AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i312_mixed26_ctra_reg_300.orf -o312_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	RCT00337	60	Chlamydia_trachomatis
#2	RCT00338	300	Chlamydia_trachomatis

Motif number 1

ATAGAACTCCGTGCCACCCTTCCCCGCCTTTT	1	11	0	GTCCCCCTTC	    0.991858	-50
TTTGCTCTTAGTTACCCCTCTTTTCGATATTT	2	15	1	GTACCCTCTT	    0.959157	-286
TGACGGCTGGGTCCCTCCTCCCCTATAGCTTT	2	124	1	GTCCCCTCCC	    0.999407	-177
TTCTAAAAAAGAACCTACCCTCGTCCTAGGTA	2	156	0	GACCACCCTC	    0.961961	-145
GTTTGGGTGTTTGCCACATCTCTAGGGAGGCG	2	201	1	TTCCCATCTC	    0.980155	-100
TCTTTGGATCTTACCGCCTCCCTAGAGATGTG	2	215	0	TTCCCCTCCC	     0.99783	-86
ATTTTGGGTTGTTCCTCCTCCCCTTTTTCTTT	2	242	0	GTCCCCTCCC	    0.999407	-59
          ** ** ******

Masking position 5
Map Score:   13.2163

Number of sites scoring better than the average of aligned sites = 50
Number in coding regions = 50
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

   TGATCTCAGAAAAGAAGTTAACTGTTC	1	44	0	AGAAAAGAAG	    0.972369	-17
GGTAACTAAGAGCAAAACAC          	2	1	0	AGCAAAACAC	     0.94472	-300
AGCCAAAGGAAACAAAAATGTATTTTTCTG	2	61	0	AACAAAAATG	    0.948898	-240
GAACACTTTTAACAAAAAAGCGTTATATCC	2	94	0	AACAAAAAAG	    0.988943	-207
CTTATATTCTAAAAAAGAACCTACCCTCGT	2	164	0	AAAAAAGAAC	    0.956648	-137
CAAACACCCAAACAAAGCAGCTTATATTCT	2	184	0	AACAAAGCAG	    0.986428	-117
GGTAAGATCCAAAGAAAAAGGGGAGGAGGA	2	232	1	AAAGAAAAAG	    0.930193	-69
          **********

Masking position 5
Map Score:   7.87937

Number of sites scoring better than the average of aligned sites = 211
Number in coding regions = 211
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

GTGCCACCCTTCCCCGCCTTTT        	1	3	0	TCCCCGCCTT	    0.996436	-58
TGCTCTTAGTTACCCCTCTTTTCGATATTT	2	17	1	TACCCCTCTT	    0.927639	-284
GGGAGGAGGGACCCAGCCGTCAGAACACTT	2	116	0	ACCCAGCCGT	    0.948813	-185
GCTGGGTCCCTCCTCCCCTATAGCTTTTAC	2	129	1	TCCTCCCCTA	    0.990434	-172
CTAAAAAAGAACCTACCCTCGTCCTAGGTA	2	156	0	ACCTACCCTC	    0.965268	-145
GGGTTGTTCCTCCTCCCCTTTTTCTTTGGA	2	239	0	TCCTCCCCTT	    0.997073	-62
          **********

Masking position 3
Map Score:   6.30935

Number of sites scoring better than the average of aligned sites = 85
Number in coding regions = 85
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

TTACCCCTCTTTTCGATATTTAAGTGAAAAA	2	26	1	TTTCGATTTT	    0.968262	-275
AATGTATTTTTCTGGAATTTTTTCACTTAAA	2	44	0	TCTGGAATTT	    0.906454	-257
AGCTGCTTTGTTTGGGTGTTTGCCACATCTC	2	192	1	TTTGGGTTTT	    0.994114	-109
CCCCTTTTTCTTTGGATCTTACCGCCTCCCT	2	224	0	TTTGGATTTA	    0.963637	-77
CCTTAAGAATTTTGGGTTGTTCCTCCTCCCC	2	251	0	TTTGGGTGTT	    0.984067	-50
CCCAAAATTCTTAAGGTTTTTCTACCTAAAA	2	266	1	TTAAGGTTTT	    0.888704	-35
          ******* ***

Masking position 10
Map Score:   3.18846

Number of sites scoring better than the average of aligned sites = 109
Number in coding regions = 109
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

TTTTTGTTTCCTTTGGCTTGAGGATATAAC	2	73	1	CTTTGGCTTG	    0.973166	-228
CCCCTATAGCTTTTACCTAGGACGAGGGTA	2	143	1	TTTTACCTAG	    0.961444	-158
CCTCCTCCCCTTTTTCTTTGGATCTTACCG	2	231	0	TTTTTCTTTG	    0.881363	-70
ACCTTAAGAATTTTGGGTTGTTCCTCCTCC	2	253	0	TTTTGGGTTG	    0.987731	-48
GATTTGTAGTTTTTAGGTAGAAAAACCTTA	2	277	0	TTTTAGGTAG	    0.973207	-24
          **********

Masking position 4
Map Score:   1.47765

Number of sites scoring better than the average of aligned sites = 89
Number in coding regions = 89
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:   2.36911e-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:   2.36911e-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:   2.36911e-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