AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i105_Manganese_Transport_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	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	     0.99829	-14
GATTTAGTGTATGATGGTGATTTTAAGGTG	3	16	0	ATGATGGTGA	     0.99324	-276
ACTGCCCTAAAGGATGGGGATTTCGGTAAT	3	60	0	AGGATGGGGA	    0.997088	-232
AGAATGACTCATGATGTGGTCTGCTATTAT	3	100	0	ATGATGTGGT	    0.983092	-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	    0.990738	-65
AATCAGTAAGTTGGCAGCATTACCGAAATCCCCA	3	42	1	TTGCAGTACC	    0.990738	-250
TCTGCTATTATTGACATCCTCACTGCCCTAAAGG	3	77	0	TTGCATTACT	    0.981746	-215
ACCACATCATGAGTCATTCTGACCGACACATGCC	3	110	1	GAGCATTACC	    0.987974	-182
TTGTTTCCAATAGACATTTTTAACATGTTGTTTT	3	192	0	TAGCATTAAC	    0.976361	-100
TTATTTCCAATTGTAATGATAACCATTCTCATAT	3	228	1	TTGAATTACC	    0.978305	-64
AATTATCACGTAGTCATATTAATATGAGAATGGT	3	249	0	TAGCATTATA	    0.864644	-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

ACATGTTGTTTTTCTAAGTGTTATAAGGTA	3	174	0	TTTCTAAGTG	    0.976898	-118
AATAAAATTGTTTCCAATAGACATTTTTAA	3	203	0	TTTCCAATAG	    0.987312	-89
AACAATTTTATTTCCAATTGTAATGATAAC	3	221	1	TTTCCAATTG	    0.992766	-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	    0.997966	-32
ATTCCAGCTAAAAGCCCGGCAAGCCGGGCG	1	19	0	AAAGCCCGGC	    0.998215	-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

ATCGAAATAAGAATTATTTTCC        	2	3	0	GAATTATTTT	    0.846768	-84
ACCTTCCCCATCATCATTTTTGTTGTGTTC	2	67	0	TCATCATTTT	    0.916436	-20
ACCACATCATGAGTCATTCTGACCGACACA	3	110	1	GAGTCATTCT	    0.972204	-182
TTGTTTCCAATAGACATTTTTAACATGTTG	3	196	0	TAGACATTTT	    0.958438	-96
ATGTCTATTGGAAACAATTTTATTTCCAAT	3	209	1	GAAACAATTT	    0.826774	-83
ATTGTAATGATAACCATTCTCATATTAATA	3	237	1	TAACCATTCT	    0.915287	-55
AATTATCACGTAGTCATATTAATATGAGAA	3	253	0	TAGTCATATT	    0.899355	-39
          **********

Masking position 6
Map Score:   1.95537

Number of sites scoring better than the average of aligned sites = 428
Number in coding regions = 336
Number in noncoding regions = 92
Number of orfs with sites within 600 bp upstream = 115
Fraction of orfs with sites within 600 bp upstream = 0.0184709


Motif number 6

          **********

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 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