AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -icynR_ecoli_hinf_100.orf -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	cynR_cynT	108	cynR: cyn operon positive regulator, cynT: carbonic anhydrase
#2	cynS	30	cyanate aminohydrolase, cyanase
#3	cynX	32	cyanate transport
#4	HI0775	205	transcriptional regulator

Motif number 1

TGAGTTCCATTGGATTTACTTATAGGTTGCG	1	87	1	TGGATTACTT	    0.855611	-22
        CGTGAACGTCTTTTGATGGTTGC	3	20	0	TGAAGTCTTT	    0.982265	-13
ACTTATTTGTTGATATTCTTTCTTTTAATCT	4	29	0	TGATTTCTTT	    0.977363	-177
ATATTTCAAATGGATATGTTTCTTGCGATGA	4	65	1	TGGAATGTTT	    0.895008	-141
ATGTTTCTTGCGATGATCCTTGATAGGCAAT	4	80	1	CGATATCCTT	    0.883354	-126
TTAATATCAATCTAGTTCCTTTATTGCCTAT	4	102	0	TCTATTCCTT	    0.811012	-104
ATTTCTTTTACGAAATTCTTTTTGCTATTTT	4	132	0	CGAATTCTTT	    0.975747	-74
CTAAGAAAGATGTATTTCTTTTACGAAATTC	4	145	0	TGTATTCTTT	    0.972831	-61
TAAGTTATTTTGATAGTGTTTTAAACAATCC	4	183	1	TGATGTGTTT	     0.91134	-23
          **** ******

Masking position 7
Map Score:   5.37307

Number of sites scoring better than the average of aligned sites = 844
Number in coding regions = 710
Number in noncoding regions = 134
Number of orfs with sites within 600 bp upstream = 155
Fraction of orfs with sites within 600 bp upstream = 0.0248956


Motif number 2

AAATCCAATGGAACTCATCATAAATGAGACT	1	73	0	GAACTCATAT	    0.992633	-36
      GGTGGAACTCCTGATGGTTTAAAAA	2	16	0	GAACTCCTAT	    0.997286	-15
       AGAGACCTCCTAATAACGAGATTA	4	4	1	GACCTCCTAT	    0.996773	-202
          ******** **

Masking position 2
Map Score:   2.19283

Number of sites scoring better than the average of aligned sites = 6
Number in coding regions = 4
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 3

    TCGCAACCTATAAGTAAATCCAATGG	1	93	0	CCTATAAGTA	    0.841781	-16
         CCTTATTTTTAAACCATCAGG	2	2	1	CTTATTTTTA	    0.968619	-29
TTTTAATCTCGTTATTAGGAGGTCTCT   	4	8	0	GTTATTAGGA	    0.955685	-198
ATATAAGATACTTATTTGTTGATATTCTTT	4	39	0	CTTATTTGTT	    0.922921	-167
AATTCTTTTTGCTATTTTTAATATCAATCT	4	120	0	GCTATTTTTA	    0.962391	-86
GCGGGTATAAGTTATTTTGATAGTGTTTTA	4	176	1	GTTATTTTGA	    0.962391	-30
          **********

Masking position 5
Map Score:   1.8663

Number of sites scoring better than the average of aligned sites = 208
Number in coding regions = 151
Number in noncoding regions = 57
Number of orfs with sites within 600 bp upstream = 69
Fraction of orfs with sites within 600 bp upstream = 0.0110826


Motif number 4

ACTACTCGCCGATTGTCATAAGGTAAAAGTCT	1	46	1	GATGCATAAG	     0.96045	-63
TGGAACTCCTGATGGTTTAAAAATAAGG    	2	7	0	GATGTTAAAA	    0.980368	-24
GATGATCCTTGATAGGCAATAAAGGAACTAGA	4	91	1	GATGCAATAA	    0.981788	-115
AAAGGAACTAGATTGATATTAAAAATAGCAAA	4	111	1	GATGTATTAA	    0.972107	-95
       AAGGATTGTTTAAAACACTATCAAA	4	191	0	GATGTTAAAA	    0.980368	-15
          *** * ******

Masking position 3
Map Score:   1.58911

Number of sites scoring better than the average of aligned sites = 126
Number in coding regions = 116
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 5

         CGTTAACCTCTGTCTGTCTCT	1	2	1	GTTAACCTCT	    0.981321	-107
GTTAACCTCTGTCTGTCTCTGGAATGAGAG	1	12	1	GTCTGTCTCT	    0.982391	-97
TCGGCGAGTAGTCTGCCTCTCATTCCAGAG	1	28	0	GTCTGCCTCT	    0.995509	-81
         CGTGAACGTCTTTTGATGGTT	3	22	0	GTGAACGTCT	    0.966718	-11
          **********

Masking position 8
Map Score:   1.68569

Number of sites scoring better than the average of aligned sites = 105
Number in coding regions = 95
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 6

          **********

No masking
Map Score:   3.43493e-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:   3.43493e-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:   3.43493e-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