AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i211_transcription_translation_hinf_reg_100.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	    0.842566	-237
TATTCTAATTAAAAATCAAATAAATAACAATC	1	53	1	AAAAATCATA	    0.799958	-194
CTAGACGGCTAAACTTCCAAAATAAGTTCTTA	1	84	1	AAACTTCAAA	    0.801855	-163
ACTTCCAAAATAAGTTCTTAAAAAAAGTGCGA	1	96	1	TAAGTTCAAA	     0.88877	-151
GTTCTTAAAAAAAGTGCGATGATTTTTATATT	1	109	1	AAAGTGCTGA	    0.906131	-138
ATTTTTATATTAAATGCTAATAAAAGCTAGAC	1	130	1	TAAATGCATA	    0.965454	-117
   AAAAAGAAAAGTGCGGTTAAAAATGCTGA	2	8	1	AAAGTGCTTA	    0.954698	-169
AGTGCGGTTAAAAATGCTGATGATTTTACACG	2	20	1	AAAATGCATG	    0.939406	-157
TTATACTGAAAAAATGCAGATAAACAAGCTCT	2	57	0	AAAATGCATA	    0.968186	-120
GTGTGGGGAGAAAGTTCCTATAGCGGCGTGGC	2	136	1	AAAGTTCATA	    0.982386	-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	     0.95403	-203
TCTAATTAAAAATCAAATAAATAACAATCTA	1	56	1	AATCAATAAA	    0.764701	-191
TTTATATTAAATGCTAATAAAAGCTAGACAG	1	133	1	ATGCAATAAA	    0.985758	-114
GGTAATTTACGTGCCATTCAAAGGGTGCAAG	1	178	1	GTGCATTCAA	    0.818083	-69
CAAGCCCACCATTCGAATAATCAATTCTTAT	1	205	1	ATTCAATAAT	    0.937774	-42
CGAATAATCAATTCTTATTAATTCCAACATT	1	218	1	ATTCTATTAA	    0.788086	-29
AAAAAGAAAAGTGCGGTTAAAAATGCTGATG	2	11	1	GTGCGTTAAA	    0.897508	-166
GCGGTTAAAAATGCTGATGATTTTACACGAA	2	23	1	ATGCGATGAT	    0.914422	-154
TACTGAAAAAATGCAGATAAACAAGCTCTAT	2	55	0	ATGCGATAAA	     0.98022	-122
ACCAAATAGGTTGCGAATTATACTGAAAAAA	2	75	0	TTGCAATTAT	    0.856539	-102
AACCTATTTGGTGCCAATTATGGCGTATTAT	2	94	1	GTGCAATTAT	     0.95955	-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

AAATAACAATCTAGACGGCTAAACTTCCAA	1	74	1	CTAGACGGCT	    0.986889	-173
CTAATAAAAGCTAGACAGCGTAGGGTTTTA	1	146	1	CTAGACAGCG	    0.987426	-101
AACTTTCTCCCCACACCGCGTGAGTGAATA	2	122	0	CCACACCGCG	    0.996932	-55
CAAAATGAAGCCACGCCGCTATAGGAACTT	2	147	0	CCACGCCGCT	    0.992049	-30
          **********

Masking position 3
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