AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00480_mjan_reg_100.orf -o00480_mjan_100.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.31 -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 =  	0.31
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	MJ0720	194	3-isopropylmalate dehydrogenase 1 (leuB1)
#2	MJ1596	226	3-isopropylmalate dehydrogenase 2 (leuB2)

Motif number 1

TTAATCACCAAAATGATTTTAAAATTAAAAAT	1	11	1	AAAATTTTAA	    0.958252	-184
ACTTCCCTTAAAAGTTTTATTTTTAATTTTAA	1	29	0	AAATTTATTT	    0.710506	-166
TAAGGGAAGTAATGCATTATAAGTATTTATAT	1	51	1	AATATTATAA	    0.796238	-144
AAAACAACACAAAATATAAATACTTATAATGC	1	64	0	AAAATAAATA	    0.907503	-131
ACCATATCAAAAATGATTAAAATACTCAACAA	1	96	0	AAAATTAAAA	    0.865565	-99
TTGGTGACTTAAACCATATCAAAAATGATTAA	1	108	0	AAAATATCAA	     0.72586	-87
AGTCACCAACAAAACATTTTTATGTGAAAGTA	1	131	1	AAAATTTTTA	    0.977794	-64
TTTTTATGTGAAAGTATTTTTATTAATATTGC	1	147	1	AAAATTTTTA	     0.97807	-48
TTATCACCAAAAAGATTAATTATAGCAATATT	1	171	0	AAATTAATTA	    0.960217	-24
TATTTCTATTAAACGTTAATAAGAGGGATAAA	2	12	0	AAATTAATAA	    0.918998	-215
ATAGAAATAGAAACAATAAATATACCGTATTA	2	35	1	AAAATAAATA	    0.914683	-192
TTAATACTTAAAAATATCTTTAAACTATACTG	2	64	1	AAAATCTTTA	    0.865875	-163
ATTTATTAATAAACTTTAATTAATTTTGAAGA	2	96	0	AAATTAATTA	    0.960227	-131
ATTTATTGTCAAATATTTATTAATAAACTTTA	2	110	0	AAATTTATTA	    0.967158	-117
AATATTTGACAATAAATATTTAAATGCCTTCC	2	125	1	AATATATTTA	    0.839174	-102
GTGTCTTTCAAAAACATTTTGAAGTAACCAGT	2	178	0	AAAATTTTGA	    0.894172	-49
GACAGCACCAAAAACTTTTTTATATAGTGTCT	2	204	0	AAATTTTTTA	    0.964835	-23
          ***  *******

Masking position 7
Map Score:   26.4579

Number of sites scoring better than the average of aligned sites = 1680
Number in coding regions = 1147
Number in noncoding regions = 533
Number of orfs with sites within 600 bp upstream = 419
Fraction of orfs with sites within 600 bp upstream = 0.0672984


Motif number 2

      TTAATCACCAAAATGATTTTAAAA	1	5	1	TCACCAAAAT	    0.991312	-190
ATTAAAATACTCAACAAAAAACAACACAAA	1	83	0	TCAACAAAAA	    0.986217	-112
ATGGTTTAAGTCACCAACAAAACATTTTTA	1	123	1	TCACCAACAA	    0.994366	-72
AAAAATACTTTCACATAAAAATGTTTTGTT	1	138	0	TCACATAAAA	    0.936928	-57
     ACTTATCACCAAAAAGATTAATTAT	1	180	0	TCACCAAAAA	    0.996202	-15
ATAGTGTCTTTCAAAAACATTTTGAAGTAA	2	183	0	TCAAAAACAT	    0.851058	-44
     AGACAGCACCAAAAACTTTTTTATA	2	212	0	GCACCAAAAA	    0.987761	-15
          **********

Masking position 7
Map Score:   13.9059

Number of sites scoring better than the average of aligned sites = 292
Number in coding regions = 200
Number in noncoding regions = 92
Number of orfs with sites within 600 bp upstream = 101
Fraction of orfs with sites within 600 bp upstream = 0.0162223


Motif number 3

TGATTTTAAAATTAAAAATAAAACTTTTAA	1	24	1	ATTAAAAATA	    0.960605	-171
CATTACTTCCCTTAAAAGTTTTATTTTTAA	1	35	0	CTTAAAAGTT	    0.948261	-160
GAAGTAATGCATTATAAGTATTTATATTTT	1	56	1	ATTATAAGTA	    0.685207	-139
AATACTTTCACATAAAAATGTTTTGTTGGT	1	135	0	CATAAAAATG	     0.94001	-60
TAGCAATATTAATAAAAATACTTTCACATA	1	151	0	AATAAAAATA	     0.88512	-44
CGTATTAATACTTAAAAATATCTTTAAACT	2	60	1	CTTAAAAATA	    0.986737	-167
TTAAAAATATCTTTAAACTATACTGTCTTC	2	71	1	CTTTAAACTA	    0.826169	-156
ACTATACTGTCTTCAAAATTAATTAAAGTT	2	87	1	CTTCAAAATT	    0.948256	-140
CTACTGGTTACTTCAAAATGTTTTTGAAAG	2	176	1	CTTCAAAATG	     0.96591	-51
          **********

Masking position 6
Map Score:   8.9236

Number of sites scoring better than the average of aligned sites = 651
Number in coding regions = 487
Number in noncoding regions = 164
Number of orfs with sites within 600 bp upstream = 166
Fraction of orfs with sites within 600 bp upstream = 0.0266624


Motif number 4

TAAGGGAAGTAATGCATTATAAGTATTTATA	1	51	1	AATGCATATA	     0.96939	-144
AACAAAAAACAACACAAAATATAAATACTTA	1	70	0	AACACAAATA	    0.947328	-125
TTTAAGTATTAATACGGTATATTTATTGTTT	2	45	0	AATACGTATA	    0.953269	-182
ATTAATTTTGAAGACAGTATAGTTTAAAGAT	2	79	0	AAGACATATA	    0.989905	-148
ATGTTTTTGAAAGACACTATATAAAAAAGTT	2	193	1	AAGACATATA	    0.990865	-34
          ****** ****

Masking position 9
Map Score:   3.88971

Number of sites scoring better than the average of aligned sites = 65
Number in coding regions = 43
Number in noncoding regions = 22
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 5

          **********

No masking
Map Score:   -7.01005e-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:   -7.01005e-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:   -7.01005e-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