AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i191_dna_gyrase_ctra_reg_300.orf -o191_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	RCT00631	300	Chlamydia_trachomatis

Motif number 1

ATATTGGTATAAAAATACGAAACAAAGAGA	1	20	0	AAAAATACGA	    0.914854	-281
AGAGAGTCTCAAAAATATTGGTATAAAAAT	1	34	0	AAAAATATTG	    0.963682	-267
TCTGCATTGAAAAAATTTTGTAGTCTGGAG	1	70	1	AAAAATTTTG	    0.923833	-231
GAAGACTAAAAGAAATACTACGCCTTACAT	1	189	1	AGAAATACTA	    0.914854	-112
CTCTCTTTAGAAAAATAATGTAAGGCGTAG	1	206	0	AAAAATAATG	    0.965071	-95
ACAATCAGCTAATAGTTATGCTCTCTTTAG	1	226	0	AATAGTTATG	    0.738624	-75
TTGTTTTCTCAGAAATTATAGAACCCGAAT	1	252	1	AGAAATTATA	    0.908329	-49
GGAATAAGGCAAAAGTTTGATTCGGGTTCT	1	271	0	AAAAGTTTGA	    0.849243	-30
          **********

Masking position 4
Map Score:   5.47198

Number of sites scoring better than the average of aligned sites = 361
Number in coding regions = 361
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

TGGTATAAAAATACGAAACAAAGAGAATGAG	1	15	0	ATACGAAACA	    0.967254	-286
TTTCGTCTCCAGACTACAAAATTTTTTCAAT	1	75	0	AGACTACAAA	    0.982462	-226
TGTAGTCTGGAGACGAAAATAGAAAAACCGT	1	88	1	AGACGAAAAA	    0.982465	-213
AGGACTTGAGATACTAAGATTAAGCCGTGGA	1	132	0	ATACTAAGAT	     0.94995	-169
GTGAGACAGAAGACTAAAAGAAATACTACGC	1	181	1	AGACTAAAAA	    0.985419	-120
ACTAAAAGAAATACTACGCCTTACATTATTT	1	193	1	ATACTACGCT	     0.92523	-108
          ********* *

Masking position 6
Map Score:   3.98002

Number of sites scoring better than the average of aligned sites = 53
Number in coding regions = 52
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 3

         TTGGCTCATTCTCTTTGTTTC	1	2	1	TGGCTCATTC	    0.974156	-299
GCCGTGGAAACGCCTTTTTTAACGGTTTTT	1	110	0	CGCCTTTTTT	    0.918145	-191
GGCGTTTCCACGGCTTAATCTTAGTATCTC	1	126	1	CGGCTTAATC	    0.981568	-175
CAAGTCCTCACCGCTCACACTGCTTAGTGA	1	155	1	CCGCTCACAC	    0.936702	-146
AGAAATACTACGCCTTACATTATTTTTCTA	1	199	1	CGCCTTACAT	    0.963377	-102
ATCAAACTTTTGCCTTATTCCACACACTCT	1	280	1	TGCCTTATTC	    0.978479	-21
          **********

Masking position 5
Map Score:   2.4572

Number of sites scoring better than the average of aligned sites = 138
Number in coding regions = 138
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

     TTGGCTCATTCTCTTTGTTTCGTAT	1	6	1	TCATTCTCTT	    0.965886	-295
AATATTTTTGAGACTCTCTTCGTTCTCTGC	1	45	1	AGACTCTCTT	    0.993566	-256
GCTAATAGTTATGCTCTCTTTAGAAAAATA	1	219	0	ATGCTCTCTT	    0.983885	-82
GCCTTATTCCACACACTCTT          	1	291	1	ACACACTCTT	    0.991188	-10
          **********

Masking position 7
Map Score:   2.2247

Number of sites scoring better than the average of aligned sites = 97
Number in coding regions = 97
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:   7.91135e-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:   7.91135e-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:   7.91135e-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