AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i211_transcription_translation_hinf_reg_300.orf -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -g0.38 -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 =  	0.38
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	HI0295	246	transcription termination factor (rho)
#2	HI0758	176	ribosomal protein L31 (rpL31)

Motif number 1

 AATTTCCCTTAAGTGCTTATTGATAACCTTA	1	10	1	TAAGTGCATT	    0.845281	-237
TATTCTAATTAAAAATCAAATAAATAACAATC	1	53	1	AAAAATCATA	    0.819076	-194
CTAGACGGCTAAACTTCCAAAATAAGTTCTTA	1	84	1	AAACTTCAAA	    0.820842	-163
ACTTCCAAAATAAGTTCTTAAAAAAAGTGCGA	1	96	1	TAAGTTCAAA	    0.900458	-151
GTTCTTAAAAAAAGTGCGATGATTTTTATATT	1	109	1	AAAGTGCTGA	     0.91615	-138
ATTTTTATATTAAATGCTAATAAAAGCTAGAC	1	130	1	TAAATGCATA	     0.96876	-117
   AAAAAGAAAAGTGCGGTTAAAAATGCTGA	2	8	1	AAAGTGCTTA	    0.955335	-169
AGTGCGGTTAAAAATGCTGATGATTTTACACG	2	20	1	AAAATGCATG	    0.946044	-157
TTATACTGAAAAAATGCAGATAAACAAGCTCT	2	57	0	AAAATGCATA	    0.967694	-120
GTGTGGGGAGAAAGTTCCTATAGCGGCGTGGC	2	136	1	AAAGTTCATA	    0.984404	-41
          *******  ***

Masking position 3
Map Score:   9.82743

Number of sites scoring better than the average of aligned sites = 706
Number in coding regions = 511
Number in noncoding regions = 195
Number of orfs with sites within 600 bp upstream = 144
Fraction of orfs with sites within 600 bp upstream = 0.0231288


Motif number 2

AATTGTCCGTATTCTAATTAAAAATCAAATA	1	44	1	ATTCAATTAA	    0.958615	-203
TCTAATTAAAAATCAAATAAATAACAATCTA	1	56	1	AATCAATAAA	    0.783906	-191
TTTATATTAAATGCTAATAAAAGCTAGACAG	1	133	1	ATGCAATAAA	    0.987204	-114
GGTAATTTACGTGCCATTCAAAGGGTGCAAG	1	178	1	GTGCATTCAA	    0.833878	-69
CAAGCCCACCATTCGAATAATCAATTCTTAT	1	205	1	ATTCAATAAT	    0.943881	-42
CGAATAATCAATTCTTATTAATTCCAACATT	1	218	1	ATTCTATTAA	    0.805852	-29
AAAAAGAAAAGTGCGGTTAAAAATGCTGATG	2	11	1	GTGCGTTAAA	    0.907189	-166
GCGGTTAAAAATGCTGATGATTTTACACGAA	2	23	1	ATGCGATGAT	    0.922641	-154
TACTGAAAAAATGCAGATAAACAAGCTCTAT	2	55	0	ATGCGATAAA	    0.982242	-122
ACCAAATAGGTTGCGAATTATACTGAAAAAA	2	75	0	TTGCAATTAT	    0.869527	-102
AACCTATTTGGTGCCAATTATGGCGTATTAT	2	94	1	GTGCAATTAT	    0.963608	-83
          **** ******

Masking position 10
Map Score:   9.48555

Number of sites scoring better than the average of aligned sites = 711
Number in coding regions = 620
Number in noncoding regions = 91
Number of orfs with sites within 600 bp upstream = 70
Fraction of orfs with sites within 600 bp upstream = 0.0112432


Motif number 3

TTGGAAGTTTAGCCGTCTAGATTGTTATTT	1	74	0	AGCCGTCTAG	    0.986889	-173
TAAAACCCTACGCTGTCTAGCTTTTATTAG	1	146	0	CGCTGTCTAG	    0.987426	-101
TATTCACTCACGCGGTGTGGGGAGAAAGTT	2	122	1	CGCGGTGTGG	    0.996932	-55
AAGTTCCTATAGCGGCGTGGCTTCATTTTG	2	147	1	AGCGGCGTGG	    0.992049	-30
          **********

Masking position 8
Map Score:   2.48596

Number of sites scoring better than the average of aligned sites = 12
Number in coding regions = 10
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 4

          **********

No masking
Map Score:   7.76924e-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:   7.76924e-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:   7.76924e-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