AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i227_rna_methyltransferase_ctra_reg_300.orf -o227_ctra_300.ace -a/home/amcguire/alignace/lib/ORF_ctra.txt -z/skink1/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	RCT00751	254	Chlamydia_trachomatis

Motif number 1

TGTCGTTATTTCTAACGAACAAGTAAGGAGT	1	19	0	TCTACGAACA	    0.963627	-236
AAATAACGACACCATCGAAAACCCAGAGAAC	1	39	1	ACCTCGAAAA	    0.938691	-216
CCCAAAGCAGCTTTTCGAACACTTTTCGTGT	1	76	1	CTTTCGAACA	    0.882088	-179
AAAAAAGAATATACACGAAAAGTGTTCGAAA	1	88	0	ATAACGAAAA	    0.919502	-167
TTTGTTTGCTTTTAATGAAAAAAAGAATATA	1	106	0	TTTATGAAAA	    0.908335	-149
CAAAGATTCTACTCTTGAAAACGACATAGCT	1	133	1	ACTTTGAAAA	    0.951168	-122
TATGCTTCTGATTTTGGAATATTTTCTATTC	1	163	1	ATTTGGAATA	    0.929689	-92
GCATTCCTTGTTAAAGGAATAGAAAATATTC	1	179	0	TTAAGGAATA	    0.772426	-76
GAATCCCCGCTCTGTGGAAAAATTCTATAGA	1	211	1	TCTTGGAAAA	    0.979028	-44
AATTCTATAGACTAAGGAGAAAAGGTTGCTT	1	231	1	ACTAGGAGAA	    0.923205	-24
          *** *******

Masking position 8
Map Score:   7.09489

Number of sites scoring better than the average of aligned sites = 485
Number in coding regions = 484
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

ATTCCTACTCCTTACTTGTTCGTTAGAAAT	1	13	1	CTTACTTGTT	    0.852107	-242
TTTCGTGTATATTCTTTTTTTCATTAAAAG	1	99	1	ATTCTTTTTT	    0.972806	-156
TCAAGAGTAGAATCTTTGTTTGCTTTTAAT	1	121	0	AATCTTTGTT	    0.982463	-134
CTGATTTTGGAATATTTTCTATTCCTTTAA	1	170	1	AATATTTTCT	    0.909248	-85
GGGATTCAGCATTCCTTGTTAAAGGAATAG	1	188	0	ATTCCTTGTT	    0.979002	-67
   GATAAGCAACCTTTTCTCCTTAGTCTA	1	238	0	AACCTTTTCT	    0.915555	-17
          **********

Masking position 6
Map Score:   3.49865

Number of sites scoring better than the average of aligned sites = 329
Number in coding regions = 328
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 3

TGGGAGAGGGGTTCTCTGGGTTTTCGATGG	1	50	0	GTTCTCTGGG	    0.978075	-205
GTTCGAAAAGCTGCTTTGGGAGAGGGGTTC	1	66	0	CTGCTTTGGG	    0.996401	-189
AACAAAGATTCTACTCTTGAAAACGACATA	1	131	1	CTACTCTTGA	    0.930355	-124
AGCTATGCTTCTGATTTTGGAATATTTTCT	1	160	1	CTGATTTTGG	    0.959156	-95
TGCTGAATCCCCGCTCTGTGGAAAAATTCT	1	207	1	CCGCTCTGTG	     0.98177	-48
          **********

Masking position 5
Map Score:   2.27399

Number of sites scoring better than the average of aligned sites = 167
Number in coding regions = 166
Number in noncoding regions = 1
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:   -4.30999e-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:   -4.30999e-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:   -4.30999e-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