AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i212_translation_transcription_bsub_reg_300.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
#2	yugG	147	similar to transcriptional regulator (Lrp/AsnC family)

Motif number 1

GAACAAAAGGTTCGTATCTTTTTTTATGTTGTTTT	1	91	0	TTACTTTTTT	    0.964057	-204
CTTTCTAGTATTCCCCCCTTTTATTGGATGCGAAC	1	122	0	TCCCTTTATT	    0.988847	-173
GTATTTTCAGTTTACCCCCTTTTTGCTGTGCATAA	1	163	1	TCCCTTTTTG	    0.992448	-132
TTGCTGTGCATAAACCTGATTTTTTATAAAAAAGT	1	185	1	TCCGTTTTTT	    0.987958	-110
    TCTGTGTCACTCCCTTTTTTTGATGGTTGTA	2	7	1	TTCCTTTTTT	    0.995187	-141
TAGCGGAAGTTTCTCCTCGTTTTTTCTTAGCATTC	2	65	1	TCCCTTTTTT	    0.997664	-83
CTCATGACATTATATCACGTTTTTTGACGAATGCT	2	93	0	TTCCTTTTTT	    0.995187	-55
          *   ** * ******

Masking position 10
Map Score:   12.2826

Number of sites scoring better than the average of aligned sites = 231
Number in coding regions = 179
Number in noncoding regions = 52
Number of orfs with sites within 600 bp upstream = 60
Fraction of orfs with sites within 600 bp upstream = 0.00963701


Motif number 2

TATTCCGTTGTTCATACGCAACCTCGATTG	1	17	1	TTCATACGCA	    0.951293	-278
AATGAAACGCTTCCTGCACAAAACAACATA	1	72	1	TTCCTGCACA	    0.972587	-223
ATACGAACCTTTTGTTCGCATCCAATAAAA	1	109	1	TTTGTTCGCA	    0.966307	-186
AAAAATCAGGTTTATGCACAGCAAAAAGGG	1	179	0	TTTATGCACA	    0.975427	-116
TAAATATCTGTTTATACGCAATTTAAAATT	1	252	0	TTTATACGCA	    0.971836	-43
GAATTGACAATTTCAGGGCATAATACAACC	2	35	0	TTTCAGGGCA	    0.873202	-113
CTCCTCGTTTTTTCTTAGCATTCGTCAAAA	2	77	1	TTTCTTAGCA	    0.929999	-71
TGTCATGAGATTTCTTGACATTGCAAAGGT	2	119	1	TTTCTTGACA	    0.947574	-29
          TTGATTCACACCTTTGCAAT	2	138	0	TTGATTCACA	    0.910047	-10
          **********

Masking position 2
Map Score:   10.3399

Number of sites scoring better than the average of aligned sites = 662
Number in coding regions = 576
Number in noncoding regions = 86
Number of orfs with sites within 600 bp upstream = 74
Fraction of orfs with sites within 600 bp upstream = 0.0118856


Motif number 3

TGAACAACGGAATATATCCC          	1	1	0	AATATATCCC	    0.962691	-294
AAGGCTTTCTAGTATTCCCCCCTTTTATTG	1	131	0	AGTATTCCCC	    0.974142	-164
TGGTATTTTCAGTTTACCCCCTTTTTGCTG	1	161	1	AGTTTACCCC	    0.981788	-134
GCAATTTAAAATTATATCACACATGTCTTA	1	235	0	ATTATATCAC	    0.946614	-60
TGATGGTTGTATTATGCCCTGAAATTGTCA	2	31	1	ATTATGCCCT	    0.906417	-117
TTCTAGCGGAAGTTTCTCCTCGTTTTTTCT	2	62	1	AGTTTCTCCT	    0.845783	-86
ATCTCATGACATTATATCACGTTTTTTGAC	2	100	0	ATTATATCAC	    0.946614	-48
          **********

Masking position 1
Map Score:   4.31963

Number of sites scoring better than the average of aligned sites = 288
Number in coding regions = 221
Number in noncoding regions = 67
Number of orfs with sites within 600 bp upstream = 80
Fraction of orfs with sites within 600 bp upstream = 0.0128493


Motif number 4

GGCTTTCTAGTATTCCCCCCTTTTATTGGA	1	129	0	TATTCCCCCC	    0.978509	-166
GGTATTTTCAGTTTACCCCCTTTTTGCTGT	1	162	1	GTTTACCCCC	    0.984898	-133
       TCTGTGTCACTCCCTTTTTTTGA	2	4	1	GTGTCACTCC	    0.961474	-144
TCTAGCGGAAGTTTCTCCTCGTTTTTTCTT	2	63	1	GTTTCTCCTC	    0.959829	-85
        TTGATTCACACCTTTGCAATGT	2	136	0	GATTCACACC	    0.974775	-12
          **********

Masking position 4
Map Score:   1.03018

Number of sites scoring better than the average of aligned sites = 297
Number in coding regions = 212
Number in noncoding regions = 85
Number of orfs with sites within 600 bp upstream = 92
Fraction of orfs with sites within 600 bp upstream = 0.0147767


Motif number 5

CCGTTGTTCATACGCAACCTCGATTGAACAGCT	1	21	1	TCGCAACCGA	     0.97878	-274
GAACCTTTTGTTCGCATCCAATAAAAGGGGGGA	1	113	1	TCGCATCATA	     0.91924	-182
AAATCAGGTTTATGCACAGCAAAAAGGGGGTAA	1	174	0	TTGCACGAAA	    0.909171	-121
ATGTCTTATTTCCGCAAAGAAAAACTTTTTTAT	1	210	0	TCGCAAGAAA	    0.993576	-85
TATCTGTTTATACGCAATTTAAAATTATATCAC	1	245	0	TCGCAATAAA	    0.978023	-50
GATTCACACCTTTGCAATGTCAAGAAATCTCAT	2	123	0	TTGCAAGCAA	    0.915855	-25
          * ***** * ***

Masking position 6
Map Score:   0.682293

Number of sites scoring better than the average of aligned sites = 241
Number in coding regions = 219
Number in noncoding regions = 22
Number of orfs with sites within 600 bp upstream = 26
Fraction of orfs with sites within 600 bp upstream = 0.00417604


Motif number 6

          **********

No masking
Map Score:   2.29806e-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 7

          **********

No masking
Map Score:   2.29806e-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 8

          **********

No masking
Map Score:   2.29806e-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