AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -imalT_aquae_opreg_300.orf -g0.435 -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 =  	0.435
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	glgP	110	glycogen phosphorylase
#2	gltX	279	glutamyl-tRNA synthetase

Motif number 1

GTGTAAGCAGTTTTTTAAAATGAATCTTGTG	1	22	0	TTTTTTAAAT	    0.796951	-89
TACTTGTATTTTATAGTAAATCCGCGGGCTA	1	90	0	TTATAGTAAT	    0.969097	-21
CTCCCTGTTTTTGTATAAAATCTATAGCCCT	2	48	1	TTGTATAAAT	     0.96215	-232
GGAATTCTCCTTGTTGAAATTGACGGTGAAG	2	93	0	TTGTTGAAAT	    0.970409	-187
AACTTTGACGTTGTAGTAAACATAAGGAGGG	2	144	0	TTGTAGTAAC	    0.960387	-136
TTTGTATGGTTTGTAAAAACTTTGACGTTGT	2	161	0	TTGTAAAAAT	    0.885606	-119
TTTCTTCAGGGTATATTAATTGAAGCCTTAC	2	210	1	GTATATTAAT	    0.822121	-70
ATGATAAGTTTTATTGTAATTCAAAGGTTAA	2	248	1	TTATTGTAAT	    0.962225	-32
    GAGAGTTTATTTTAACCTTTGAATTAC	2	263	0	TTATTTTAAC	     0.88699	-17
          ********* *

Masking position 4
Map Score:   7.35311

Number of sites scoring better than the average of aligned sites = 181
Number in coding regions = 150
Number in noncoding regions = 31
Number of orfs with sites within 600 bp upstream = 40
Fraction of orfs with sites within 600 bp upstream = 0.00642467


Motif number 2

TAAAATGAATCTTGTGAGGTCACTCAA      	1	5	0	CTGAGGTCAC	    0.932862	-106
AAACTGCTTACACAGGCGGCTTCTGTCCCCGTA	1	40	1	CAGCGGCTTC	     0.73226	-71
CCGCGTATCTATGATACGGGGACAGAAGCCGCC	1	54	0	ATACGGGGAC	    0.961507	-57
TTTTATAGTAAATCCGCGGGCTAAAACCGCGTA	1	80	0	AAGCGGGCTA	    0.968373	-31
AGGTTCAACCCATAGAAGGGCAAATATTCACCG	2	12	0	CAAAGGGCAA	    0.961131	-268
AGCGGAAGAAATAGAAAGGGCTATAGATTTTAT	2	62	0	ATAAGGGCTA	    0.969816	-218
TCCTTGTTGAAATTGACGGTGAAGCGGAAGAAA	2	84	0	AAACGGTGAA	    0.869455	-196
TGTAGTAAACATAAGGAGGGCACAGGTTTCACA	2	131	0	ATGAGGGCAC	     0.98312	-149
CAAACCATACAAAGTACAGGCTCCTTGACCTTT	2	179	1	AAACAGGCTC	    0.810403	-101
ATATACCCTGAAGAAAAGGTCAAGGAGCCTGTA	2	193	0	AAAAGGTCAA	    0.949688	-87
TATCATGAACATGGTAAGGCTTCAATTAATATA	2	221	0	ATAAGGCTTC	    0.836964	-59
TTTTATTGTAATTCAAAGGTTAAAATAAACTCT	2	256	1	ATAAGGTTAA	    0.841923	-24
          **   ********

Masking position 9
Map Score:   7.20215

Number of sites scoring better than the average of aligned sites = 1046
Number in coding regions = 977
Number in noncoding regions = 69
Number of orfs with sites within 600 bp upstream = 58
Fraction of orfs with sites within 600 bp upstream = 0.00931577


Motif number 3

ATTCATTTTAAAAAACTGCTTACACAGGCG	1	28	1	AAAAACTGCT	    0.951397	-83
ATCCGCGGGCTAAAACCGCGTATCTATGAT	1	72	0	TAAAACCGCG	    0.995308	-39
TATTTTATAGTAAATCCGCGGGCTAAAACC	1	85	0	TAAATCCGCG	    0.988229	-26
GATTTTATACAAAAACAGGGAGTGGAGGTT	2	40	0	AAAAACAGGG	    0.966681	-240
          **********

Masking position 4
Map Score:   1.48977

Number of sites scoring better than the average of aligned sites = 73
Number in coding regions = 68
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 4

          **********

No masking
Map Score:   2.43208e-15

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:   2.43208e-15

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:   2.43208e-15

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