AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -irhaS_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	PH0864	300	208aa long hypothetical transcription initiation factor IIB

Motif number 1

GAACACATATCTCCCAAGGCTATCACTTCGAAA	1	13	1	CTCCAAGTAT	    0.988951	-288
AAGGCTATCACTTCGAAAAGTGGAAGATAATAA	1	28	1	CTTCAAATGG	    0.981734	-273
TAAAGTTTACCTTCCAAGTATATATAATATGGG	1	113	1	CTTCAAGTAT	    0.992538	-188
TAATATGGGGGATCCAAGATTAGGTGTCCAGTT	1	137	1	GATCAAGTAG	    0.960104	-164
GTTTGTGGTTCTTCAAAAATTATTTATGACCCC	1	167	1	CTTCAAATAT	    0.988316	-134
AGAAGAAAATGTTCTAACCCTAGTATCAAAGGA	1	245	0	GTTCAACTAG	    0.977397	-56
AGTTCCCTTACTCCTAAACTTAGGGGGAGAAGA	1	272	0	CTCCAAATAG	    0.991564	-29
          **** ***  ***

Masking position 7
Map Score:   8.34306

Number of sites scoring better than the average of aligned sites = 143
Number in coding regions = 134
Number in noncoding regions = 9
Number of orfs with sites within 600 bp upstream = 8
Fraction of orfs with sites within 600 bp upstream = 0.00128493


Motif number 2

GTGATAGCCTTGGGAGATATGTGTTCGG  	1	9	0	TGGGAGATAT	     0.97357	-292
CTTCGAAAAGTGGAAGATAATAAAAACAAC	1	38	1	TGGAAGATAA	    0.988081	-263
AATTTTTTAGAGAAAGGTATTTAAAGTTTA	1	92	1	AGAAAGGTAT	    0.930496	-209
TATATATACTTGGAAGGTAAACTTTAAATA	1	109	0	TGGAAGGTAA	    0.992387	-192
TCCTAAACTTAGGGGGAGAAGAAAATGTTC	1	264	0	AGGGGGAGAA	    0.954199	-37
TAAGTTTAGGAGTAAGGGAACTTCGGAT  	1	283	1	AGTAAGGGAA	    0.953935	-18
          **********

Masking position 9
Map Score:   4.21991

Number of sites scoring better than the average of aligned sites = 820
Number in coding regions = 762
Number in noncoding regions = 58
Number of orfs with sites within 600 bp upstream = 73
Fraction of orfs with sites within 600 bp upstream = 0.011725


Motif number 3

          **********

No masking
Map Score:   7.91135e-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 4

          **********

No masking
Map Score:   7.91135e-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:   7.91135e-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