AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i129_Transmembrane_Transport_3_hpyl_reg_300.orf -o129_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	RHP01395	225	AE000511
#2	RHP01396	21	AE000511

Motif number 1

ATCCTTCTTGTTGAATTAAAGTTACACCCTAAG	1	16	1	TTGTTAAAGT	    0.971729	-210
GATCGGTTATTTTTCTAAAAGTTTTAATTTTTT	1	48	1	TTTTAAAAGT	    0.992728	-178
AATCTTCATCTTTGATAAAAAATTAAAACTTTT	1	64	0	TTTTAAAAAT	    0.985102	-162
AGTGAAAATGTTGGTTAAATACTAATAAGTGGG	1	101	1	TTGTAAATAT	    0.972122	-125
TAAAAATTTGTATTTTAAAAGTTTGAGGCGGTT	1	150	0	TATTAAAAGT	    0.982752	-76
TACCTATTTGTATCTTAAAAATTTGTATTTTAA	1	165	0	TATTAAAAAT	     0.96593	-61
AGAACTCCCTTTGATTAAATGATTGGAATTGGT	1	203	0	TTGTAAATGT	    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

ATTAAAGTTACACCCTAAGATCGGTTATTT	1	30	1	CACCCTAAGA	    0.992604	-196
CCAACATTTTCACTCTAAAATCTTCATCTT	1	85	0	CACTCTAAAA	    0.982932	-141
AAGTGGGATACACCCACAAAACAAACCGCC	1	127	1	CACCCACAAA	    0.992912	-99
ACAAAACAAACCGCCTCAAACTTTTAAAAT	1	142	1	CCGCCTCAAA	    0.987252	-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 3

TAACCGATCTTAGGGTGTAACTTTAATTCAAC	1	25	0	TAGGTGAACT	    0.979754	-201
TCTTTGATAAAAAATTAAAACTTTTAGAAAAA	1	57	0	AAAATAAACT	    0.926755	-169
ATTTTTTATCAAAGATGAAGATTTTAGAGTGA	1	74	1	AAAGTGAGAT	    0.932424	-152
ATGAAGATTTTAGAGTGAAAATGTTGGTTAAA	1	88	1	TAGATGAAAT	    0.973768	-138
CTCAAACTTTTAAAATACAAATTTTTAAGATA	1	156	1	TAAATAAAAT	    0.966074	-70
TACAAATTTTTAAGATACAAATAGGTATAATC	1	171	1	TAAGTAAAAT	    0.978155	-55
          **** ** ****

Masking position 6
Map Score:   2.63856

Number of sites scoring better than the average of aligned sites = 106
Number in coding regions = 86
Number in noncoding regions = 20
Number of orfs with sites within 600 bp upstream = 17
Fraction of orfs with sites within 600 bp upstream = 0.00273049


Motif number 4

    AATAAATCCTTCTTGTTGAATTAAAGT	1	7	1	TCCTTCTTTT	     0.95574	-219
CACCCTAAGATCGGTTATTTTTCTAAAAGTT	1	40	1	TCGGTTATTT	    0.946025	-186
TGTGGGTGTATCCCACTTATTAGTATTTAAC	1	114	0	TCCCACTTTT	    0.963067	-112
AAAGTTTGAGGCGGTTTGTTTTGTGGGTGTA	1	135	0	GCGGTTTGTT	    0.955627	-91
     AGAACTCCCTTTGATTAAATGATTGG	1	210	0	TCCCTTTGTT	    0.988478	-16
       TGCTCGCCTTTTTTATGCGTT   	2	8	0	TCGCCTTTTT	       0.979	-14
          ******** **

Masking position 10
Map Score:   1.33555

Number of sites scoring better than the average of aligned sites = 469
Number in coding regions = 426
Number in noncoding regions = 43
Number of orfs with sites within 600 bp upstream = 42
Fraction of orfs with sites within 600 bp upstream = 0.0067459


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