    0.855246	-140
CTATTGGAAACAATTTTATTTCCAATTGTA	3	213	1	CAATTTTATT	    0.930054	-79
TAATGATAACCATTCTCATATTAATATGAC	3	241	1	CATTCTCATA	    0.945455	-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

CTTATTTCGATTGTCCTTTTTACCCTTCTC	2	22	1	TTGTCCTTTT	     0.94623	-65
TCTGCTATTATTGACATCCTCACTGCCCTA	3	81	0	TTGACATCCT	    0.926165	-211
ACCACATCATGAGTCATTCTGACCGACACA	3	110	1	GAGTCATTCT	    0.935853	-182
TTGTTTCCAATAGACATTTTTAACATGTTG	3	196	0	TAGACATTTT	    0.962676	-96
ATGATAACCATTCTCATATTAATATGACTA	3	243	1	TTCTCATATT	    0.885074	-49
AATTATCACGTAGTCATATTAATATGAGAA	3	253	0	TAGTCATATT	    0.971088	-39
          **********

Masking position 7
Map Score:   1.29023

Number of sites scoring better than the average of aligned sites = 260
Number in coding regions = 202
Number in noncoding regions = 58
Number of orfs with sites within 600 bp upstream = 76
Fraction of orfs with sites within 600 bp upstream = 0.0122069


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