AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -ihipB_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	PH1748	271	192aa long hypothetical protein

Motif number 1

TGATGATCCTTGCCCAGCCTGAGGA      	1	5	0	TGCCCAGCCG	    0.976888	-267
CAAGGATCATCATCCGCCCACAAGAATTTTA	1	24	1	CATCCGCCCC	    0.993399	-248
GAGGGTATTGTACCCTCGCTGTCGGCGATTA	1	74	0	TACCCTCGCG	    0.948244	-198
GAGGGTACAATACCCTCGCAAGGGCTCGGTC	1	88	1	TACCCTCGCA	    0.836912	-184
GGGCTCGGTCAACCCGCCCCCGCAAGGTTTC	1	109	1	AACCCGCCCC	    0.992855	-163
ACACCCCGCTCATCGACCCCGAAACCTTGCG	1	129	0	CATCGACCCG	    0.988858	-143
GCTCGGCGTGAGCACACCCCGCTCATCGACC	1	142	0	AGCACACCCG	    0.936365	-130
GGTGTGCTCACGCCGAGCCTACAGGGCCGGT	1	155	1	CGCCGAGCCA	    0.941735	-117
CGGGCGGATGCACCGGCCCTGTAGGCTCGGC	1	166	0	CACCGGCCCG	    0.998244	-106
AGGGCCGGTGCATCCGCCCGCGGGATTAATG	1	177	1	CATCCGCCCC	    0.993399	-95
GGGCCGGCAACAGAGACCCAGCGGTCATTAA	1	202	0	CAGAGACCCG	    0.891032	-70
GGGTCTCTGTTGCCGGCCCACAATAAAGTTT	1	214	1	TGCCGGCCCC	    0.993547	-58
          ********* *

Masking position 9
Map Score:   22.9642

Number of sites scoring better than the average of aligned sites = 456
Number in coding regions = 359
Number in noncoding regions = 97
Number of orfs with sites within 600 bp upstream = 78
Fraction of orfs with sites within 600 bp upstream = 0.0125281


Motif number 2

TCTTGTGGGCGGATGATGATCCTTGCCCAGCC	1	17	0	GGTGATGACC	    0.880765	-255
CCTCGCTGTCGGCGATTAAAATTAATAAATTA	1	60	0	GGGATTAAAT	     0.81279	-212
GCCCTTGCGAGGGTATTGTACCCTCGCTGTCG	1	81	0	GGTATTGTCC	    0.939315	-191
CCTTGCGGGGGCGGGTTGACCGAGCCCTTGCG	1	104	0	GCGGTTGACG	    0.964046	-168
AAGGTTTCGGGGTCGATGAGCGGGGTGTGCTC	1	132	1	GGCGATGACG	    0.983517	-140
TAATCCCGCGGGCGGATGCACCGGCCCTGTAG	1	173	0	GGGGATGCCC	    0.916666	-99
GAGACCCAGCGGTCATTAATCCCGCGGGCGGA	1	189	0	GGCATTAACC	    0.979314	-83
ATTAAGAAGGGGATATTAAACTTTATTGTGGG	1	230	0	GGTATTAACT	    0.955348	-42
ATTAATAGATGGAGGCTAATCT          	1	260	1	GGGGCTAACT	    0.969501	-12
          ** ****** **

Masking position 7
Map Score:   7.36895

Number of sites scoring better than the average of aligned sites = 521
Number in coding regions = 481
Number in noncoding regions = 40
Number of orfs with sites within 600 bp upstream = 30
Fraction of orfs with sites within 600 bp upstream = 0.0048185


Motif number 3

GATGATGATCCTTGCCCAGCCTGAGGA   	1	8	0	CTTGCCCAGC	    0.987726	-264
AGGATCATCATCCGCCCACAAGAATTTTAA	1	26	1	TCCGCCCACA	    0.765689	-246
ATTAATTTTAATCGCCGACAGCGAGGGTAC	1	66	1	ATCGCCGACA	    0.921338	-206
CGGGGGCGGGTTGACCGAGCCCTTGCGAGG	1	101	0	TTGACCGAGC	    0.950396	-171
ACCCCGAAACCTTGCGGGGGCGGGTTGACC	1	115	0	CTTGCGGGGG	    0.685225	-157
GCACACCCCGCTCATCGACCCCGAAACCTT	1	132	0	CTCATCGACC	    0.895683	-140
GGGGTGTGCTCACGCCGAGCCTACAGGGCC	1	153	1	CACGCCGAGC	    0.991811	-119
GCCGGCAACAGAGACCCAGCGGTCATTAAT	1	201	0	GAGACCCAGC	    0.848282	-71
CTGGGTCTCTGTTGCCGGCCCACAATAAAG	1	212	1	GTTGCCGGCC	    0.970621	-60
          **********

Masking position 5
Map Score:   1.57211

Number of sites scoring better than the average of aligned sites = 752
Number in coding regions = 660
Number in noncoding regions = 92
Number of orfs with sites within 600 bp upstream = 69
Fraction of orfs with sites within 600 bp upstream = 0.0110826


Motif number 4

          **********

No masking
Map Score:   -3.17312e-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:   -3.17312e-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:   -3.17312e-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