AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i260_ecoli_mtub_100.orf -o260_ecoli_mtub_100.ace -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.58 -x5 -e 
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 =  	0.58
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	fliC_fliD	265	fliC: flagellar biosynthesis; flagellin, filament structural protein, fliD: flagellar biosynthesis; filament capping protein; enables filament assembly
#2	fliS	24	flagellar biosynthesis; repressor of class 3a and 3b operons (RflA activity)

Motif number 1

        GCGATTTCCTTTTATCTTTCGA	1	3	1	GATTTCCTTT	    0.976819	-263
GATAACCCCGGTATTCGTTTTACGTGTCGA	1	29	0	GTATTCGTTT	     0.97376	-237
ATTGCGCAAAGTTTACGTTTAATTGTTTTT	1	66	1	GTTTACGTTT	    0.987748	-200
CGTCAACCCTGTTATCGTCTGTCGTAAAAC	1	181	0	GTTATCGTCT	    0.979292	-85
GCAAGTCGTTGATTACGTATTGGGTTTCCA	1	228	0	GATTACGTAT	    0.967903	-38
     GATTCGTTATCCTATATTGCAAGTC	1	251	0	GTTATCCTAT	    0.967114	-15
          **********

Masking position 8
Map Score:   7.26182

Number of sites scoring better than the average of aligned sites = 297
Number in coding regions = 249
Number in noncoding regions = 48
Number of orfs with sites within 600 bp upstream = 56
Fraction of orfs with sites within 600 bp upstream = 0.00899454


Motif number 2

GGTATTCGTTTTACGTGTCGAAAGATAAAAGGA	1	17	0	TAGGTCGAAA	    0.983614	-249
GTTATCGGTCTGAATTGCGCAAAGTTTACGTTT	1	53	1	TATGCGCAAA	    0.976615	-213
ATTGTTTTTTTTAATAGCGGGAATAAGGGGCAG	1	87	1	TATGCGGGAA	    0.987558	-179
ATAGCGGGAATAAGGGGCAGAGAAAAGAGTATT	1	100	1	TAGGCAGAGA	     0.95958	-166
CCATTTTTTGTTAGTCGCCGAAATACTCTTTTC	1	121	0	TATGCCGAAA	     0.99529	-145
ACCCGTCGGCTCAATCGCCGTCAACCCTGTTAT	1	196	0	TATGCCGTCA	    0.951279	-70
GCGATTGAGCCGACGGGTGGAAACCCAATACGT	1	211	1	CAGGTGGAAA	    0.956495	-55
          * * * *******

Masking position 3
Map Score:   3.44995

Number of sites scoring better than the average of aligned sites = 732
Number in coding regions = 654
Number in noncoding regions = 78
Number of orfs with sites within 600 bp upstream = 88
Fraction of orfs with sites within 600 bp upstream = 0.0141343


Motif number 3

CTTTCGACACGTAAAACGAATACCGGGGTT	1	26	1	GTAAAACGAA	    0.852663	-240
CGAATACCGGGGTTATCGGTCTGAATTGCG	1	42	1	GGTTATCGGT	    0.946321	-224
AGAGAAAAGAGTATTTCGGCGACTAACAAA	1	118	1	GTATTTCGGC	     0.96881	-148
TCTAAAGGTTGTTTTACGACAGACGATAAC	1	171	1	GTTTTACGAC	    0.973421	-95
ACGATAACAGGGTTGACGGCGATTGAGCCG	1	193	1	GGTTGACGGC	    0.987123	-73
TTGCAATATAGGATAACGAATC        	1	254	1	GGATAACGAA	    0.973605	-12
          **********

Masking position 7
Map Score:   2.80645

Number of sites scoring better than the average of aligned sites = 1907
Number in coding regions = 1792
Number in noncoding regions = 115
Number of orfs with sites within 600 bp upstream = 131
Fraction of orfs with sites within 600 bp upstream = 0.0210408


Motif number 4

GTTTACGTTTAATTGTTTTTTTTAATAGCGGG	1	76	1	AATGTTTTTT	    0.986045	-190
TTAGTCGCCGAAATACTCTTTTCTCTGCCCCT	1	112	0	AATACTTTTT	    0.958891	-154
ACTAACAAAAAATGGCTGTTTTTGAAAAAAAT	1	139	1	AAGGCTTTTT	    0.994142	-127
AAAAAATTCTAAAGGTTGTTTTACGACAGACG	1	164	1	AAGGTTTTTT	    0.990619	-102
          ** **** ****

Masking position 7
Map Score:   2.2123

Number of sites scoring better than the average of aligned sites = 68
Number in coding regions = 45
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 30
Fraction of orfs with sites within 600 bp upstream = 0.0048185


Motif number 5

CGTAAAACGAATACCGGGGTTATCGGTCTGA	1	35	1	ATACGGGGTT	    0.981871	-231
GTTTTTTTTAATAGCGGGAATAAGGGGCAGA	1	90	1	ATACGGGAAT	    0.979035	-176
ACGACAGACGATAACAGGGTTGACGGCGATT	1	186	1	ATACAGGGTT	    0.992846	-80
          *** *******

Masking position 3
Map Score:   1.25512

Number of sites scoring better than the average of aligned sites = 10
Number in coding regions = 8
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 6

          **********

No masking
Map Score:   -5.44113e-14

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:   -5.44113e-14

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:   -5.44113e-14

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