AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i113_Amino_Acid_Transport_4_hpyl_reg_300.orf -o113_hpyl_300.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

    GGAATTTCTTTTTTAAACCCTAGTTT	1	7	1	TCTTTTTTAA	    0.959682	-34
    AAAAACTCCTTAATAAACTAGGGTTT	1	25	0	TCCTTAATAA	    0.941742	-16
GCTGATAGTCCCTTTAATAAA         	2	2	0	CCTTTAATAA	    0.973262	-20
AAAAGCATTTTCTATAATAAGCCATAATAA	3	65	1	TCTATAATAA	    0.965082	-236
GCTTGCAAGCCCTTTTATTATGGCTTATTA	3	79	0	CCTTTTATTA	    0.947585	-222
TTTGTTGTCATCAATTTTAAAGCTACCACT	3	110	0	TCAATTTTAA	    0.863043	-191
ATATTTTTTACCCATATTTAGAAATTCTTA	3	165	0	CCCATATTTA	    0.881462	-136
TATACAATACCTTATAATAAGATGAAAATT	3	192	1	CTTATAATAA	    0.706883	-109
CGTTTTGCGCTCATTTTTTATTTCTTTATT	3	227	1	TCATTTTTTA	    0.815931	-74
ATTTTTTATTTCTTTATTAATTTGATTGCA	3	239	1	TCTTTATTAA	    0.965082	-62
TGTTATGTCAGCTATTATTATGCAATCAAA	3	259	0	GCTATTATTA	    0.812057	-42
          **********

Masking position 10
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

         AAAAACTCCTTAATAAACTAGGGT	1	27	0	AAAACCTAAT	    0.895946	-14
CATTGCCACTAAAAGAGGGCAAAGCCGCAATCT	3	13	0	AAAAGGGAAA	    0.970014	-288
GAGTGTCTGTAAAAATGCTCAAAAGCATTTTCT	3	45	1	AAAAGCTAAA	    0.991483	-256
AAGCCATAATAAAAGGGCTTGCAAGCGAGTGGT	3	83	1	AAAAGCTGCA	    0.945312	-218
TGGTAGCTTTAAAATTGATGACAACAAAGCCTA	3	112	1	AAAAGATACA	    0.902493	-189
ATTGATGACAACAAAGCCTAAAACTCAAACAAA	3	125	1	ACAACCTAAA	    0.966852	-176
AAACTCAAACAAAACCCGTTTAAGAATTTCTAA	3	145	1	AAAACGTTAA	    0.808619	-156
AAGAATTTCTAAATATGGGTAAAAAATATACAA	3	166	1	AAATGGGAAA	     0.88921	-135
TAAAAAATATACAATACCTTATAATAAGATGAA	3	185	1	ACAACCTATA	    0.839419	-116
AAGAAATAAAAAATGAGCGCAAAACGCCATGAA	3	220	0	AAATGCGAAA	    0.947618	-81
TGATTGCATAATAATAGCTGACATAACACATCA	3	261	1	ATAAGCTACA	    0.928907	-40
          ****  *** ***

Masking position 3
Map Score:   8.10367

Number of sites scoring better than the average of aligned sites = 3014
Number in coding regions = 2632
Number in noncoding regions = 382
Number of orfs with sites within 600 bp upstream = 260
Fraction of orfs with sites within 600 bp upstream = 0.0417604


Motif number 3

AACTAGGGTTTAAAAAAGAAATTCC     	1	6	0	TAAAAAAGAA	    0.893976	-35
AACCCTAGTTTATTAAGGAGTTTTT     	1	26	1	TATTAAGGAG	    0.939941	-15
        TTTATTAAAGGGACTATCAGC 	2	3	1	TATTAAAGGG	    0.989413	-19
TCATTGCCACTAAAAGAGGGCAAAGCCGCA	3	17	0	TAAAAGAGGG	    0.925984	-284
TATTATGGCTTATTATAGAAAATGCTTTTG	3	64	0	TATTATAGAA	    0.908852	-237
TAATAAGCCATAATAAAAGGGCTTGCAAGC	3	79	1	TAATAAAAGG	     0.95531	-222
ATTTTCATCTTATTATAAGGTATTGTATAT	3	191	0	TATTATAAGG	    0.902702	-110
GCAATCAAATTAATAAAGAAATAAAAAATG	3	238	0	TAATAAAGAA	    0.958387	-63
          **********

Masking position 5
Map Score:   7.43528

Number of sites scoring better than the average of aligned sites = 645
Number in coding regions = 516
Number in noncoding regions = 129
Number of orfs with sites within 600 bp upstream = 110
Fraction of orfs with sites within 600 bp upstream = 0.0176678


Motif number 4

          GCTGATAGTCCCTTTAATAAA 	2	10	0	GCTGATAGCC	    0.903505	-12
GCCACTAAAAGAGGGCAAAGCCGCAATCTGT 	3	10	0	GAGGGCAACC	    0.977647	-291
GCTACCACTCGCTTGCAAGCCCTTTTATTATG	3	87	0	GCTTGCAACC	    0.983421	-214
CTTTAAAATTGATGACAACAAAGCCTAAAACT	3	118	1	GATGACAAAA	     0.82371	-183
TGACAACAAAGCCTAAAACTCAAACAAAACCC	3	130	1	GCCTAAAACA	    0.876553	-171
CTTATAATAAGATGAAAATTCATGGCGTTTTG	3	202	1	GATGAAAACA	    0.967792	-99
TAAAAAATGAGCGCAAAACGCCATGAATTTTC	3	215	0	GCGCAAAACC	     0.93773	-86
CATAATAATAGCTGACATAACACATCATCATA	3	267	1	GCTGACATCA	    0.943759	-34
          GATTGAAACTCCTATGATGATG	3	289	0	GATTGAAACC	    0.950086	-12
          ********  **

Masking position 7
Map Score:   3.18124

Number of sites scoring better than the average of aligned sites = 853
Number in coding regions = 802
Number in noncoding regions = 51
Number of orfs with sites within 600 bp upstream = 41
Fraction of orfs with sites within 600 bp upstream = 0.00658529


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


Motif number 7

          **********

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