AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -imetR_mjan_opreg_300.orf -g0.314 -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 =  	0.314
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	MJ0138	49	cobyric acid synthase (cbiP)
#2	MJ1597	226	serine hydroxymethyltransferase (glyA)

Motif number 1

AATATTTGTTATAAAAATTTCAAATTGGGA	1	16	0	ATAAAAATTT	    0.981936	-34
GGATATCACCAAAAATATTTGTTATAAAAA	1	29	0	AAAAATATTT	     0.91854	-21
GACACTATATAAAAAAGTTTTTGGTGCTGT	2	13	0	AAAAAAGTTT	      0.9615	-214
AGTGTCTTTCAAAAACATTTTGAAGTAACC	2	37	1	AAAAACATTT	    0.973531	-190
ATATTTGACAATAAATATTTAAATGCCTTC	2	92	0	ATAAATATTT	    0.986212	-135
AAGTTTATTAATAAATATTTGACAATAAAT	2	106	0	ATAAATATTT	    0.986212	-121
TTCAAAATTAATTAAAGTTTATTAATAAAT	2	120	0	ATTAAAGTTT	    0.946232	-107
ATTAATACTTAAAAATATCTTTAAACTATA	2	155	0	AAAAATATCT	    0.920764	-72
AATATACCGTATTAATACTTAAAAATATCT	2	165	0	ATTAATACTT	    0.892117	-62
TATCCCTCTTATTAACGTTTAATAGAAATA	2	204	0	ATTAACGTTT	    0.949993	-23
          **********

Masking position 5
Map Score:   20.9723

Number of sites scoring better than the average of aligned sites = 768
Number in coding regions = 510
Number in noncoding regions = 258
Number of orfs with sites within 600 bp upstream = 238
Fraction of orfs with sites within 600 bp upstream = 0.0382268


Motif number 2

      TGGATATCACCAAAAATATTTGTTA	1	35	0	TACACCAAAA	    0.975019	-15
       AGACAGCACCAAAAACTTTTTTAT	2	4	1	CACACCAAAA	    0.963326	-223
TTTTATATAGTGTCTTTCAAAAACATTTTGA	2	29	1	TGCTTTCAAA	    0.953034	-198
AAGCTACTGGTTACTTCAAAATGTTTTTGAA	2	44	0	TTCTTCAAAA	     0.97592	-183
AGCTTATGAACACCTTCCAAAGGAAGGCATT	2	70	1	CACTTCCAAA	    0.983708	-157
TAAACTATACTGTCTTCAAAATTAATTAAAG	2	133	0	TGCTTCAAAA	    0.991035	-94
TACTTAAAAATATCTTTAAACTATACTGTCT	2	149	0	TACTTTAAAC	    0.917984	-78
          ** ********

Masking position 9
Map Score:   5.97819

Number of sites scoring better than the average of aligned sites = 642
Number in coding regions = 555
Number in noncoding regions = 87
Number of orfs with sites within 600 bp upstream = 97
Fraction of orfs with sites within 600 bp upstream = 0.0155798


Motif number 3

TGTTTTTGAAAGACACTATATAAAAAAGTT	2	24	0	AGACACTATA	    0.993172	-203
ATATTTATTAATAAACTTTAATTAATTTTG	2	118	1	ATAAACTTTA	    0.896989	-109
TTAATTTTGAAGACAGTATAGTTTAAAGAT	2	139	1	AGACAGTATA	    0.990085	-88
TTAAGTATTAATACGGTATATTTATTGTTT	2	173	1	ATACGGTATA	      0.9523	-54
TAATAGAAATAGAAACAATAAATATACCGT	2	185	0	AGAAACAATA	    0.951505	-42
          **********

Masking position 3
Map Score:   3.99615

Number of sites scoring better than the average of aligned sites = 114
Number in coding regions = 89
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 30
Fraction of orfs with sites within 600 bp upstream = 0.0048185


Motif number 4

          TTATATCCCAATTTGAAATT	1	1	1	TTATATCCCA	    0.987475	-49
CAATAAATATTTAAATGCCTTCCTTTGGAA	2	84	0	TTAAATGCCT	    0.977258	-143
          TTTTATCCCTCTTATTAACG	2	217	0	TTTTATCCCT	    0.987511	-10
          **********

Masking position 5
Map Score:   0.36219

Number of sites scoring better than the average of aligned sites = 83
Number in coding regions = 76
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 5

          **********

No masking
Map Score:   -1.17788e-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:   -1.17788e-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:   -1.17788e-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