AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i060_Diaminopimelate_Pathway_aquae_reg_300.orf -o060_aquae_300.ace -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -g0.44 -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 =  	0.44
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Purged sequences:
RAA00088	35	Aquifex_aeolicus

Input sequences:
#1	RAA00115	81	Aquifex_aeolicus
#2	RAA00117	33	Aquifex_aeolicus
#3	RAA00083	41	Aquifex_aeolicus
#4	RAA00786	300	Aquifex_aeolicus

Motif number 1

GAGGTAATTTCTTATAAATGTCCACAAAAAC	1	34	1	CTATAAATGT	    0.892017	-48
TATAAATGTCCACAAAAACTTAATTATATCT	1	46	1	CCAAAAACTT	    0.971985	-36
        AACTTAAAAATTTTAAGATATAA	1	69	0	CTAAAAATTT	    0.993031	-13
        AGCACAAAAATTTTATACTTGTT	3	3	1	CCAAAAATTT	    0.983941	-39
TTCCACGACTCCTAAAAATTTTCCATCAGGT	4	32	0	CTAAAAATTT	    0.993031	-269
AAAAAGTTTCCATCAAATTTTCCCGTTGTTT	4	142	0	CTCAAATTTT	    0.892017	-159
ATTATCGTATCTTAAAAAGTTTCCATCAAAT	4	155	0	CTAAAAAGTT	    0.987759	-146
ACATCTTAAAGGTAAAAAGTTCCCTTATAAA	4	209	1	GTAAAAAGTT	    0.912652	-92
AAAAAGTTCCCTTATAAATTTACGGATATTG	4	222	1	CTATAAATTT	    0.975376	-79
CAAAATCGTTCTTAAAATCTTCTATCAATTG	4	255	0	CTAAAATCTT	     0.95732	-46
          * *********

Masking position 6
Map Score:   18.9614

Number of sites scoring better than the average of aligned sites = 104
Number in coding regions = 83
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 24
Fraction of orfs with sites within 600 bp upstream = 0.0038548


Motif number 2

TAAGAAATTACCTCCCCTTCAGGAACCAAGG	1	17	0	CTCCCCTTCA	    0.933885	-65
ATTTCTTATAAATGTCCACAAAAACTTAATT	1	40	1	ATGTCCACAA	    0.944758	-42
          AATCTCCTCCTTTAGAGTTAT	2	23	0	ATCTCCTCCT	    0.976133	-11
          CCTTTCCTCCTTTTAATTAAC	3	31	0	CTTTCCTCCT	    0.972455	-11
ACTCCTAAAAATTTTCCATCAGGTGAAAATA	4	25	0	ATTTCCATCA	     0.98139	-276
TCCATATCTTCATTTCCACGACTCCTAAAAA	4	45	0	CTTTCCACGA	    0.906428	-256
ATCTTTTGGTACTTTCCATATCTTCATTTCC	4	59	0	ATTTCCATAT	    0.929919	-242
TATCTTAAAAAGTTTCCATCAAATTTTCCCG	4	148	0	ATTTCCATCA	     0.98139	-153
AGATGTTTATGGTGTCCTTCACATTGATAAT	4	184	0	GTGTCCTTCA	     0.90408	-117
AAAGGTAAAAAGTTCCCTTATAAATTTACGG	4	216	1	ATTCCCTTAT	    0.858191	-85
     TTCACAACCTCCTCAATTAATTTTTC	4	285	0	ACCTCCTCAA	    0.847904	-16
          * *********

Masking position 6
Map Score:   8.73907

Number of sites scoring better than the average of aligned sites = 1246
Number in coding regions = 1167
Number in noncoding regions = 79
Number of orfs with sites within 600 bp upstream = 80
Fraction of orfs with sites within 600 bp upstream = 0.0128493


Motif number 3

AAAACTTAATTATATCTTAAAATTTTTAAG	1	60	1	TATATCTTAA	    0.942369	-22
TAAAACGGAGCGTATTTTCACCTGATGGAA	4	13	1	CGTATTTTCA	    0.937838	-288
TGGTACTTTCCATATCTTCATTTCCACGAC	4	54	0	CATATCTTCA	    0.981772	-247
TGATAATTATCGTATCTTAAAAAGTTTCCA	4	161	0	CGTATCTTAA	    0.981772	-140
GGACACCATAAACATCTTAAAGGTAAAAAG	4	198	1	AACATCTTAA	    0.928517	-103
CAATTGATAGAAGATTTTAAGAACGATTTT	4	255	1	AAGATTTTAA	    0.814441	-46
          **********

Masking position 5
Map Score:   2.77953

Number of sites scoring better than the average of aligned sites = 84
Number in coding regions = 70
Number in noncoding regions = 14
Number of orfs with sites within 600 bp upstream = 20
Fraction of orfs with sites within 600 bp upstream = 0.00321234


Motif number 4

          **********

No masking
Map Score:   -3.81261e-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:   -3.81261e-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:   -3.81261e-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