AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i212_translation_transcription_bsub_reg_100.orf -aORF_bsub.txt -zbsub.fna -g0.435 -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 =  	0.435
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	yugI	294	similar to polyribonucleotide nucleotidyltransferase

Motif number 1

TATTCCGTTGTTCATACGCAACCTCGATTGAACAGCT	1	17	1	TTCTCGCACA	    0.991601	-278
AATGAAACGCTTCCTGCACAAAACAACATAAAAAAAG	1	72	1	TTCTCACAAC	    0.975545	-223
ATACGAACCTTTTGTTCGCATCCAATAAAAGGGGGGA	1	109	1	TTTTCGCAAA	    0.997429	-186
AAAAATCAGGTTTATGCACAGCAAAAAGGGGGTAAAC	1	172	0	TTTTCACAAA	    0.967368	-123
ACACATGTCTTATTTCCGCAAAGAAAAACTTTTTTAT	1	210	0	TATTCGCAAA	     0.98966	-85
TAAATATCTGTTTATACGCAATTTAAAATTATATCAC	1	245	0	TTTTCGCAAA	    0.997399	-50
          *** * ****    * *

Masking position 10
Map Score:   7.11592

Number of sites scoring better than the average of aligned sites = 70
Number in coding regions = 60
Number in noncoding regions = 10
Number of orfs with sites within 600 bp upstream = 10
Fraction of orfs with sites within 600 bp upstream = 0.00160617


Motif number 2

AACGCTTCTTGAAGCTGTTCAATCGAGGTT	1	36	0	GAAGCTGTTC	    0.894519	-259
ACAGCTTCAAGAAGCGTTAGTCAGAATGAA	1	48	1	GAAGCGTTAG	    0.982125	-247
TTTTGTGCAGGAAGCGTTTCATTCTGACTA	1	65	0	GAAGCGTTTC	    0.745128	-230
AAAAAGATACGAACCTTTTGTTCGCATCCA	1	103	1	GAACCTTTTG	    0.975455	-192
GGAATACTAGAAAGCCTTTGGTATTTTCAG	1	143	1	AAAGCCTTTG	    0.977554	-152
TTTTTATAAAAAAGTTTTTCTTTGCGGAAA	1	205	1	AAAGTTTTTC	    0.919987	-90
          **********

Masking position 3
Map Score:   6.85714

Number of sites scoring better than the average of aligned sites = 1208
Number in coding regions = 1149
Number in noncoding regions = 59
Number of orfs with sites within 600 bp upstream = 63
Fraction of orfs with sites within 600 bp upstream = 0.0101189


Motif number 3

ATATTCCGTTGTTCATACGCAACCTCGATT	1	16	1	GTTCATACGC	    0.969713	-279
AGGCTTTCTAGTATTCCCCCCTTTTATTGG	1	130	0	GTATTCCCCC	    0.972008	-165
GGTATTTTCAGTTTACCCCCTTTTTGCTGT	1	162	1	GTTTACCCCC	    0.991785	-133
AAAAAATCAGGTTTATGCACAGCAAAAAGG	1	180	0	GTTTATGCAC	    0.934701	-115
CACACATGTCTTATTTCCGCAAAGAAAAAC	1	218	0	TTATTTCCGC	    0.904204	-77
TTAAATATCTGTTTATACGCAATTTAAAAT	1	253	0	GTTTATACGC	     0.98697	-42
          **********

Masking position 2
Map Score:   4.25506

Number of sites scoring better than the average of aligned sites = 714
Number in coding regions = 630
Number in noncoding regions = 84
Number of orfs with sites within 600 bp upstream = 84
Fraction of orfs with sites within 600 bp upstream = 0.0134918


Motif number 4

GGATGCGAACAAAAGGTTCGTATCTTTTTT	1	102	0	AAAAGGTTCG	    0.972192	-193
CGCATCCAATAAAAGGGGGGAATACTAGAA	1	125	1	AAAAGGGGGG	     0.99792	-170
ATGCACAGCAAAAAGGGGGTAAACTGAAAA	1	166	0	AAAAGGGGGT	    0.994341	-129
          **********

Masking position 4
Map Score:   1.22243

Number of sites scoring better than the average of aligned sites = 48
Number in coding regions = 25
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 31
Fraction of orfs with sites within 600 bp upstream = 0.00497912


Motif number 5

          **********

No masking
Map Score:   -4.02005e-14

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:   -4.02005e-14

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 7

          **********

No masking
Map Score:   -4.02005e-14

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