AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i066_Lysine_Biosynthesis_ctra_reg_100.orf -o066_ctra_100.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	RCT00412	49	Chlamydia_trachomatis
#2	RCT00414	300	Chlamydia_trachomatis

Motif number 1

CCAAAATGAAACTGTTTCCTGCTCCAGAAT	1	22	0	ACTGTTTCCT	     0.93538	-28
          CGATTCTCCCAAAATGAAAC	1	40	0	CGATTCTCCC	    0.867679	-10
       AAGCTTTTTTCCTAGTAGGAAGC	2	4	1	CTTTTTTCCT	    0.953433	-297
ACCAAGCGCCCCATTTTCCCTAGTCGCTTA	2	98	0	CCATTTTCCC	    0.970422	-203
AAGCATCGTTTCTTTTTCTTATAGTTATAG	2	139	1	TCTTTTTCTT	    0.908368	-162
AAATAAATCCTCTTTCTCCTAGAAAGTTTA	2	172	1	TCTTTCTCCT	    0.990758	-129
GAAAGTTTAGACTTTCTCATCAAAAGATTA	2	193	1	ACTTTCTCAT	    0.893099	-108
TACCCACTCTCCCTTATCCTTTATGGGAAT	2	224	0	CCCTTATCCT	    0.967986	-77
GCAGAGGCACTCTTTATCCTCTACCCACTC	2	245	0	TCTTTATCCT	    0.979415	-56
          **********

Masking position 5
Map Score:   9.28925

Number of sites scoring better than the average of aligned sites = 492
Number in coding regions = 490
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 2

ATGAAACTGTTTCCTGCTCCAGAATATAAA	1	17	0	TTCCTGCTCC	    0.985364	-33
TTTAATACCATTGCAGCTTCAGTTGATCAT	2	57	0	TTGCAGCTTC	    0.966648	-244
TGCAATGGTATTAAAGCACCTTATGGTAAG	2	72	1	TTAAAGCACC	    0.913985	-229
GAAACGATGCTTCCAAGACCATTACCAAGC	2	121	0	TTCCAAGACC	    0.984449	-180
TGATTAAACCTTGCAAGACCTTGCAGAGGC	2	267	0	TTGCAAGACC	    0.977508	-34
        ATTTCCACCTCCACTGATTAAA	2	289	0	TTCCACCTCC	    0.990272	-12
          **********

Masking position 2
Map Score:   4.9779

Number of sites scoring better than the average of aligned sites = 163
Number in coding regions = 162
Number in noncoding regions = 1
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 3

    CGATTCTCCCAAAATGAAACTGTTTC	1	34	0	TCCCAAAATG	    0.978453	-16
 AAGCTTTTTTCCTAGTAGGAAGCTTCTTG	2	10	1	TCCTAGTAGG	    0.978526	-291
CCTAGTCGCTTACCATAAGGTGCTTTAATA	2	80	0	TACCATAAGG	    0.976654	-221
ATCCTCTTTCTCCTAGAAAGTTTAGACTTT	2	178	1	TCCTAGAAAG	    0.989789	-123
AAGATTAGATTCCCATAAAGGATAAGGGAG	2	216	1	TCCCATAAAG	    0.992966	-85
          **********

Masking position 5
Map Score:   4.81128

Number of sites scoring better than the average of aligned sites = 78
Number in coding regions = 78
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

GTAGGAAGCTTCTTGACTTTTGCTGTAAGA	2	25	1	TCTTGACTTT	    0.978642	-276
AGAGGATTTATTTTAACTATAACTATAAGA	2	155	0	TTTTAACTAT	    0.886123	-146
GATGAGAAAGTCTAAACTTTCTAGGAGAAA	2	184	0	TCTAAACTTT	     0.98736	-117
TTTATGGGAATCTAATCTTTTGATGAGAAA	2	205	0	TCTAATCTTT	    0.968668	-96
          **********

Masking position 3
Map Score:   1.46044

Number of sites scoring better than the average of aligned sites = 43
Number in coding regions = 43
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:   2.79544e-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:   2.79544e-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:   2.79544e-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