AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00480_mjan_reg_300.orf -o00480_mjan_300.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

ATTTTTAATTTTAAAATCATTTTGGTGATTAA	1	11	0	TTAAAATTTT	     0.94612	-184
TTAAAATTAAAAATAAAACTTTTAAGGGAAGT	1	29	1	AAATAAATTT	    0.764093	-166
ATATAAATACTTATAATGCATTACTTCCCTTA	1	51	0	TTATAATATT	      0.7938	-144
GCATTATAAGTATTTATATTTTGTGTTGTTTT	1	64	1	TATTTATTTT	     0.90818	-131
TTGTTGAGTATTTTAATCATTTTTGATATGGT	1	96	1	TTTTAATTTT	     0.89182	-99
TACTTTCACATAAAAATGTTTTGTTGGTGACT	1	131	0	TAAAAATTTT	    0.971377	-64
GCAATATTAATAAAAATACTTTCACATAAAAA	1	147	0	TAAAAATTTT	    0.972672	-48
AATATTGCTATAATTAATCTTTTTGGTGATAA	1	171	1	TAATTAATTT	    0.961122	-24
TTTATCCCTCTTATTAACGTTTAATAGAAATA	2	12	1	TTATTAATTT	    0.897036	-215
TAATACGGTATATTTATTGTTTCTATTTCTAT	2	35	0	TATTTATTTT	    0.933258	-192
AAATATACCGTATTAATACTTAAAAATATCTT	2	52	1	TATTAATTTA	    0.644399	-175
CAGTATAGTTTAAAGATATTTTTAAGTATTAA	2	64	0	TAAAGATTTT	    0.777349	-163
TCTTCAAAATTAATTAAAGTTTATTAATAAAT	2	96	1	TAATTAATTT	    0.961216	-131
TAAAGTTTATTAATAAATATTTGACAATAAAT	2	110	1	TAATAAATTT	    0.967915	-117
GGAAGGCATTTAAATATTTATTGTCAAATATT	2	125	0	TAAATATATT	    0.754679	-102
ACTGGTTACTTCAAAATGTTTTTGAAAGACAC	2	178	1	TCAAAATTTT	    0.890544	-49
AGACACTATATAAAAAAGTTTTTGGTGCTGTC	2	204	1	TAAAAAATTT	      0.9663	-23
          *******  ***

Masking position 6
Map Score:   26.4587

Number of sites scoring better than the average of aligned sites = 1692
Number in coding regions = 1146
Number in noncoding regions = 546
Number of orfs with sites within 600 bp upstream = 425
Fraction of orfs with sites within 600 bp upstream = 0.0682621


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

      TTAATCACCAAAATGATTTTAAAA	1	5	1	TCACCAAAAT	    0.835712	-190
ATGATTTTAAAATTAAAAATAAAACTTTTA	1	23	1	AATTAAAAAT	    0.939002	-172
TGATTAAAATACTCAACAAAAAACAACACA	1	85	0	ACTCAACAAA	    0.755564	-110
ACTTAAACCATATCAAAAATGATTAAAATA	1	104	0	TATCAAAAAT	    0.916445	-91
AAATACTTTCACATAAAAATGTTTTGTTGG	1	136	0	ACATAAAAAT	    0.909372	-59
ATTATAGCAATATTAATAAAAATACTTTCA	1	155	0	TATTAATAAA	    0.687913	-40
CCGTATTAATACTTAAAAATATCTTTAAAC	2	59	1	ACTTAAAAAT	    0.973003	-168
AACTATACTGTCTTCAAAATTAATTAAAGT	2	86	1	TCTTCAAAAT	     0.96253	-141
AATTAAAGTTTATTAATAAATATTTGACAA	2	107	1	TATTAATAAA	    0.687913	-120
GCTACTGGTTACTTCAAAATGTTTTTGAAA	2	175	1	ACTTCAAAAT	    0.962508	-52
          **********

Masking position 6
Map Score:   9.3155

Number of sites scoring better than the average of aligned sites = 1522
Number in coding regions = 1195
Number in noncoding regions = 327
Number of orfs with sites within 600 bp upstream = 288
Fraction of orfs with sites within 600 bp upstream = 0.0462576


Motif number 4

TATAAATACTTATAATGCATTACTTCCCTTA	1	51	0	TATATGCATT	     0.96775	-144
TAAGTATTTATATTTTGTGTTGTTTTTTGTT	1	70	1	TATTTGTGTT	    0.944565	-125
AAACAATAAATATACCGTATTAATACTTAAA	2	45	1	TATACGTATT	    0.952476	-182
ATCTTTAAACTATACTGTCTTCAAAATTAAT	2	79	1	TATATGTCTT	    0.989457	-148
AACTTTTTTATATAGTGTCTTTCAAAAACAT	2	193	0	TATATGTCTT	    0.990366	-34
          **** ******

Masking position 3
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