AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i129_Transmembrane_Transport_3_aquae_reg_300.orf -o129_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	RAA01040	264	Aquifex_aeolicus
#2	RAA00172	40	Aquifex_aeolicus
#3	RAA00567	43	Aquifex_aeolicus

Motif number 1

CCATTTCTGGAAAGGATAAC          	1	1	0	AAAGGATAAC	    0.962122	-264
AACCGCTTAAAAAGCCTATAATACATATTG	1	40	0	AAAGCCTATA	    0.890175	-225
CTTTCGTTGTAAAGGAAACCGCTTAAAAAG	1	56	0	AAAGGAAACC	    0.955538	-209
CTTTACAACGAAAGCATATACAGAAGAGCC	1	72	1	AAAGCATATA	    0.947349	-193
AAGAGCCAAAAAAGGGAAAAATCCCATAGT	1	95	1	AAAGGGAAAA	    0.956702	-170
ACCTCACGGGAAAGGTTACTATGGGATTTT	1	112	0	AAAGGTTACT	     0.87476	-153
AGTAAACGATAAAGAAAACAAGAACGCTGA	1	151	0	AAAGAAAACA	    0.837243	-114
TCAGCCTTGTAAAAGTAAACGATAAAGAAA	1	164	0	AAAAGTAAAC	    0.864696	-101
GGGAAATCGTAAAGAGAATAGCCCCTTCAG	1	190	0	AAAGAGAATA	    0.813117	-75
TTTTTTAGAGTAAGGTTAAATTAGTAGTT 	1	246	1	TAAGGTTAAA	    0.827897	-19
GAATTACAATAAAACTTATC          	2	1	0	AAAACTTATC	    0.811832	-40
ATTGTAATTCAAAGGTTAAAATAAACTCTC	2	21	1	AAAGGTTAAA	    0.978357	-20
ACCAGCTTTAAAAACTAATAATATAATACG	3	13	0	AAAACTAATA	    0.819071	-31
          **********

Masking position 3
Map Score:   12.2724

Number of sites scoring better than the average of aligned sites = 2428
Number in coding regions = 2266
Number in noncoding regions = 162
Number of orfs with sites within 600 bp upstream = 128
Fraction of orfs with sites within 600 bp upstream = 0.0205589


Motif number 2

TAGTAACCTTTCCCGTGAGGTTTTTCCTCCTCA	1	121	1	TCCTGAGGTT	    0.964159	-144
TGAGGTTTTTCCTCCTCAGCGTTCTTGTTTTCT	1	136	1	CCCTCAGCTT	    0.998579	-129
AAGAGAATAGCCCCTTCAGCCTTGTAAAAGTAA	1	176	0	CCCTCAGCTT	    0.998614	-89
GATTTCCCACCTTCTCGGGCGTTTCTTCCAGCT	1	212	1	CTCCGGGCTT	    0.978781	-53
   GCTATCACCTCACCAGCTTTAAAAACTAAT	3	24	0	CCCCCAGCTT	    0.998716	-20
          ** * ***** **

Masking position 12
Map Score:   4.9018

Number of sites scoring better than the average of aligned sites = 73
Number in coding regions = 66
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 3

     GTTATCCTTTCCAGAAATGGAACGT	1	6	1	CCTTTCCAGA	    0.963833	-259
GGAGGAAAAACCTCACGGGAAAGGTTACTA	1	121	0	CCTCACGGGA	    0.976993	-144
TGAGGTTTTTCCTCCTCAGCGTTCTTGTTT	1	136	1	CCTCCTCAGC	    0.989777	-129
AAGAGAATAGCCCCTTCAGCCTTGTAAAAG	1	179	0	CCCCTTCAGC	    0.984024	-86
GATTTCCCACCTTCTCGGGCGTTTCTTCCA	1	212	1	CTTCTCGGGC	    0.971557	-53
   GCTATCACCTCACCAGCTTTAAAAACT	3	27	0	CCTCACCAGC	    0.996769	-17
          **********

Masking position 9
Map Score:   6.99794

Number of sites scoring better than the average of aligned sites = 247
Number in coding regions = 222
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 4

CCGTGAGGTTTTTCCTCCTCAGCGTTCTTG	1	133	1	TTTCCTCCTC	    0.977859	-132
AGAATAGCCCCTTCAGCCTTGTAAAAGTAA	1	176	0	CTTCAGCCTT	    0.956745	-89
TCTTTACGATTTCCCACCTTCTCGGGCGTT	1	205	1	TTCCCACCTT	    0.976542	-60
TCGGGCGTTTCTTCCAGCTCTTTTTTAGAG	1	226	1	CTTCCAGCTC	     0.98127	-39
 GAGAGTTTATTTTAACCTTTGAATTACAA	2	22	0	TTTTAACCTT	    0.913428	-19
         GCTATCACCTCACCAGCTTTA	3	33	0	CTATCACCTC	    0.959127	-11
          **********

Masking position 2
Map Score:   3.05032

Number of sites scoring better than the average of aligned sites = 925
Number in coding regions = 841
Number in noncoding regions = 84
Number of orfs with sites within 600 bp upstream = 93
Fraction of orfs with sites within 600 bp upstream = 0.0149374


Motif number 5

          **********

No masking
Map Score:   7.2008e-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:   7.2008e-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:   7.2008e-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