AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -iompR_mthe_opreg_100.orf -g0.495 -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 =  	0.495
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	MTH425	90	unknown
#2	MTH426	36	unknown
#3	MTH1343	218	imidazoleglycerol-phosphate synthase (cyclase)

Motif number 1

   TGTGAGACCCTCGGTGGTGCTTATGTTGATGT	2	15	0	CCCGGTGGCT	    0.997717	-22
GTTCAAATCCCCCCGGGTCCGCTTTTTTATTAACT	3	19	0	CCCGGTCCTT	    0.995797	-200
GACTTCGGATCCCAAGGTCGGGGGTTCAAATCCCC	3	42	0	CCCGGTCGGT	    0.998426	-177
GACCTTGGGATCCGAAGTCCCACGTCATATTCCAG	3	58	1	TCCAGTCACT	    0.972397	-161
GTGTAGGGGGCCCGTAGTCTAGCCTGGAATATGAC	3	81	0	CCCAGTCGCT	    0.999165	-138
GTCTGCTGTCCCCTGAGTCTGGTCTTCGGCTGACA	3	161	0	CCCAGTCGTT	    0.998138	-58
          ***  ****  ** *

Masking position 8
Map Score:   9.81658

Number of sites scoring better than the average of aligned sites = 63
Number in coding regions = 58
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 2

TCATCCATATATCAACGTGAGGGATGTATT      	1	5	0	ATCAATGAGG	     0.99353	-86
AGATTATGTTATAAAATGGAAAGGGGATAAGC    	1	69	1	ATAAAGGAGG	    0.987798	-22
GGGACTTCGGATCCCAAGGTCGGGGGTTCAAATCCC	3	43	0	ATCCCGGTGG	    0.975069	-176
TTAACTTTAAATAGAGATGTGTGTAGGGGGCCCGTA	3	100	0	ATAGATGTGG	    0.987955	-119
ATATTTTCTCATCAACGTGTCAGCCGAAGACCAGAC	3	144	1	ATCAATGTGG	    0.996522	-75
GGCATTTAGTATAAAGCTGTCTGCTGTCCCCTGAGT	3	178	0	ATAAATGTGG	    0.994541	-41
          *****  ***  *  *

Masking position 2
Map Score:   5.00248

Number of sites scoring better than the average of aligned sites = 47
Number in coding regions = 40
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 3

ATATCAACGTGAGGGATGTATT        	1	3	0	GAGGGATGTA	    0.979386	-88
AGCGGACCCGGGGGGATTTGAACCCCCGAC	3	31	1	GGGGGATTTG	    0.990346	-188
GGAATATGACGTGGGACTTCGGATCCCAAG	3	61	0	GTGGGACTTC	    0.965222	-158
ATGTGTGTAGGGGGCCCGTAGTCTAGCCTG	3	90	0	GGGGCCCGTA	    0.984368	-129
TATTAATTAAGGGGCATTTAGTATAAAGCT	3	196	0	GGGGCATTTA	     0.99174	-23
          **********

Masking position 9
Map Score:   3.3662

Number of sites scoring better than the average of aligned sites = 182
Number in coding regions = 170
Number in noncoding regions = 12
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 4

      GCTTATCCCCTTTCCATTTTATAA	1	77	0	ATCCCCTTTC	    0.962106	-14
      TGTGAGACCCTCGGTGGTGCTTAT	2	23	0	AGACCCTCGG	    0.813176	-14
GGGGGTTCAAATCCCCCCGGGTCCGCTTTT	3	28	0	ATCCCCCCGG	    0.980842	-191
GGGGGATTTGAACCCCCGACCTTGGGATCC	3	41	1	AACCCCCGAC	    0.972906	-178
GGGATCCGAAGTCCCACGTCATATTCCAGG	3	64	1	GTCCCACGTC	    0.895147	-155
CTAGACTACGGGCCCCCTACACACATCTCT	3	94	1	GGCCCCCTAC	    0.990956	-125
GCTGTCTGCTGTCCCCTGAGTCTGGTCTTC	3	169	0	GTCCCCTGAG	    0.985603	-50
TTATACTAAATGCCCCTTAATTAATAAAT 	3	200	1	TGCCCCTTAA	    0.769152	-19
          **********

Masking position 5
Map Score:   3.76013

Number of sites scoring better than the average of aligned sites = 2029
Number in coding regions = 1922
Number in noncoding regions = 107
Number of orfs with sites within 600 bp upstream = 84
Fraction of orfs with sites within 600 bp upstream = 0.0134918


Motif number 5

          **********

No masking
Map Score:   9.48026e-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 6

          **********

No masking
Map Score:   9.48026e-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:   9.48026e-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