AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i113_Amino_Acid_Transport_4_hpyl_reg_100.orf -o113_hpyl_100.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -g0.39 -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 =  	0.39
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RHP00357	40	AE000511
#2	RHP00358	21	AE000511
#3	RHP00359	300	AE000511

Motif number 1

AAACTAGGGTTTAAAAAAGAAATTCC    	1	7	0	TTAAAAAAGA	    0.956445	-34
AAACCCTAGTTTATTAAGGAGTTTTT    	1	25	1	TTATTAAGGA	    0.937296	-16
         TTTATTAAAGGGACTATCAGC	2	2	1	TTATTAAAGG	    0.971084	-20
TTATTATGGCTTATTATAGAAAATGCTTTT	3	65	0	TTATTATAGA	    0.962383	-236
TAATAAGCCATAATAAAAGGGCTTGCAAGC	3	79	1	TAATAAAAGG	    0.943429	-222
AGTGGTAGCTTTAAAATTGATGACAACAAA	3	110	1	TTAAAATTGA	    0.853311	-191
TAAGAATTTCTAAATATGGGTAAAAAATAT	3	165	1	TAAATATGGG	    0.872769	-136
AATTTTCATCTTATTATAAGGTATTGTATA	3	192	0	TTATTATAAG	     0.68994	-109
AATAAAGAAATAAAAAATGAGCGCAAAACG	3	227	0	TAAAAAATGA	    0.803525	-74
TGCAATCAAATTAATAAAGAAATAAAAAAT	3	239	0	TTAATAAAGA	    0.962383	-62
TTTGATTGCATAATAATAGCTGACATAACA	3	259	1	TAATAATAGC	    0.799431	-42
          **********

Masking position 6
Map Score:   12.0573

Number of sites scoring better than the average of aligned sites = 1086
Number in coding regions = 839
Number in noncoding regions = 247
Number of orfs with sites within 600 bp upstream = 196
Fraction of orfs with sites within 600 bp upstream = 0.0314809


Motif number 2

          GGAATTTCTTTTTTAAACCC	1	1	1	GGAATTTCTT	    0.868499	-40
TAGTTTATTAAGGAGTTTTT          	1	31	1	AGGAGTTTTT	    0.949936	-10
AATGCTTTTGAGCATTTTTACAGACACTCA	3	44	0	AGCATTTTTA	    0.974192	-257
AATGCTCAAAAGCATTTTCTATAATAAGCC	3	58	1	AGCATTTTCT	    0.967741	-243
AACCCGTTTAAGAATTTCTAAATATGGGTA	3	157	1	AGAATTTCTA	    0.958738	-144
CAAAACGCCATGAATTTTCATCTTATTATA	3	204	0	TGAATTTTCA	    0.890157	-97
ACATCATCATAGGAGTTTCAATC       	3	288	1	AGGAGTTTCA	    0.955882	-13
          **********

Masking position 4
Map Score:   4.71121

Number of sites scoring better than the average of aligned sites = 519
Number in coding regions = 450
Number in noncoding regions = 69
Number of orfs with sites within 600 bp upstream = 70
Fraction of orfs with sites within 600 bp upstream = 0.0112432


Motif number 3

 ACAGATTGCGGCTTTGCCCTCTTTTAGTGGCAA	3	10	1	GGTTTGCTCT	    0.997486	-291
CATAATAAAAGGGCTTGCAAGCGAGTGGTAGCTT	3	87	1	GGCTTGCGCA	    0.961588	-214
TTGAGTTTTAGGCTTTGTTGTCATCAATTTTAAA	3	119	0	GGTTTGTTCT	    0.994354	-182
TTCTTAAACGGGTTTTGTTTGAGTTTTAGGCTTT	3	137	0	GGTTTGTGAT	    0.973284	-164
AAATTCATGGCGTTTTGCGCTCATTTTTTATTTC	3	217	1	CGTTTGCTCT	    0.991205	-84
          ** *****  ** *

Masking position 6
Map Score:   1.94877

Number of sites scoring better than the average of aligned sites = 131
Number in coding regions = 112
Number in noncoding regions = 19
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 4

          **********

No masking
Map Score:   -1.17788e-14

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:   -1.17788e-14

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:   -1.17788e-14

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