AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -imetJ_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	MTH777	48	conserved protein
#2	MTH778	68	unknown
#3	MTH779	300	conserved protein

Motif number 1

TCATTCACCAGCTGGGACCGC          	1	1	0	GCTGGGCCGC	    0.895807	-48
ATCTCTGGTTTCAGGGTCCGGATTTTTGCCC	2	42	1	TCAGGGCCGG	    0.993967	-27
AAGTTTAAAGGGAGTCACCGGGATGTCC   	3	8	0	GGAGTCCCGG	    0.995506	-293
AGTTTTGAGTGGACTGGCCGGGATTTGAACC	3	159	1	GGACTGCCGG	    0.992294	-142
TTGGCATGGCGGAGGCCCCGGGTTCAAATCC	3	179	0	GGAGGCCCGG	    0.995603	-122
TGTATACTTTGTTGGGGCTGGTAGCTCAGGT	3	225	0	GTTGGGCTGG	    0.971736	-76
          ****** ****

Masking position 8
Map Score:   7.87252

Number of sites scoring better than the average of aligned sites = 408
Number in coding regions = 382
Number in noncoding regions = 26
Number of orfs with sites within 600 bp upstream = 18
Fraction of orfs with sites within 600 bp upstream = 0.0028911


Motif number 2

GGAAGTGCCCAATGATTTTTAAGTTTAAAG	3	29	0	AATGATTTTT	    0.980281	-272
TGTGGCCTGGAATGATTTTTTTATTTTAAT	3	60	1	AATGATTTTT	    0.980281	-241
ATTGTCCTGCATTTATTTTTACTGATTAAA	3	111	0	ATTTATTTTT	    0.937946	-190
CTGTTTTTTAAACTGTTTTTATTGTCCTGC	3	131	0	AACTGTTTTT	    0.982975	-170
GTCCACTCAAAACTGTTTTTTAAACTGTTT	3	143	0	AACTGTTTTT	    0.982975	-158
          **********

Masking position 6
Map Score:   5.42739

Number of sites scoring better than the average of aligned sites = 67
Number in coding regions = 30
Number in noncoding regions = 37
Number of orfs with sites within 600 bp upstream = 34
Fraction of orfs with sites within 600 bp upstream = 0.00546097


Motif number 3

GATTTTTTTATTTTAATAAGGAAACCTGAA	3	73	1	TTTTAATAAG	    0.981324	-228
GAAAAACTTCATTTAATCAGTAAAAATAAA	3	100	1	ATTTAATCAG	    0.975375	-201
CAAAACTGTTTTTTAAACTGTTTTTATTGT	3	136	0	TTTTAAACTG	    0.923317	-165
ACATTAAGCCTTTTAATATTTAAAGTTAAC	3	253	1	TTTTAATATT	    0.875495	-48
TCCGTCGAAGATTTAATAAGGTTAACTTTA	3	273	0	ATTTAATAAG	    0.973417	-28
          **********

Masking position 5
Map Score:   3.29062

Number of sites scoring better than the average of aligned sites = 36
Number in coding regions = 17
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 19
Fraction of orfs with sites within 600 bp upstream = 0.00305172


Motif number 4

CATATCTCTGGTTTCAGGGTCCGGATTTTT	2	39	1	GTTTCAGGGT	    0.997234	-30
          GTTTCAGGGCAAAAATCCGG	2	59	0	GTTTCAGGGC	    0.996711	-10
TAAATGAAGTTTTTCAGGTTTCCTTATTAA	3	85	0	TTTTCAGGTT	    0.979782	-216
          **********

Masking position 6
Map Score:   2.31606

Number of sites scoring better than the average of aligned sites = 56
Number in coding regions = 50
Number in noncoding regions = 6
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 5

       GTTTCAGGGCAAAAATCCGGACC	2	56	0	TCAGGGCAAA	    0.900067	-13
AAAAATCATTCCAGGCCACAGGGAAGTGCC	3	50	0	CCAGGCCACA	    0.994536	-251
AAAAATAAATGCAGGACAATAAAAACAGTT	3	121	1	GCAGGACAAT	    0.920466	-180
CAAATCCCGGCCAGTCCACTCAAAACTGTT	3	156	0	CCAGTCCACT	    0.963899	-145
TTGGCATGGCGGAGGCCCCGGGTTCAAATC	3	180	0	GGAGGCCCCG	    0.937353	-121
GGGGCCTCCGCCATGCCAAGGCGACGCTCT	3	191	1	CCATGCCAAG	    0.966319	-110
ACCTGAGCTACCAGCCCCAACAAAGTATAC	3	225	1	CCAGCCCCAA	    0.969315	-76
          **********

Masking position 3
Map Score:   2.93777

Number of sites scoring better than the average of aligned sites = 785
Number in coding regions = 722
Number in noncoding regions = 63
Number of orfs with sites within 600 bp upstream = 39
Fraction of orfs with sites within 600 bp upstream = 0.00626405


Motif number 6

          **********

No masking
Map Score:   -7.8627e-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:   -7.8627e-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:   -7.8627e-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