AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -ifruR_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	MTH184	125	isocitrate dehydrogenase
#2	MTH1041	195	triosephosphate isomerase
#3	MTH1119	132	ribosomal protein L10
#4	MTH1386	300	3-isopropylmalate dehydratase, LeuD subunit

Motif number 1

GCATGGGATAATATTTTAAGGCTGTAATGA	1	65	0	ATATTTTAAG	    0.831309	-61
TTTACAATTTAATTTTTCACTGGTTTAACA	2	18	1	AATTTTTCAC	    0.934249	-178
ATGTATCCTTATATTTTCAGGTTATCTATT	3	24	1	ATATTTTCAG	    0.980495	-109
CATTTCATAGTTATTCTCACAGGATCACAG	3	102	1	TTATTCTCAC	    0.884142	-31
AATAACTTATTAGTTTTCAGGAGCTCACCA	4	57	0	TAGTTTTCAG	     0.83492	-244
TTTTACATCTATATTTTCACCCGGCCCTAT	4	120	0	ATATTTTCAC	    0.984193	-181
AATTCAGACGAGTTTTTCAGTATGAAGGCG	4	148	1	AGTTTTTCAG	    0.870613	-153
TGATGTCCCCATATGTTCACTGGATAACTG	4	183	0	ATATGTTCAC	    0.935682	-118
AAAGAGGCTCTAATTTTCACAGACTGCCCC	4	220	1	TAATTTTCAC	    0.953183	-81
          **********

Masking position 4
Map Score:   6.96101

Number of sites scoring better than the average of aligned sites = 170
Number in coding regions = 122
Number in noncoding regions = 48
Number of orfs with sites within 600 bp upstream = 46
Fraction of orfs with sites within 600 bp upstream = 0.00738837


Motif number 2

CTGAATGATCTGCATGGGATAATATTTTAAGG	1	74	0	TGAGGGATAA	    0.974171	-52
TAAATTCCTCTTGAAGTGTTCTCATGAAGCTG	1	103	0	TTAGTGTTCT	    0.861921	-23
AATTTAATTTTTCACTGGTTTAACATCATCCA	2	23	1	TTATGGTTTA	    0.810924	-173
CCCCACATAGTGAAGGTGTTAAATGCAGAAAG	2	59	0	TGAGTGTTAA	    0.931101	-137
CGGGAGTTGTTGAAGGGGTTCATGAATGAATT	2	112	0	TGAGGGTTCA	    0.984929	-84
        GATTAATGGGATATCTCATAGTAT	2	182	0	TTAGGGATAT	     0.93372	-14
TCCCCATATGTTCACTGGATAACTGTCTTTCG	4	176	0	TTATGGATAA	    0.897906	-125
AGCAGAATAATTGAAGGGTTCATAAAGGTTCC	4	264	0	TTAGGGTTCA	    0.986715	-37
          ** * *******

Masking position 4
Map Score:   5.39777

Number of sites scoring better than the average of aligned sites = 337
Number in coding regions = 286
Number in noncoding regions = 51
Number of orfs with sites within 600 bp upstream = 44
Fraction of orfs with sites within 600 bp upstream = 0.00706714


Motif number 3

TTTTCACTGGTTTAACATCATCCAACAGCTT	2	31	1	TTAACATCAT	     0.76494	-165
CCCGCACGGATGTCACAGCATATTTTATAAT	2	140	1	TTCACAGCAT	    0.986764	-56
TAATGGGATATCTCATAGTATGGTTGAGGTG	2	172	0	TTCATAGTAT	    0.881743	-24
TCATAGTTATTCTCACAGGATCACAGGAGGA	3	106	1	TTCACAGGAT	    0.975909	-27
ACGCCCCGTCTATAAAAGACTTGGTGAGCTC	4	36	1	TTAAAAGACT	    0.806581	-265
TAAATCTTATTATCAAAGTATTTATAGGGCC	4	97	1	TTCAAAGTAT	    0.929318	-204
AGGCTCTAATTTTCACAGACTGCCCCATGGA	4	224	1	TTCACAGACT	    0.975062	-77
TCTATCCTCCTTTAGCAGAATAATTGAAGGG	4	278	0	TTAGCAGAAT	    0.877602	-23
          * *********

Masking position 7
Map Score:   2.88322

Number of sites scoring better than the average of aligned sites = 206
Number in coding regions = 179
Number in noncoding regions = 27
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 4

    ATAAAAGGGAATATGAAGACATCATAA	1	7	1	GGGATATGAA	    0.894495	-119
GGAATATGAAGACATCATAAAAACCCCCAGC	1	18	1	GACTCATAAA	    0.880979	-108
CTCTTGAAGTGTTCTCATGAAGCTGAATGAT	1	97	0	GTTTCATGAA	    0.927418	-29
GTTGTTGAAGGGGTTCATGAATGAATTTGCC	2	108	0	GGGTCATGAA	    0.993388	-88
AGAGTTAATAGATAACCTGAAAATATAAGGA	3	29	0	GATACCTGAA	    0.904321	-104
AAGACTTGGTGAGCTCCTGAAAACTAATAAG	4	51	1	GAGTCCTGAA	    0.984686	-250
AATAATTGAAGGGTTCATAAAGGTTCCAGCA	4	260	0	GGGTCATAAA	    0.976183	-41
          *** *******

Masking position 10
Map Score:   3.19461

Number of sites scoring better than the average of aligned sites = 449
Number in coding regions = 412
Number in noncoding regions = 37
Number of orfs with sites within 600 bp upstream = 30
Fraction of orfs with sites within 600 bp upstream = 0.0048185


Motif number 5

          **********

No masking
Map Score:   3.64809e-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 6

          **********

No masking
Map Score:   3.64809e-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:   3.64809e-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