AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00740_ctra_reg_100.orf -o00740_ctra_100.ace -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -g0.41 -x5 -e 
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 =  	0.41
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	truB	37	tRNA Pseudouridine Synthase
#2	nusA	117	Transcription antitermination factor
#3	ribC	300	Riboflavin Synthase
#4	ribA/ribB	109	GTP Cyclohydratase and DHBP Synthase

Motif number 1

      CAAAAAGACAATCCTTCTGAACTCCA	1	5	1	AAGACAACTT	    0.977088	-33
         TAACACAATTCTTGATTGTGATT	3	2	1	AACACAACTT	    0.993332	-299
AAAAAAAATCACCACAAATCACAATCAAGAAT	3	18	0	ACCACAACAC	    0.990622	-283
GGTTCTTTTCAACACAAGACACAGGATTTTAT	3	107	0	AACACAACAC	    0.992212	-194
CTAGGTCGTGACAACAATACTTTTTAGCAATC	3	260	0	ACAACAACTT	    0.960028	-41
CGCAGAGTATAACACAAACCTCTACTTTCTGC	4	15	0	AACACAACTC	    0.995811	-95
          *******  ***

Masking position 6
Map Score:   7.73145

Number of sites scoring better than the average of aligned sites = 27
Number in coding regions = 27
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 2

TTCGTTAGTGAAGAGCAAACATAAGAGCAGAG	2	28	1	AGAGCAAAAT	    0.855648	-90
GAGCAAACATAAGAGCAGAGCTCTAGGGCTCT	2	40	1	AGAGCAGACT	    0.974846	-78
ATAATGCTAACGGAGCAGAGCCCTAGAGCTCT	2	56	0	CGAGCAGACC	     0.97671	-62
TAGGCGACTTTTGAAAAAAAATCACCACAAAT	3	31	0	TGAAAAAAAT	     0.73578	-270
TTTATTTTAATGGATAAAATCCTGTGTCTTGT	3	94	1	TGATAAAACC	    0.947935	-207
GTGTCTTGTGTTGAAAAGAACCTCTTCTTAGA	3	117	1	TGAAAAGACC	    0.959084	-184
AGACCGCCCGTAGAGAAAACCTTTCTAAGAAG	3	140	0	TGAGAAAACT	    0.981075	-161
GCTGTTTGCCTTGATCAGATCCGGAGAGGGCT	3	205	1	TGATCAGACC	    0.973808	-96
TACCCCGTTTTTGAGGAAAACTTAGCCAGTGG	4	80	0	TGAGGAAACT	    0.958938	-30
          * ******* **

Masking position 7
Map Score:   6.51487

Number of sites scoring better than the average of aligned sites = 243
Number in coding regions = 243
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 3

ATTAAAATAAAAACCGTGGTATCTTGAGCGT	3	74	0	AAACCGGGTA	    0.986668	-227
AAACCTTTCTAAGAAGAGGTTCTTTTCAACA	3	125	0	AAGAAGGGTT	     0.98639	-176
TGATCAAGGCAAACAGCGGTTACTTATAATC	3	191	0	AAACAGGGTT	    0.989283	-110
 GGTCGCAGAAAGTAGAGGTTTGTGTTATAC	4	10	1	AAGTAGGGTT	     0.97628	-100
GTTTTCCTCAAAAACGGGGTAGATTGAGA  	4	91	1	AAAACGGGTA	    0.980645	-19
          ****** ****

Masking position 2
Map Score:   4.01675

Number of sites scoring better than the average of aligned sites = 35
Number in coding regions = 35
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

 TCTCTTTACTAATAATCTTCGTTAGTGAAG	2	10	1	TAATAATCTC	    0.951369	-108
          TAATACTCCTCTTATGGGTAA	2	107	0	TAATACTCCC	     0.98579	-11
CAAAAAATAATTATACTCCGAGACCGCCCGT	3	161	0	TTATACTCCA	    0.977646	-140
CAGCGGTTACTTATAATCAAAAAATAATTAT	3	178	0	TTATAATCAA	    0.874961	-123
GAGGTTTGTGTTATACTCTGCGCACAGCGAG	4	25	1	TTATACTCTC	    0.982887	-85
CGTTCTTTGTCTATAATCCCCTCGCTGTGCG	4	45	0	CTATAATCCC	    0.967851	-65
          ********* *

Masking position 5
Map Score:   3.75225

Number of sites scoring better than the average of aligned sites = 34
Number in coding regions = 34
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

 TAACACAATTCTTGATTGTGATTTGTGGTG	3	10	1	TCTTGTTGTG	    0.952496	-291
TAAAAACCGTGGTATCTTGAGCGTCCTGCAG	3	67	0	GGTATTTGAG	    0.966646	-234
GATAAAATCCTGTGTCTTGTGTTGAAAAGAA	3	106	1	TGTGTTTGTG	     0.91466	-195
TCCGGAGAGGGCTTTTTCGTGTATCTAGTTT	3	224	1	GCTTTTCGTG	    0.969027	-77
AAATACCTTTGCTAGGTCGTGACAACAATAC	3	272	0	GCTAGTCGTG	    0.986012	-29
TCAAAAACGGGGTAGATTGAGA         	4	98	1	GGTAGTTGAG	    0.978528	-12
          ***** *****

Masking position 7
Map Score:   1.6034

Number of sites scoring better than the average of aligned sites = 60
Number in coding regions = 60
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:   7.69818e-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:   7.69818e-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:   7.69818e-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