AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i061_Glutamate_Synthase_mtub_reg_300.orf -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -g0.66 -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 =  	0.66
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	gltB	300	gltB

Motif number 1

GTGGCCAGCAACCGACCGTATCGTCACATG	1	12	0	ACCGACCGTA	    0.871317	-289
TTGCTGGCCACGCGGCAGCTACGGTGCCGC	1	31	1	CGCGGCAGCT	    0.596972	-270
GCGGCAGCTACGGTGCCGCCGGCTGACGAG	1	42	1	CGGTGCCGCC	     0.99067	-259
CCAATACTAACTCGTCAGCCGGCGGCACCG	1	52	0	CTCGTCAGCC	    0.969202	-249
GGGGCTTCGTCCGTGCAGCAGTGAACGCTT	1	149	0	CCGTGCAGCA	    0.986681	-152
CGGACGAAGCCCCGACCGGATCACGCCCGC	1	166	1	CCCGACCGGA	    0.974869	-135
CGCCCGCTTGACGGACAGCCTATCGACAAG	1	189	1	ACGGACAGCC	     0.95744	-112
CGGGCAAGACCCCTTCGGTCTTGTCGATAG	1	208	0	CCCTTCGGTC	    0.861166	-93
GGGTCTTGCCCGCTACCTCCGGGTGCGGCC	1	226	1	CGCTACCTCC	    0.942447	-75
GCGGATTCGACGGGGCCGCACCCGGAGGTA	1	239	0	CGGGGCCGCA	    0.986842	-62
AGACTTTCTGCGCGGCCGCCTTTGCGGATT	1	262	0	CGCGGCCGCC	    0.733412	-39
ACCCACCTAACCCTTCAGCAGACTTTCTGC	1	281	0	CCCTTCAGCA	    0.982752	-20
          **********

Masking position 6
Map Score:   23.1979

Number of sites scoring better than the average of aligned sites = 30007
Number in coding regions = 28229
Number in noncoding regions = 1778
Number of orfs with sites within 600 bp upstream = 1000
Fraction of orfs with sites within 600 bp upstream = 0.160617


Motif number 2

     GCATGTGACGATACGGTCGGTTGCT	1	6	1	TGACGATACG	    0.803095	-295
GGTCGGTTGCTGGCCACGCGGCAGCTACGG	1	25	1	TGGCCACGCG	    0.968696	-276
ACTCGTCAGCCGGCGGCACCGTAGCTGCCG	1	43	0	CGGCGGCACC	    0.975378	-258
TAAAACGATATGACAAAACCCGCTTGACAT	1	92	0	TGACAAAACC	    0.942963	-209
GAATCGGACTCGACAAGTCGTAAAACGATA	1	112	0	CGACAAGTCG	    0.871099	-189
TCCGATTCCAGGGCCAAGCGTTCACTGCTG	1	134	1	GGGCCAAGCG	    0.980184	-167
ACTGCTGCACGGACGAAGCCCCGACCGGAT	1	157	1	GGACGAAGCC	    0.986291	-144
AGCCCCGACCGGATCACGCCCGCTTGACGG	1	173	1	GGATCACGCC	    0.891883	-128
GACAGCCTATCGACAAGACCGAAGGGGTCT	1	202	1	CGACAAGACC	     0.97217	-99
CGGAGGTAGCGGGCAAGACCCCTTCGGTCT	1	217	0	GGGCAAGACC	    0.984515	-84
GGATTCGACGGGGCCGCACCCGGAGGTAGC	1	237	0	GGGCCGCACC	    0.975478	-64
GGTGCGGCCCCGTCGAATCCGCAAAGGCGG	1	247	1	CGTCGAATCC	     0.80135	-54
          **********

Masking position 9
Map Score:   16.7644

Number of sites scoring better than the average of aligned sites = 21268
Number in coding regions = 20065
Number in noncoding regions = 1203
Number of orfs with sites within 600 bp upstream = 750
Fraction of orfs with sites within 600 bp upstream = 0.120463


Motif number 3

GTCGGTTGCTGGCCACGCGGCAGCTACGGT	1	26	1	GGCCACGCGG	    0.995246	-275
AATACTAACTCGTCAGCCGGCGGCACCGTA	1	50	0	CGTCAGCCGG	    0.986252	-251
AAAGTTGGCATGTCAAGCGGGTTTTGTCAT	1	83	1	TGTCAAGCGG	    0.997248	-218
CCGATTCCAGGGCCAAGCGTTCACTGCTGC	1	135	1	GGCCAAGCGT	    0.986285	-166
ATAGGCTGTCCGTCAAGCGGGCGTGATCCG	1	182	0	CGTCAAGCGG	    0.998195	-119
CCTTCGGTCTTGTCGATAGGCTGTCCGTCA	1	197	0	TGTCGATAGG	     0.79713	-104
          **********

Masking position 4
Map Score:   8.20589

Number of sites scoring better than the average of aligned sites = 2041
Number in coding regions = 1853
Number in noncoding regions = 188
Number of orfs with sites within 600 bp upstream = 167
Fraction of orfs with sites within 600 bp upstream = 0.026823


Motif number 4

          **********

No masking
Map Score:   7.91135e-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:   7.91135e-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:   7.91135e-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