AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i307_mixed21_hpyl_reg_100.orf -o307_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	RHP01463	37	AE000511
#2	RHP01464	263	AE000511

Motif number 1

TTAATCCCATTAAATTAAAAATAGTGTC     	1	20	1	TAATTAAAAA	    0.805316	-18
TTTTAAGTTTAAATTTAAAAATAAAGGATACTT	2	12	0	AAATTAAAAA	    0.803695	-252
TTTTAAATTTAAACTTAAAATTATAGCATAAGT	2	25	1	AAATTAAAAA	    0.968582	-239
TAAGTCATAATAAATTAAAACCACTCTAAAGTT	2	53	1	TAATTAAAAA	    0.989549	-211
AAACCACTCTAAAGTTAAATAAAATTTGACTTT	2	70	1	AAATTAAATA	    0.927718	-194
AAAATTTGACTTTGTTAAAAAAATTATGATAGC	2	90	1	TTTTTAAAAA	    0.934219	-174
AAGCTAAAGCATTCTTAAAAAATTAGTGTAACC	2	181	0	ATTTTAAAAT	     0.78965	-83
TTGTTGCAATTAAGATAAAAATACAAAAAGCTA	2	208	0	TAAATAAAAA	     0.94281	-56
GAAATCTCTTTTTGTTAAAAGGAAATTTA    	2	245	1	TTTTTAAAAA	    0.967438	-19
          *** ******  *

Masking position 7
Map Score:   15.3015

Number of sites scoring better than the average of aligned sites = 314
Number in coding regions = 201
Number in noncoding regions = 113
Number of orfs with sites within 600 bp upstream = 103
Fraction of orfs with sites within 600 bp upstream = 0.0165435


Motif number 2

         CAAGTATCCTTTATTTTTAAAT	2	2	1	AAGTTCCTTT	    0.992373	-262
TATTTAACTTTAGAGTGGTTTTAATTTATTA	2	60	0	TAGATGGTTT	    0.903733	-204
GGCCACTTATTAGCATCTTTTGGTTACACTA	2	160	1	TAGCTCTTTT	    0.947907	-104
CTAATTTTTTAAGAATGCTTTAGCTTTTTGT	2	188	1	AAGATGCTTT	    0.979238	-76
AACAAACTAGAAATCTCTTTTTGTTAAAAGG	2	236	1	AAATTCTTTT	    0.910555	-28
         TAAATTTCCTTTTAACAAAAAG	2	252	0	AAATTCCTTT	    0.977301	-12
          **** ******

Masking position 6
Map Score:   3.02619

Number of sites scoring better than the average of aligned sites = 254
Number in coding regions = 205
Number in noncoding regions = 49
Number of orfs with sites within 600 bp upstream = 45
Fraction of orfs with sites within 600 bp upstream = 0.00722775


Motif number 3

ATGCCACAAGTGTTGAATTTCGTAATTCTTTGCTATG	2	122	0	TTGATGTATT	    0.991959	-142
ATTCAACACTTGTGGCATGGGCCACTTATTAGCATCT	2	141	1	TTGATCCATT	    0.989181	-123
TATTAGCATCTTTTGGTTACACTAATTTTTTAAGAAT	2	167	1	TTGTTCTATT	    0.991772	-97
TTAAGAATGCTTTAGCTTTTTGTATTTTTATCTTAAT	2	196	1	TTGTTGTATT	    0.994375	-68
AAAAGAGATTTCTAGTTTGTTGCAATTAAGATAAAAA	2	220	0	TTGTTGCATT	    0.994782	-44
          * * * **   *** **

Masking position 8
Map Score:   3.38408

Number of sites scoring better than the average of aligned sites = 33
Number in coding regions = 28
Number in noncoding regions = 5
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 4

CACTATTTTTAATTTAATGGGATTAATTAGGG	1	14	0	AATTAATGGA	    0.954578	-24
GAGTGGTTTTAATTTATTATGACTTATGCTAT	2	47	0	AATTATTTGA	    0.985258	-217
TCTAAAGTTAAATAAAATTTGACTTTGTTAAA	2	77	1	AATAAATTGA	    0.972834	-187
GACTTTGTTAAAAAAATTATGATAGCATAGCA	2	97	1	AAAAATTTGA	     0.97272	-167
ATAGCATAGCAAAGAATTACGAAATTCAACAC	2	118	1	AAAAATTCGA	    0.954561	-146
TGGTTACACTAATTTTTTAAGAATGCTTTAGC	2	180	1	AATTTTTAGA	     0.86714	-84
          *** **** ***

Masking position 8
Map Score:   1.64183

Number of sites scoring better than the average of aligned sites = 89
Number in coding regions = 75
Number in noncoding regions = 14
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


Motif number 5

        AATCCCTAATTAATCCCATTAA	1	3	1	TCCCTAATTA	    0.955772	-35
CTAATTAATCCCATTAAATTAAAAATAGTG	1	16	1	CCATTAAATT	    0.862482	-22
         GACACTATTTTTAATTTAATG	1	27	0	ACACTATTTT	    0.922961	-11
    CAAGTATCCTTTATTTTTAAATTTAA	2	7	1	TCCTTTATTT	    0.879623	-257
GTGGCATGGGCCACTTATTAGCATCTTTTG	2	152	1	CCACTTATTA	     0.95581	-112
TCTTTTGGTTACACTAATTTTTTAAGAATG	2	175	1	ACACTAATTT	    0.978458	-89
          **********

Masking position 5
Map Score:   1.79051

Number of sites scoring better than the average of aligned sites = 486
Number in coding regions = 431
Number in noncoding regions = 55
Number of orfs with sites within 600 bp upstream = 45
Fraction of orfs with sites within 600 bp upstream = 0.00722775


Motif number 6

          **********

No masking
Map Score:   -4.80737e-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:   -4.80737e-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 8

          **********

No masking
Map Score:   -4.80737e-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