AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i129_Transmembrane_Transport_3_hpyl_reg_100.orf -o129_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	RHP01395	225	AE000511
#2	RHP01396	21	AE000511

Motif number 1

CTTAGGGTGTAACTTTAATTCAACAAGAAGGAT	1	16	0	ACTTTAACAA	    0.971729	-210
AAAAAATTAAAACTTTTAGAAAAATAACCGATC	1	48	0	ACTTTTAAAA	    0.992728	-178
AAAAGTTTTAATTTTTTATCAAAGATGAAGATT	1	64	1	ATTTTTAAAA	    0.985102	-162
CCCACTTATTAGTATTTAACCAACATTTTCACT	1	101	0	ATATTTACAA	    0.972122	-125
AACCGCCTCAAACTTTTAAAATACAAATTTTTA	1	150	1	ACTTTTAATA	    0.982752	-76
TTAAAATACAAATTTTTAAGATACAAATAGGTA	1	165	1	ATTTTTAATA	     0.96593	-61
ACCAATTCCAATCATTTAATCAAAGGGAGTTCT	1	203	1	ACATTTACAA	    0.986237	-23
          * ******  ***

Masking position 8
Map Score:   10.4012

Number of sites scoring better than the average of aligned sites = 426
Number in coding regions = 328
Number in noncoding regions = 98
Number of orfs with sites within 600 bp upstream = 84
Fraction of orfs with sites within 600 bp upstream = 0.0134918


Motif number 2

ACTTTAATTCAACAAGAAGGATTTATT       	1	4	0	AAAGAGATTT	    0.933029	-222
ATCTTTGATAAAAAATTAAAACTTTTAGAAAAAT	1	56	0	AAATTAACTT	    0.867745	-170
ATTTTTTATCAAAGATGAAGATTTTAGAGTGAAA	1	74	1	AAATGAATTT	     0.87615	-152
GGTGTATCCCACTTATTAGTATTTAACCAACATT	1	107	0	ACATTGATTT	    0.986149	-119
TTTGTATCTTAAAAATTTGTATTTTAAAAGTTTG	1	158	0	AAATTGATTT	    0.970235	-68
TGGTGATTATACCTATTTGTATCTTAAAAATTTG	1	173	0	ACATTGATCT	    0.974287	-53
CCTTTGATTAAATGATTGGAATTGGTGATTATAC	1	195	0	AAATTGATTG	    0.982607	-31
          **  *** * ****

Masking position 5
Map Score:   4.57276

Number of sites scoring better than the average of aligned sites = 219
Number in coding regions = 178
Number in noncoding regions = 41
Number of orfs with sites within 600 bp upstream = 38
Fraction of orfs with sites within 600 bp upstream = 0.00610344


Motif number 3

ATTAAAGTTACACCCTAAGATCGGTTATTT	1	30	1	CACCCTAAGA	    0.992302	-196
CCAACATTTTCACTCTAAAATCTTCATCTT	1	85	0	CACTCTAAAA	    0.982242	-141
AAGTGGGATACACCCACAAAACAAACCGCC	1	127	1	CACCCACAAA	    0.992622	-99
ACAAAACAAACCGCCTCAAACTTTTAAAAT	1	142	1	CCGCCTCAAA	    0.986735	-84
          **********

Masking position 8
Map Score:   3.13676

Number of sites scoring better than the average of aligned sites = 281
Number in coding regions = 261
Number in noncoding regions = 20
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


Motif number 4

ACCCTAAGATCGGTTATTTTTCTAAAAGTT	1	41	1	CGGTTATTTT	    0.975121	-185
AAGTTTGAGGCGGTTTGTTTTGTGGGTGTA	1	135	0	CGGTTTGTTT	    0.993514	-91
    AGAACTCCCTTTGATTAAATGATTGG	1	210	0	CCCTTTGATT	    0.957657	-16
      TGCTCGCCTTTTTTATGCGTT   	2	8	0	CGCCTTTTTT	    0.983077	-14
          **********

Masking position 5
Map Score:   1.24451

Number of sites scoring better than the average of aligned sites = 365
Number in coding regions = 344
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 5

          **********

No masking
Map Score:   -4.09683e-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:   -4.09683e-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:   -4.09683e-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