AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -iglpR_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	PH1363	211	493aa long hypothetical protein
#2	PH1497	109	197aa long hypothetical protein

Motif number 1

         AGATGTTGTTAAACTGCATAAGGAG	1	2	1	GAGTGTTAAT	    0.984049	-210
ACTGCATAAGGAGCTCTTTAAAAAAGTTCCGATA	1	23	1	GACTTTTAAA	    0.924407	-189
CCAAGCTGAAAACGTCTTTGATTTTGCAATTGCT	1	95	1	AAGTTTTATT	    0.942776	-117
TTGCTAACCTAATGTTTTATAAATTATGACTTTA	1	151	1	AAGTTTAAAT	    0.942776	-61
AATTCAACATTACCTATGTAAAGTCATAATTTAT	1	169	0	TACTTGTAAT	    0.943911	-43
GGTAATGTTGAATTTGTTTCAATTTTTGGAGGG 	1	189	1	AATTTTTAAT	    0.941719	-23
TTCATCTGTCGAGCTTGGTTAATTGAGAAGATTT	2	33	1	GACTGGTAAT	    0.948808	-77
TTCTTCACCATAAGTCTTTTAAATCTTCTCAATT	2	53	0	TAGTTTTAAT	    0.982461	-57
ATGGTGAAGAAAAGTATTTTAAATCGCCTGAAAA	2	76	1	AAGTTTTAAT	    0.990522	-34
          ** ** *** ** *

Masking position 5
Map Score:   7.40286

Number of sites scoring better than the average of aligned sites = 162
Number in coding regions = 129
Number in noncoding regions = 33
Number of orfs with sites within 600 bp upstream = 41
Fraction of orfs with sites within 600 bp upstream = 0.00658529


Motif number 2

TCTATCGGAACTTTTTTAAAGAGCTCCTTA	1	29	0	CTTTTTTAAA	    0.963037	-183
TTTTCTCACTCTTTTCTATCGGAACTTTTT	1	43	0	CTTTTCTATC	    0.978426	-169
CCCTTGCAACCTTTATTTTCTCACTCTTTT	1	58	0	CTTTATTTTC	    0.876778	-154
TGCTTCCGGCCTTCTTTAACCTTTTTTTGC	1	125	1	CTTCTTTAAC	    0.943045	-87
CTTCTTTAACCTTTTTTTGCTAACCTAATG	1	135	1	CTTTTTTTGC	    0.960384	-77
ATTTAAAATACTTTTCTTCACCATAAGTCT	2	70	0	CTTTTCTTCA	    0.934098	-40
          CTTTCCTAAATTTTCAGGCG	2	100	0	CTTTCCTAAA	     0.92003	-10
          **********

Masking position 7
Map Score:   4.47937

Number of sites scoring better than the average of aligned sites = 420
Number in coding regions = 379
Number in noncoding regions = 41
Number of orfs with sites within 600 bp upstream = 49
Fraction of orfs with sites within 600 bp upstream = 0.00787022


Motif number 3

   AGATGTTGTTAAACTGCATAAGGAGCT	1	8	1	GTTAAACTGC	    0.930559	-204
CTCTTTGCCCTTGCAACCTTTATTTTCTCA	1	65	0	TTGCAACCTT	    0.930559	-147
GTCTTTGATTTTGCAATTGCTTCCGGCCTT	1	108	1	TTGCAATTGC	    0.930559	-104
TCCGGCCTTCTTTAACCTTTTTTTGCTAAC	1	129	1	TTTAACCTTT	    0.824056	-83
GTTGAATTTGTTTCAATTTTTGGAGGG   	1	195	1	TTTCAATTTT	    0.938353	-17
TTTAGTCATCGTTCATCTGTCGAGCTTGGT	2	22	1	GTTCATCTGT	     0.81825	-88
CCATAAGTCTTTTAAATCTTCTCAATTAAC	2	50	0	TTTAAATCTT	    0.903904	-60
AGAAAAGTATTTTAAATCGCCTGAAAATTT	2	83	1	TTTAAATCGC	    0.935996	-27
          **********

Masking position 5
Map Score:   2.48747

Number of sites scoring better than the average of aligned sites = 658
Number in coding regions = 587
Number in noncoding regions = 71
Number of orfs with sites within 600 bp upstream = 83
Fraction of orfs with sites within 600 bp upstream = 0.0133312


Motif number 4

          **********

No masking
Map Score:   -7.93376e-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:   -7.93376e-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:   -7.93376e-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