AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i149_Thioredoxin_hpyl_reg_100.orf -o149_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	RHP00243	173	AE000511
#2	RHP00247	88	AE000511

Motif number 1

AGAATTTTTAAATCAGCCTTAAAA        	1	3	0	AATAGCTTAA	    0.969896	-171
CTTCTATGCAAACGCCCACCAACAGCACCACG	1	37	0	AACCCCCCAA	    0.977274	-137
AAAAAACTTCAAACAGCTCTAATTCTTCTATG	1	61	0	AAAAGCCTAA	    0.981734	-113
CATTCAATGAAAAACCCGCTAAAAAAACTTCA	1	82	0	AAACCCCTAA	    0.990603	-92
TTGCGGTTATAAAGCCCCTCCATTCAATGAAA	1	102	0	AAACCCTCCA	    0.958008	-72
CGCTTGTAGCAATAACCATTCAAGCTTGCGGT	1	127	0	AATACCTTCA	    0.948036	-47
TGGTTATTGCTACAAGCGCTAAAAAGCATGTT	1	141	1	TACAGCCTAA	    0.872601	-33
AATGTTAATGAAATCGCATTTACTTTCTGTAA	2	15	0	AAACGCTTTA	    0.944605	-74
AAGCTAATATAATTCTCGTTAATCAAAATCAT	2	50	1	AATCTCTTAA	    0.923836	-39
          *** *** ****

Masking position 2
Map Score:   8.26931

Number of sites scoring better than the average of aligned sites = 2086
Number in coding regions = 1872
Number in noncoding regions = 214
Number of orfs with sites within 600 bp upstream = 159
Fraction of orfs with sites within 600 bp upstream = 0.0255381


Motif number 2

GCACCACGCCAGAATTTTTAAATCAGCCTT	1	15	0	AGAATTTTTA	    0.952585	-159
ACCGCAAGCTTGAATGGTTATTGCTACAAG	1	127	1	TGAATGGTTA	     0.93501	-47
AGCGCTAAAAAGCATGTTAAGATCAGTTT 	1	155	1	AGCATGTTAA	    0.985475	-19
  ATTTTTACAGAAAGTAAATGCGATTTCA	2	9	1	AGAAAGTAAA	    0.932947	-80
TATTAGCTTAAGAATGTTAATGAAATCGCA	2	29	0	AGAATGTTAA	    0.993375	-60
          **********

Masking position 4
Map Score:   3.65133

Number of sites scoring better than the average of aligned sites = 142
Number in coding regions = 118
Number in noncoding regions = 24
Number of orfs with sites within 600 bp upstream = 24
Fraction of orfs with sites within 600 bp upstream = 0.0038548


Motif number 3

          TTTTAAGGCTGATTTAAAAA	1	1	1	TTTTAAGGCT	    0.964246	-173
TGCATAGAAGAATTAGAGCTGTTTGAAGTT	1	59	1	AATTAGAGCT	    0.916278	-115
TTTGAAGTTTTTTTAGCGGGTTTTTCATTG	1	80	1	TTTTAGCGGG	    0.977541	-94
TTAACATGCTTTTTAGCGCTTGTAGCAATA	1	145	0	TTTTAGCGCT	    0.992945	-29
AAAATCATATATTTAGGAGTAACTA     	2	74	1	ATTTAGGAGT	    0.928163	-15
          **********

Masking position 5
Map Score:   1.33784

Number of sites scoring better than the average of aligned sites = 1191
Number in coding regions = 1093
Number in noncoding regions = 98
Number of orfs with sites within 600 bp upstream = 70
Fraction of orfs with sites within 600 bp upstream = 0.0112432


Motif number 4

          **********

No masking
Map Score:   3.22176e-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:   3.22176e-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:   3.22176e-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