AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -inarP_pyro_opreg_100.orf -g0.419 -x5 
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 =  	0.419
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	PH1509	300	440aa long hypothetical NADH oxidase
#2	PH1670	300	102aa long hypothetical protein

Motif number 1

AGGAGCATCTCTCCGATTATCTTTATCGCGCA	1	166	0	CTCCATATCT	    0.988179	-135
CGGAGAGATGCTCCTGAACTCTAGACAAAAAA	1	183	1	CTCCGACTCT	    0.945117	-118
TGAACGAATGCCCTCATTTTCTCCCCAACATT	1	240	1	CCCTATTTCT	     0.95274	-61
CTCATTTTCTCCCCAACATTTTAATATCTCTT	1	252	1	CCCCAATTTT	    0.810019	-49
TATCTCTTAACCCTTTCTCTCTTGGGTGGAGA	1	276	1	CCCTTTCTCT	    0.959721	-25
      GGAGATCCTTTTCTCTAGAGGTTTCT	2	5	1	ATCCTTCTCT	      0.7897	-296
GAGGTTTCTCCCCTAATTATCTCGACTTTTGC	2	28	1	CCCTATATCT	    0.978876	-273
TCGACTTTTGCCCCAAGAATCTTTGAGAGGAA	2	49	1	CCCCAAATCT	    0.991165	-252
CAATTGTCAACTCCTTCAATCTTGTTCTCCTT	2	151	1	CTCCTAATCT	    0.967691	-150
GCACTTTCCTCACCCAATATCTTTTCTACGAA	2	236	1	CACCATATCT	    0.962132	-65
          **** * *****

Masking position 10
Map Score:   11.3511

Number of sites scoring better than the average of aligned sites = 537
Number in coding regions = 495
Number in noncoding regions = 42
Number of orfs with sites within 600 bp upstream = 42
Fraction of orfs with sites within 600 bp upstream = 0.0067459


Motif number 2

TAAGGAAGGAAAGGCCAACAAAATGTCAACAT	1	123	1	AAGGCACAAA	       0.987	-178
CCTCCAGTTAAAGGGGAGGCAAATAAGGAACT	2	88	0	AAGGGAGCAA	    0.980801	-213
AAAATAGAATAAGGATAAGCATAAAAGCTCCT	2	117	0	AAGGAAGCAT	    0.934942	-184
ACCAAACTCCAAGGAGAACAAGATTGAAGGAG	2	161	0	AAGGAACAAG	    0.983139	-140
GAAAGTGCTTAAGGAAACCAAAGATGGAACAA	2	212	0	AAGGAACAAA	     0.98598	-89
CCTTTCATCGAAGGGTATTAAATCTTCGTAGC	2	271	1	AAGGGATAAA	    0.950272	-30
     TGGCCAAGGCTACGAAGATTTAATACC	2	284	0	AAGGCAGAAG	    0.984361	-17
          ***** * ****

Masking position 7
Map Score:   6.38674

Number of sites scoring better than the average of aligned sites = 249
Number in coding regions = 220
Number in noncoding regions = 29
Number of orfs with sites within 600 bp upstream = 31
Fraction of orfs with sites within 600 bp upstream = 0.00497912


Motif number 3

CCCTCATAGCGAGCTTCTCAGCTTTTCGGG	1	37	0	GAGCTTCTCA	    0.908192	-264
TTATTTCGATAAACCTCTCCTTATCGAATG	1	96	0	AAACCTCTCC	    0.949223	-205
TTTATCGCGCAAAGATCTCCAAATGTTGAC	1	147	0	AAAGATCTCC	    0.935042	-154
TAGAGTTCAGGAGCATCTCTCCGATTATCT	1	176	0	GAGCATCTCT	    0.915722	-125
GCATTCGTTCAAATTTTTCCTTCATATTTC	1	221	0	AAATTTTTCC	    0.708215	-80
CTCTAGAGAAAAGGATCTCC          	2	1	0	AAGGATCTCC	    0.980414	-300
TTTTCTCTAGAGGTTTCTCCCCTAATTATC	2	19	1	AGGTTTCTCC	    0.946368	-282
GGAACTTATAAAGTTCCTCTCAAAGATTCT	2	64	0	AAGTTCCTCT	    0.894133	-237
ATAAGCATAAAAGCTCCTCCAGTTAAAGGG	2	105	0	AAGCTCCTCC	    0.987057	-196
          **********

Masking position 8
Map Score:   6.05225

Number of sites scoring better than the average of aligned sites = 1070
Number in coding regions = 1007
Number in noncoding regions = 63
Number of orfs with sites within 600 bp upstream = 66
Fraction of orfs with sites within 600 bp upstream = 0.0106007


Motif number 4

ATCTTTTTGACTAAAGAGGATTGACTCCCG	1	11	1	CTAAAGAGGA	     0.78305	-290
ATTGACTCCCGAAAAGCTGAGAAGCTCGCT	1	30	1	GAAAAGCTGA	    0.750333	-271
GAGGTTTATCGAAATAAGGAAGGAAAGGCC	1	109	1	GAAATAAGGA	     0.95347	-192
CAAAGATCTCCAAATGTTGACATTTTGTTG	1	138	0	CAAATGTTGA	     0.86923	-163
AAAACTCACTGAAATATGAAGGAAAAATTT	1	211	1	GAAATATGAA	    0.702721	-90
GAAACCTCTAGAGAAAAGGATCTCC     	2	6	0	GAGAAAAGGA	    0.826218	-295
ATTCTTGGGGCAAAAGTCGAGATAATTAGG	2	39	0	CAAAAGTCGA	    0.873147	-262
AAAGGGGAGGCAAATAAGGAACTTATAAAG	2	81	0	CAAATAAGGA	    0.944998	-220
TTGACAATTGGAAAAATAGAATAAGGATAA	2	131	0	GAAAAATAGA	    0.804971	-170
TTAAGGAAACCAAAGATGGAACAATAATTC	2	206	0	CAAAGATGGA	    0.954241	-95
ACCCTTCGATGAAAGGTGGTTCGTAGAAAA	2	257	0	GAAAGGTGGT	    0.809195	-44
          **********

Masking position 4
Map Score:   4.46464

Number of sites scoring better than the average of aligned sites = 923
Number in coding regions = 846
Number in noncoding regions = 77
Number of orfs with sites within 600 bp upstream = 67
Fraction of orfs with sites within 600 bp upstream = 0.0107613


Motif number 5

          **********

No masking
Map Score:   1.30983e-12

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:   1.30983e-12

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:   1.30983e-12

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