AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i160_Porphyrin_Biosynthesis_aquae_reg_300.orf -o160_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

Input sequences:
#1	RAA01200	29	Aquifex_aeolicus
#2	RAA01210	157	Aquifex_aeolicus
#3	RAA01123	300	Aquifex_aeolicus

Motif number 1

GCGCGTCTGCCAGTTCCGCCACTCCGGCTTACC	2	53	0	CAGTCCGCCT	    0.990803	-105
CGCCCGTAAAGGGCACCGTCCCCTCAAGACGGC	2	84	0	GGGACCGCCC	    0.688341	-74
TACGGGCGTGCGGGTTCGACTCCCGCCTCCGGC	2	109	1	CGGTTCGCCC	    0.992744	-49
GTTCGACTCCCGCCTCCGGCACCACAAAATCCC	2	122	1	CGCTCCGCCC	    0.998403	-36
AGCCCTTTTTGGGCTCCGGCTCCTTGGCAATTG	3	194	0	GGGTCCGCCC	    0.990855	-107
          *** **** * **

Masking position 7
Map Score:   8.31376

Number of sites scoring better than the average of aligned sites = 25
Number in coding regions = 16
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 6
Fraction of orfs with sites within 600 bp upstream = 0.000963701


Motif number 2

ACTTGCCAAATAAAGGGCTTTTTTATAAAA	2	12	1	TAAAGGGCTT	    0.995993	-146
CGCACGCCCGTAAAGGGCACCGTCCCCTCA	2	91	0	TAAAGGGCAC	    0.987366	-67
 TTGATTATTTTAAGGGATTTTGTGGTGCC	2	139	0	TTAAGGGATT	    0.949629	-19
AGATTGAAAATCAAGGGCATAAATTTTTAC	3	88	0	TCAAGGGCAT	    0.990269	-213
CCGGAGCCCAAAAAGGGCTTTGTTTAGTAT	3	208	1	AAAAGGGCTT	    0.986937	-93
          **********

Masking position 4
Map Score:   6.76912

Number of sites scoring better than the average of aligned sites = 202
Number in coding regions = 186
Number in noncoding regions = 16
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 3

          TTGATTATTCTTTTCAGATAGG	1	1	1	TTGATATTTT	    0.969616	-29
          TTGATTATTTTAAGGGATTTTG	2	146	0	TTGATATTTA	    0.983351	-12
GGCATAAATTTTTACAATGATATACTCAAGTT	3	71	0	TTTAAATGTA	    0.944909	-230
TCCTTGGCAATTGAATATGGTAAGTGAACCTT	3	175	0	TTGATATGTA	    0.989232	-126
AAGGGCTTTGTTTAGTATTTTAAAACATTTTC	3	220	1	TTTATATTTA	    0.952862	-81
TGGAAAAAACTTGAAAATGTTTTAAAATACTA	3	232	0	TTGAAATGTT	    0.964548	-69
          **** **** **

Masking position 7
Map Score:   5.18958

Number of sites scoring better than the average of aligned sites = 20
Number in coding regions = 12
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 4

TTTATTTTATAAAAAAGCCCTTTATTTGGC	2	16	0	AAAAAAGCCC	    0.975754	-142
CTCCGGCACCACAAAATCCCTTAAAATAAT	2	135	1	ACAAAATCCC	    0.923816	-23
 TTATTAGACACCTAACCTTCACGAAACGA	3	10	1	ACCTAACCTT	    0.798724	-291
ACATCACACCATCAAAGCATCACTTATTAA	3	147	1	ATCAAAGCAT	    0.839226	-154
TAAAATACTAAACAAAGCCCTTTTTGGGCT	3	212	0	AACAAAGCCC	    0.988112	-89
ACAAACCCTGACAAAAGCTTGGAAAAAACT	3	253	0	ACAAAAGCTT	    0.946543	-48
TTTCCTTCTAAACAAACCCTGACAAAAGCT	3	264	0	AACAAACCCT	    0.972955	-37
          **********

Masking position 5
Map Score:   4.07434

Number of sites scoring better than the average of aligned sites = 326
Number in coding regions = 307
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 18
Fraction of orfs with sites within 600 bp upstream = 0.0028911


Motif number 5

          **********

No masking
Map Score:   2.29806e-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:   2.29806e-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 7

          **********

No masking
Map Score:   2.29806e-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