AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i196_mixed_replication_rec__hpyl_reg_300.orf -o196_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	RHP01073	165	AE000511
#2	RHP01276	248	AE000511
#3	RHP01277	24	AE000511

Motif number 1

CACCCTTTGCTTGACTAAAATCAAATATCT	1	28	0	TTGACTAAAA	    0.976731	-138
GACTAAACGATTCATTAAACCATAAAAACC	1	88	0	TTCATTAAAC	    0.981141	-78
GCATAGAATTTTGACTAAACGATTCATTAA	1	100	0	TTGACTAAAC	    0.971945	-66
GCTACAATCATTCATTAATAGGTATAAACA	1	128	1	TTCATTAATA	    0.908618	-38
AAGCTAATTTTTCACTTAAACGATGCGTTT	2	31	0	TTCACTTAAA	    0.942625	-218
ATCGTTTCACTTCTTTAAAAGTGCTCGTAG	2	75	1	TTCTTTAAAA	    0.958446	-174
GGGAGCGATAATGTTTAAAAACATGCAGAA	2	182	0	ATGTTTAAAA	    0.854878	-67
AAATAAATACTTGCTTAAACACGCTAGGAG	2	221	1	TTGCTTAAAC	    0.928181	-28
          ATCATTTAAAATAAAAGGAA	3	1	1	ATCATTTAAA	    0.862985	-24
          **********

Masking position 6
Map Score:   9.97269

Number of sites scoring better than the average of aligned sites = 772
Number in coding regions = 649
Number in noncoding regions = 123
Number of orfs with sites within 600 bp upstream = 110
Fraction of orfs with sites within 600 bp upstream = 0.0176678


Motif number 2

   GTTTGCATCCTTTGCATAGATATTTGA	1	8	1	TCCTTTGCAT	    0.838484	-158
CTTTGCATAGATATTTGATTTTAGTCAAGC	1	20	1	ATATTTGATT	     0.91336	-146
AGTTGGAACACCCTTTGCTTGACTAAAATC	1	36	0	CCCTTTGCTT	    0.982779	-130
GGTGTTCCAACTCTTTGATTTTTAACGCTG	1	54	1	CTCTTTGATT	    0.933282	-112
ATAGGTATAAACATTTTATTAAAGGCGTTC	1	145	1	ACATTTTATT	     0.92006	-21
GTGAAAAATTAGCTTTTCTTGCTATAATCA	2	46	1	AGCTTTTCTT	    0.947775	-203
CTCCGAGCACACCATTTCTTAATATTCTGC	2	158	1	ACCATTTCTT	    0.871463	-91
GGTAAAATAAATACTTGCTTAAACACGCTA	2	217	1	ATACTTGCTT	    0.797073	-32
ACACGCTAGGAGATTTGATT          	2	239	1	AGATTTGATT	    0.919225	-10
     ATGATTCCTTTTATTTTAAATGAT 	3	10	0	TCCTTTTATT	     0.90803	-15
          **********

Masking position 5
Map Score:   8.86708

Number of sites scoring better than the average of aligned sites = 868
Number in coding regions = 772
Number in noncoding regions = 96
Number of orfs with sites within 600 bp upstream = 76
Fraction of orfs with sites within 600 bp upstream = 0.0122069


Motif number 3

TATTAATGAATGATTGTAGCATAGAATTTT	1	118	0	TGATTGTAGC	     0.99158	-48
AGTGAAACGATGATTATAGCAAGAAAAGCT	2	56	0	TGATTATAGC	    0.975487	-193
TCTTTAAAAGTGCTCGTAGCTCAGCTGAAT	2	86	1	TGCTCGTAGC	    0.990601	-163
GTAGCTCAGCTGAATAGAGCAACAGGTTGC	2	101	1	TGAATAGAGC	    0.939162	-148
AGAAATGGTGTGCTCGGAGGGATTCAAACC	2	147	0	TGCTCGGAGG	    0.974359	-102
TATTTTACCATAATGGGAGCGATAATGTTT	2	196	0	TAATGGGAGC	    0.943834	-53
          **********

Masking position 8
Map Score:   5.201

Number of sites scoring better than the average of aligned sites = 178
Number in coding regions = 168
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 4

       GTTTGCATCCTTTGCATAGATAT	1	4	1	TGCATCCTTT	    0.985511	-162
TGTTATGGTTTTTATGGTTTAATGAATCGT	1	82	1	TTTATGGTTT	    0.890172	-84
TATGGTTTAATGAATCGTTTAGTCAAAATT	1	94	1	TGAATCGTTT	    0.978675	-72
ATAGAAAAAACGCATCGTTTAAGTGAAAAA	2	24	1	CGCATCGTTT	    0.990816	-225
TCTTGCTATAATCATCGTTTCACTTCTTTA	2	62	1	ATCATCGTTT	    0.960932	-187
CTTAATATTCTGCATGTTTTTAAACATTAT	2	175	1	TGCATGTTTT	    0.959979	-74
          **********

Masking position 5
Map Score:   5.02206

Number of sites scoring better than the average of aligned sites = 255
Number in coding regions = 232
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 5

          **********

No masking
Map Score:   -3.88366e-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:   -3.88366e-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:   -3.88366e-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