AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i160_Porphyrin_Biosynthesis_aquae_reg_100.orf -o160_aquae_100.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	RAA01210	157	Aquifex_aeolicus
#2	RAA01123	300	Aquifex_aeolicus

Motif number 1

GGTAAGCCGGAGTGGCGGAACTGGCAGACGCGC	1	53	1	AGGCGGACTG	    0.990249	-105
GCCGTCTTGAGGGGACGGTGCCCTTTACGGGCG	1	84	1	GGGCGGTCCC	    0.695267	-74
GCCGGAGGCGGGAGTCGAACCCGCACGCCCGTA	1	109	0	GGGCGAACCG	    0.992948	-49
GGGATTTTGTGGTGCCGGAGGCGGGAGTCGAAC	1	122	0	GGGCGGAGCG	    0.998353	-36
CAATTGCCAAGGAGCCGGAGCCCAAAAAGGGCT	2	194	1	GGGCGGACCC	    0.991313	-107
          ** * **** ***

Masking position 7
Map Score:   8.51013

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	1	12	1	TAAAGGGCTT	    0.996101	-146
CGCACGCCCGTAAAGGGCACCGTCCCCTCA	1	91	0	TAAAGGGCAC	    0.987703	-67
 TTGATTATTTTAAGGGATTTTGTGGTGCC	1	139	0	TTAAGGGATT	    0.950921	-19
AGATTGAAAATCAAGGGCATAAATTTTTAC	2	88	0	TCAAGGGCAT	    0.990529	-213
CCGGAGCCCAAAAAGGGCTTTGTTTAGTAT	2	208	1	AAAAGGGCTT	    0.987285	-93
          **********

Masking position 4
Map Score:   6.99622

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

ATAAAATAAAAATCTTAGGTAAGCCGGAGTG	1	36	1	AACTTAGGTA	    0.805892	-122
GCGGTTCTGCAAACTTGAGTATATCATTGTA	2	60	1	AACTTGAGTA	    0.968895	-241
CAAGGGCATAAATTTTTACAATGATATACTC	2	76	0	AATTTTACAA	    0.808528	-225
CATAGCTAAAAAGATTGAAAATCAAGGGCAT	2	98	0	AAATTGAAAA	    0.890493	-203
ATGGTAAGTGAACCTTAATAAGTGATGCTTT	2	160	0	AACTTAATAA	    0.871275	-141
AGCTTGGAAAAAACTTGAAAATGTTTTAAAA	2	237	0	AACTTGAAAA	    0.984299	-64
ACCCTGACAAAAGCTTGGAAAAAACTTGAAA	2	248	0	AACTTGGAAA	    0.968398	-53
CTTCTAAACAAACCCTGACAAAAGCTTGGAA	2	259	0	AACCTGACAA	    0.940519	-42
TTAGAAGGAAAAGTTTTAGAATTTGGAT   	2	283	1	AATTTTAGAA	    0.860157	-18
          ** ********

Masking position 6
Map Score:   4.75186

Number of sites scoring better than the average of aligned sites = 695
Number in coding regions = 642
Number in noncoding regions = 53
Number of orfs with sites within 600 bp upstream = 53
Fraction of orfs with sites within 600 bp upstream = 0.00851269


Motif number 4

GCCAAATAAAGGGCTTTTTTATAAAATAAA	1	16	1	GGGCTTTTTT	    0.995289	-142
ATTATTTTAAGGGATTTTGTGGTGCCGGAG	1	135	0	GGGATTTTGT	    0.982879	-23
AGCCCAAAAAGGGCTTTGTTTAGTATTTTA	2	212	1	GGGCTTTGTT	    0.989603	-89
AGTTTTTTCCAAGCTTTTGTCAGGGTTTGT	2	253	1	AAGCTTTTGT	    0.893335	-48
GCTTTTGTCAGGGTTTGTTTAGAAGGAAAA	2	265	1	GGGTTTGTTT	    0.959931	-36
          **********

Masking position 5
Map Score:   3.38233

Number of sites scoring better than the average of aligned sites = 203
Number in coding regions = 188
Number in noncoding regions = 15
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 5

CTGCCAGTTCCGCCACTCCGGCTTACCTAAGA	1	48	0	CGCACTCCGC	     0.97775	-110
GGCACCGTCCCCTCAAGACGGCGCGTCTGCCA	1	74	0	CCCAAGACGC	    0.976978	-84
GGAGTCGAACCCGCACGCCCGTAAAGGGCACC	1	100	0	CCCACGCCGT	    0.976567	-58
CCGCCTCCGGCACCACAAAATCCCTTAAAATA	1	131	1	CACACAAATC	    0.808527	-27
  TTATTAGACACCTAACCTTCACGAAACGAA	2	9	1	CACTAACCTC	    0.961739	-292
ATGTTAATTTCCGCTAACCCGCGGTTCTGCAA	2	40	1	CCCTAACCGC	    0.987898	-261
GATTTCAATACATCACACCATCAAAGCATCAC	2	138	1	CACACACCTC	     0.99169	-163
          ** ****** **

Masking position 4
Map Score:   2.58996

Number of sites scoring better than the average of aligned sites = 305
Number in coding regions = 266
Number in noncoding regions = 39
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 6

          **********

No masking
Map Score:   3.93231e-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:   3.93231e-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 8

          **********

No masking
Map Score:   3.93231e-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