AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i126_Biopolymer_Transport_hpyl_reg_300.orf -o126_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	RHP00530	52	AE000511
#2	RHP00533	22	AE000511
#3	RHP00535	20	AE000511
#4	RHP00538	110	AE000511
#5	RHP00542	23	AE000511
#6	RHP00543	39	AE000511
#7	RHP00544	243	AE000511

Motif number 1

TAAGATATTTATAAAATCCCCTTAAAAGCT     	1	6	0	ATAAAACTAA	    0.987486	-47
CTATCTTAACAAAAAATCGCTTAAAATTTGAGAAT	4	20	0	AAAAAACAAA	    0.946696	-91
CGCATTTGTTATAAAAACATTAACTCTATCTTAAC	4	45	0	ATAAAACACT	    0.927225	-66
TATTTCTTTCCTAAAATCCTACAAAATATTTGAAA	4	82	0	CTAAAACAAA	    0.969689	-29
     TTGAATTAAAAACAAGGAATAAC       	5	6	1	TTAAAACAAT	     0.93812	-18
TACATTATAAATAAAAAAAATGAAGAAATTGAGAT	7	66	0	ATAAAAAAAG	    0.887783	-178
TACCCTTCGCATAAAAACTACATTATAAATAAAAA	7	84	0	ATAAAACTTA	    0.951788	-160
ACAACAAAAAATAAAAAAGGCAAAAAATACCCTTC	7	111	0	ATAAAAAAAA	    0.971318	-133
GGGATTTTAAATACAAACAACAAAAAATAAAAAAG	7	127	0	ATACAACAAA	    0.963417	-117
TTGTTTGTATTTAAAATCCCTATTTTACTGAACTT	7	142	1	TTAAAACTTT	    0.661054	-102
AACTTATTGGATAAAACCTGCTTAAGTTAAATTGA	7	172	1	ATAAAACTAA	    0.987486	-72
TCATTCTATTATAAAATATAAAAAATCAAATCTTA	7	209	1	ATAAAAAAAA	    0.971318	-35
          ****** *    ***

Masking position 6
Map Score:   12.9888

Number of sites scoring better than the average of aligned sites = 1458
Number in coding regions = 1226
Number in noncoding regions = 232
Number of orfs with sites within 600 bp upstream = 206
Fraction of orfs with sites within 600 bp upstream = 0.0330871


Motif number 2

     AGCTTTTAAGGGGATTTTATAAATATCT	1	6	1	TTAAGGGATT	    0.895529	-47
AACTCCCTATTTAAGATATTTATAAAATCCCCT	1	19	0	TTAAGATTAT	    0.939228	-34
CGATTTTTTGTTAAGATAGAGTTAATGTTTTTA	4	36	1	TTAAGATGTT	    0.954211	-75
GTGGTGTGCTTTGAGATGATATTGTGAATTAGG	6	16	1	TTGAGATATT	    0.985678	-24
AAGCACAAGTTTTAGAGAACCATACG       	7	4	0	TTTAGAGAAT	    0.859445	-240
AATGAAGAAATTGAGATAACGATCGATCAGCTG	7	50	0	TTGAGATAAT	    0.977222	-194
TTATAATAGAATGAGATCAATTTAACTTAAGCA	7	190	0	ATGAGATATT	    0.925003	-54
 GATTTTCCTTTAAGATTTGATTTTTTATATTT	7	222	0	TTAAGATTTT	    0.961231	-22
          ******* *  **

Masking position 4
Map Score:   4.52843

Number of sites scoring better than the average of aligned sites = 186
Number in coding regions = 140
Number in noncoding regions = 46
Number of orfs with sites within 600 bp upstream = 52
Fraction of orfs with sites within 600 bp upstream = 0.00835207


Motif number 3

CTCTATCTTAACAAAAAATCGCTTAAAATT	4	27	0	ACAAAAAATC	     0.95584	-84
CTAAAATCCTACAAAATATTTGAAACTCGC	4	77	0	ACAAAATATT	    0.821903	-34
AGGATTTTAGGAAAGAAATAGGTT      	4	97	1	GAAAGAAATA	    0.820947	-14
TGAATTAAAAACAAGGAATAAC        	5	12	1	ACAAGGAATA	    0.889303	-12
CATTATAAATAAAAAAAATGAAGAAATTGA	7	69	0	AAAAAAAATG	    0.855169	-175
TACCCTTCGCATAAAAACTACATTATAAAT	7	89	0	ATAAAAACTA	    0.817635	-155
AATAAAAAAGGCAAAAAATACCCTTCGCAT	7	107	0	GCAAAAAATA	    0.971739	-137
AATACAAACAACAAAAAATAAAAAAGGCAA	7	123	0	ACAAAAAATA	    0.985983	-121
TCATTCTATTATAAAATATAAAAAATCAAA	7	209	1	ATAAAATATA	    0.858437	-35
          **********

Masking position 4
Map Score:   6.39667

Number of sites scoring better than the average of aligned sites = 552
Number in coding regions = 450
Number in noncoding regions = 102
Number of orfs with sites within 600 bp upstream = 89
Fraction of orfs with sites within 600 bp upstream = 0.0142949


Motif number 4

          **********

No masking
Map Score:   1.09013e-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 5

          **********

No masking
Map Score:   1.09013e-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:   1.09013e-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