AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i320_mixed5_hpyl_reg_100.orf -o320_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	RHP01145	214	AE000511
#2	RHP01148	64	AE000511
#3	RHP01149	66	AE000511
#4	RHP00049	77	AE000511
#5	RHP00050	34	AE000511
#6	RHP00589	61	AE000511

Motif number 1

ATTTTGAGTTTTTAGGAGCAGTTTTT        	1	3	0	TTTAGGATTT	    0.973275	-212
GTCAAGCGATTTTAGGTTAATTTTGAGTTTTTAG	1	22	0	TTTAGGATTT	    0.973275	-193
TGTAGTAGAATTAAGGCAGTGTTTTTGCGTCAAG	1	50	0	TTAAGGTTTT	    0.944746	-165
TTCTACTACATTTGAAATAATTTTTCTTATAAAC	1	74	1	TTTGAAATTT	    0.920239	-141
TTTTTCTCAATTTAGGTTTTGTTTATAAGAAAAA	1	94	0	TTTAGGTTTT	    0.973275	-121
CAATAGCCCCTTTGAATTGAATTTTTTCTCAATT	1	116	0	TTTGAAATTT	    0.920239	-99
GGGCTATTGTTTAAAATTTACATTTTTTAAACGC	1	141	1	TTAAAAAATT	     0.86673	-74
ATTTACATTTTTTAAACGCTATTAGATATAATAA	1	156	1	TTTAAATTTA	    0.880043	-59
ATTGTCCTTATTAAAATAATCATTCGTATTCAAA	2	39	0	TTAAAATATT	     0.86673	-26
AAATATTACCCTTAAAATATTTTT          	3	1	0	CTTAAATTTT	    0.789106	-66
AGGGTAATATTTTAAAAAATTTTTGTATAATCAA	3	23	1	TTTAAATTTT	    0.967218	-44
CCTAATTTAGTTTAAAAGGTTTTTACAAAC    	4	7	0	TTTAAATTTT	    0.967218	-71
TTAAACTAAATTAGGGTAGTATTATAGCATTTAA	4	26	1	TTAGGGTTTA	    0.624445	-52
TTGATAGGGCTTTAGGGGAAAATAG         	4	63	1	TTTAGGAATA	    0.809599	-15
TCCCTTTAAATTAAAACAAAAATTAAAT      	5	5	0	TTAAAAAATT	    0.866731	-30
TTTTAAAGATTTTAAGCTAAAATTTTAGCATACA	6	22	1	TTTAAGAATT	    0.945813	-40
          ******   * ***

Masking position 2
Map Score:   21.6005

Number of sites scoring better than the average of aligned sites = 2433
Number in coding regions = 1914
Number in noncoding regions = 519
Number of orfs with sites within 600 bp upstream = 301
Fraction of orfs with sites within 600 bp upstream = 0.0483456


Motif number 2

TTATAAGAAAAATTATTTCAAATGTAGTAG	1	76	0	AATTATTTCA	    0.861337	-139
CTTTGAATTGAATTTTTTCTCAATTTAGGT	1	111	0	AATTTTTTCT	    0.932088	-104
AACTATCCCTTATTATATCTAATAGCGTTT	1	169	0	TATTATATCT	    0.902179	-46
AAAATGGGCTTATTATAGCTTATTTCATTC	2	12	0	TATTATAGCT	    0.956257	-53
ATTACCCTTAAAATATTTTT          	3	1	0	AAATATTTTT	    0.592628	-66
TATTTTAAAAAATTTTTGTATAATCAACAA	3	30	1	AATTTTTGTA	    0.861391	-37
AATACTACCCTAATTTAGTTTAAAAGGTTT	4	19	0	TAATTTAGTT	    0.720555	-59
ATTAGGGTAGTATTATAGCATTTAATCTTT	4	35	1	TATTATAGCA	    0.908521	-43
      ATTTAATTTTTGTTTTAATTTAAA	5	5	1	AATTTTTGTT	    0.932077	-30
TGTATGCTAAAATTTTAGCTTAAAATCTTT	6	26	0	AATTTTAGCT	    0.969832	-36
          **********

Masking position 6
Map Score:   8.30949

Number of sites scoring better than the average of aligned sites = 962
Number in coding regions = 793
Number in noncoding regions = 169
Number of orfs with sites within 600 bp upstream = 150
Fraction of orfs with sites within 600 bp upstream = 0.0240925


Motif number 3

AAATTAACCTAAAATCGCTTGACGCAAAAA	1	33	1	AAAATCGCTT	    0.851432	-182
AATTTTAAACAATAGCCCCTTTGAATTGAA	1	129	0	AATAGCCCCT	    0.985616	-86
ATAGGTGGTAACTATCCCTTATTATATCTA	1	178	0	ACTATCCCTT	    0.975726	-37
ATAAGCTATAATAAGCCCATTTTGAATACG	2	19	1	ATAAGCCCAT	    0.916209	-46
        CTATTTTCCCCTAAAGCCCTAT	4	66	0	ATTTTCCCCT	    0.921842	-12
        GTTTTATCCCTTTAAATTAAAA	5	23	0	TTTATCCCTT	    0.934326	-12
         CAATAGCCCTTTTTTAAAGAT	6	2	1	AATAGCCCTT	     0.98787	-60
          **********

Masking position 10
Map Score:   5.88429

Number of sites scoring better than the average of aligned sites = 513
Number in coding regions = 447
Number in noncoding regions = 66
Number of orfs with sites within 600 bp upstream = 55
Fraction of orfs with sites within 600 bp upstream = 0.00883392


Motif number 4

AGTAGAATTAAGGCAGTGTTTTTGCGTCAA	1	51	0	AGGCAGTGTT	    0.959411	-164
TTCTCAATTTAGGTTTTGTTTATAAGAAAA	1	95	0	AGGTTTTGTT	    0.923023	-120
AATTCAAAGGGGCTATTGTTTAAAATTTAC	1	132	1	GGCTATTGTT	     0.97056	-83
AATATTTTAAGGGTAATATTTTAAAAAATT	3	14	1	GGGTAATATT	    0.950587	-53
TAAACTCCTTGTGAATTGTTGATTATACAA	3	45	0	GTGAATTGTT	    0.871189	-22
AACTAAATTAGGGTAGTATTATAGCATTTA	4	29	1	GGGTAGTATT	    0.981299	-49
          **********

Masking position 7
Map Score:   1.23726

Number of sites scoring better than the average of aligned sites = 367
Number in coding regions = 316
Number in noncoding regions = 51
Number of orfs with sites within 600 bp upstream = 44
Fraction of orfs with sites within 600 bp upstream = 0.00706714


Motif number 5

          **********

No masking
Map Score:   -5.94424e-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:   -5.94424e-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:   -5.94424e-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