AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -inagC_tpal_opreg_100.orf -g0.528 -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 =  	0.528
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	TP0861	236	glucosamine-fructose-6-phosphate aminotransferase (glmS)

Motif number 1

CCATGCCCATCCGTTGCCTTGCTGCACATCGC	1	11	0	CCTTGCCTTC	    0.966265	-226
TCGCCTGTGACCTGTGGGTTACCTTGCTCGTT	1	45	1	CCGTGGGTTC	     0.99495	-192
GGTTACCTTGCTCGTTCGTCGGGTCTCCCCTT	1	61	1	CTGTTCGTCG	    0.914148	-176
GTCGGGTCTCCCCTTGGGGGAGGTGGTGAGTC	1	78	1	CCTTGGGGGG	    0.982395	-159
GGTGAGTCTCCCTGTTGGTGCGCTGGACCGTA	1	102	1	CCGTTGGTGG	    0.993938	-135
GTGCGCTGGACCGTAGCCTGCGAGGCGGCTCG	1	119	1	CCTAGCCTGG	    0.950654	-118
TGCGAGGCGGCTCGTGGCTTGGTTGAGTCAGA	1	137	1	CTGTGGCTTG	    0.988597	-100
ATGGTTCCTACGCGTGCGTGTGTTCTGTGGGT	1	169	1	CGGTGCGTGG	    0.997003	-68
GTGCGTGTGTTCTGTGGGTTTGAGTTTAACGT	1	182	1	TCGTGGGTTG	    0.984702	-55
AACGTTCTCCCGTGTGCTTTTGCACTGAAAAG	1	209	1	CGGTGCTTTG	    0.971269	-28
          ** ******* *

Masking position 5
Map Score:   14.5689

Number of sites scoring better than the average of aligned sites = 1040
Number in coding regions = 942
Number in noncoding regions = 98
Number of orfs with sites within 600 bp upstream = 72
Fraction of orfs with sites within 600 bp upstream = 0.0115644


Motif number 2

GCGATGTGCAGCAAGGCAACGGATGGGCAT	1	11	1	GCAAGGCAAC	     0.97681	-226
CAACGGATGGGCATGGGATCGCCTGTGACC	1	27	1	GCATGGGATC	    0.995837	-210
GCATGGGATCGCCTGTGACCTGTGGGTTAC	1	37	1	GCCTGTGACC	     0.98339	-200
CGACGAACGAGCAAGGTAACCCACAGGTCA	1	52	0	GCAAGGTAAC	    0.966008	-185
CCCTGTTGGTGCGCTGGACCGTAGCCTGCG	1	111	1	GCGCTGGACC	    0.975929	-126
ACACACGCACGCGTAGGAACCATTCTGACT	1	162	0	GCGTAGGAAC	    0.988148	-75
TCCTACGCGTGCGTGTGTTCTGTGGGTTTG	1	174	1	GCGTGTGTTC	    0.955158	-63
          **********

Masking position 2
Map Score:   8.08502

Number of sites scoring better than the average of aligned sites = 365
Number in coding regions = 340
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 3

CTCGTTCGTCGGGTCTCCCCTTGGGGGAGG	1	71	1	GGGTCTCCCC	    0.994533	-166
GGGAGACTCACCACCTCCCCCAAGGGGAGA	1	84	0	CCACCTCCCC	    0.991931	-153
GGGAGGTGGTGAGTCTCCCTGTTGGTGCGC	1	95	1	GAGTCTCCCT	    0.976608	-142
AAGCCACGAGCCGCCTCGCAGGCTACGGTC	1	127	0	CCGCCTCGCA	    0.980721	-110
TTGAGTTTAACGTTCTCCCGTGTGCTTTTG	1	201	1	CGTTCTCCCG	     0.98402	-36
          **********

Masking position 6
Map Score:   3.14393

Number of sites scoring better than the average of aligned sites = 224
Number in coding regions = 189
Number in noncoding regions = 35
Number of orfs with sites within 600 bp upstream = 25
Fraction of orfs with sites within 600 bp upstream = 0.00401542


Motif number 4

          **********

No masking
Map Score:   -2.17836e-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 5

          **********

No masking
Map Score:   -2.17836e-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:   -2.17836e-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