AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -imetR_ctra_opreg_100.orf -g0.413 -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 =  	0.413
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	glyA	300	Serine Hydroxymethyltransferase
#2	CT623	200	CHLPN 76kDa Homolog

Motif number 1

AGAAGCTTCCTACTAGGAAAAAAGCTT          	1	1	0	TAGAAAAAAT	    0.933481	-300
GATCATATTCTTACAGCAAAAGTCAAGAAGCTTCCTA	1	26	0	TAGAAAAGTG	    0.987364	-275
TATGGTAAGCGACTAGGGAAAATGGGGCGCTTGGTAA	1	93	1	GAGGAAAATG	    0.781768	-208
TAACTATAACTATAAGAAAAAGAAACGATGCTTCCAA	1	135	0	TAGAAAAGAG	    0.987364	-166
CTAAACTTTCTAGGAGAAAGAGGATTTATTTTAACTA	1	166	0	TAGAAGAGGT	    0.938679	-135
GTTTAGACTTTCTCATCAAAAGATTAGATTCCCATAA	1	197	1	TATAAAAGAG	    0.908144	-104
TCCCATAAAGGATAAGGGAGAGTGGGTAGAGGATAAA	1	226	1	GAGGAGAGTT	    0.888072	-75
AGAGTGGGTAGAGGATAAAGAGTGCCTCTGCAAGGTC	1	244	1	GATAAGAGTT	    0.760626	-57
GTTCTATTCTTAAGAGAAAAAGATGTCCTAAGAGACT	2	20	0	TAGAAAAGAC	    0.937586	-181
AGAACTGTATTTTTAGAAAAAATCCTTCCTGAGCTAT	2	52	1	TAGAAAAATT	    0.933481	-149
ATCATGCTTATGTAAGTAAGAGATTTGTAACCGTTTG	2	108	1	TAGAAGAGAG	    0.987597	-93
TTTGTAACCGTTTGCGAAAAAATCAAGCGTCCCAGGA	2	131	1	TCGAAAAATG	    0.779864	-70
AAATCAAGCGTCCCAGGAAGAGAGATTTCCGTGAGCA	2	150	1	TAGAAGAGAT	    0.980295	-51
          *   ** ******   *

Masking position 9
Map Score:   12.8248

Number of sites scoring better than the average of aligned sites = 567
Number in coding regions = 566
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 1
Fraction of orfs with sites within 600 bp upstream = 0.000160617


Motif number 2

AAAAGTCAAGAAGCTTCCTACTAGGAAAAA	1	16	0	AAGCTTCCTA	    0.988182	-285
GACCATTACCAAGCGCCCCATTTTCCCTAG	1	105	0	AAGCGCCCCA	    0.993771	-196
AAAAGAAACGATGCTTCCAAGACCATTACC	1	125	0	ATGCTTCCAA	     0.96219	-176
ATCAAAAGATTAGATTCCCATAAAGGATAA	1	211	1	TAGATTCCCA	    0.950906	-90
CGAAAAAATCAAGCGTCCCAGGAAGAGAGA	2	145	1	AAGCGTCCCA	    0.997216	-56
          **********

Masking position 10
Map Score:   5.11113

Number of sites scoring better than the average of aligned sites = 54
Number in coding regions = 54
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

TTTCCTAGTAGGAAGCTTCTTGACTTTTGCT	1	18	1	GGAAGCTTCT	    0.994036	-283
AGGGAAAATGGGGCGCTTGGTAATGGTCTTG	1	107	1	GGGCGCTTGT	    0.987816	-194
TAATGGTCTTGGAAGCATCGTTTCTTTTTCT	1	127	1	GGAAGCATCT	    0.991477	-174
CTATAGCTCAGGAAGGATTTTTTCTAAAAAT	2	60	0	GGAAGGATTT	    0.923738	-141
TCTCTTCCTGGGACGCTTGATTTTTTCGCAA	2	142	0	GGACGCTTGT	    0.994474	-59
          ********* *

Masking position 8
Map Score:   4.03032

Number of sites scoring better than the average of aligned sites = 26
Number in coding regions = 26
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

GAATATGATCAACTGAAGCTGCAATGGTAT	1	53	1	AACTGAAGCT	    0.962853	-248
GATTTATTTTAACTATAACTATAAGAAAAA	1	151	0	AACTATAACT	     0.90811	-150
TTAAGAATAGAACTGTATTTTTAGAAAAAA	2	44	1	AACTGTATTT	    0.853388	-157
CCAAGCCAAAAACTATAGCTCAGGAAGGAT	2	73	0	AACTATAGCT	     0.61187	-128
          **********

Masking position 4
Map Score:   1.07089

Number of sites scoring better than the average of aligned sites = 18
Number in coding regions = 18
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

 AAGCTTTTTTCCTAGTAGGAAGCTTCTTG	1	10	1	TCCTAGTAGG	    0.970812	-291
AGTCTAAACTTTCTAGGAGAAAGAGGATTT	1	176	0	TTCTAGGAGA	     0.98267	-125
GAAAAAGATGTCCTAAGAGACTAGCTTACA	2	12	0	TCCTAAGAGA	    0.993074	-189
ACAGTTCTATTCTTAAGAGAAAAAGATGTC	2	30	0	TCTTAAGAGA	    0.971981	-171
          **********

Masking position 5
Map Score:   1.97707

Number of sites scoring better than the average of aligned sites = 25
Number in coding regions = 25
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:   8.55083e-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:   8.55083e-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:   8.55083e-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