AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i011_CTP_synthase_hinf_reg_300.orf -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -g0.38 -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 =  	0.38
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	HI1077	300	CTP synthetase (pyrG)

Motif number 1

TCAAGAGATGTGTTGGTTGAGACAAATATT	1	19	0	TGTTGGTTGA	    0.996369	-282
ACATTACAAATGTTGAATGATAAATTAAGT	1	89	0	TGTTGAATGA	    0.981341	-212
TCAATGCTAGTTTTGGCTTAATCCTTTTTA	1	141	0	TTTTGGCTTA	    0.951512	-160
TTGACCGCACTTTTGGTTGATTTTGTCTGT	1	232	1	TTTTGGTTGA	    0.991858	-69
TGATTTTGTCTGTAGGATGATTAGCTATAA	1	249	1	TGTAGGATGA	    0.988153	-52
          **********

Masking position 3
Map Score:   7.16071

Number of sites scoring better than the average of aligned sites = 74
Number in coding regions = 67
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 2

TGCCACTACATACTTATTCAAGCAGTTAAA	1	53	0	TACTTATTCA	    0.907333	-248
TGGCATTTAATACTTAATTTATCATTCAAC	1	78	1	TACTTAATTT	    0.949009	-223
GATGGTAGTTTACCTGATTTGCGCAATGAA	1	172	0	TACCTGATTT	    0.964779	-129
CCGTCTTTGATAGCTAATTATCTTCGATTT	1	202	1	TAGCTAATTA	    0.971932	-99
TAAATGATTATAGCTAATCATCCTACAGAC	1	256	0	TAGCTAATCA	    0.983876	-45
      AGGGAACCTAATCTGTATTGGAAT	1	287	0	AACCTAATCT	    0.966732	-14
          **********

Masking position 5
Map Score:   4.51117

Number of sites scoring better than the average of aligned sites = 179
Number in coding regions = 142
Number in noncoding regions = 37
Number of orfs with sites within 600 bp upstream = 28
Fraction of orfs with sites within 600 bp upstream = 0.00449727


Motif number 3

CATATTTTAATATTTGTCTCAACCAACACA	1	11	1	TATTTGTCTC	    0.924381	-290
TCTCTTGATGTTTTTAACTGCTTGAATAAG	1	41	1	TTTTTAACTG	    0.970917	-260
GGCTTAATCCTTTTTATCCTTGGAAAGGAT	1	127	0	TTTTTATCCT	    0.928576	-174
TTATCTTCGATTTTTGACCGCACTTTTGGT	1	219	1	TTTTTGACCG	    0.987838	-82
CTTTTGGTTGATTTTGTCTGTAGGATGATT	1	241	1	ATTTTGTCTG	    0.970387	-60
          **********

Masking position 5
Map Score:   1.90053

Number of sites scoring better than the average of aligned sites = 406
Number in coding regions = 304
Number in noncoding regions = 102
Number of orfs with sites within 600 bp upstream = 87
Fraction of orfs with sites within 600 bp upstream = 0.0139737


Motif number 4

CTTGAATAAGTATGTAGTGGCATTTAATACTTA	1	61	1	TTGTATGGAT	     0.99573	-240
TCATTCAACATTTGTAATGTGATTGTGGATCCT	1	99	1	TTGTATGTAT	    0.993405	-202
GTTGATTTTGTCTGTAGGATGATTAGCTATAAT	1	247	1	TTGTAGATAT	    0.957009	-54
GGGAACCTAATCTGTATTGGAATATAAATGATT	1	277	0	TTGTATGGAT	    0.995724	-24
          * **** *** **

Masking position 6
Map Score:   2.05663

Number of sites scoring better than the average of aligned sites = 14
Number in coding regions = 11
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 5

CAAGCAGTTAAAAACATCAAGAGATGTGTT	1	35	0	AAAACATCAA	    0.936666	-266
TTATCCTTGGAAAGGATCCACAATCACATT	1	114	0	AAAGGATCCA	    0.984479	-187
CCAAGGATAAAAAGGATTAAGCCAAAACTA	1	134	1	AAAGGATTAA	     0.93165	-167
CCTACAGACAAAATCAACCAAAAGTGCGGT	1	235	0	AAATCAACCA	    0.935468	-66
TGATTATAGCTAATCATCCTACAGACAAAA	1	252	0	TAATCATCCT	    0.885966	-49
ATTGGAATATAAATGATTATAGCTAATCAT	1	265	0	AAATGATTAT	    0.871251	-36
          **********

Masking position 6
Map Score:   1.32918

Number of sites scoring better than the average of aligned sites = 513
Number in coding regions = 447
Number in noncoding regions = 66
Number of orfs with sites within 600 bp upstream = 50
Fraction of orfs with sites within 600 bp upstream = 0.00803084


Motif number 6

TACAAATGTTGAATGATAAATTAAGTATTAA	1	84	0	GAATGTAAAT	    0.960405	-217
GCAATGAACTCAATGCTAGTTTTGGCTTAAT	1	149	0	CAATGTAGTT	    0.962627	-152
ATCAAAGACGGGATGGTAGTTTACCTGATTT	1	182	0	GGATGTAGTT	    0.988309	-119
GGTCAAAAATCGAAGATAATTAGCTATCAAA	1	207	0	CGAAGTAATT	    0.974039	-94
AATCTGTATTGGAATATAAATGATTATAGCT	1	271	0	GGAATTAAAT	    0.879644	-30
          ***** *****

Masking position 7
Map Score:   0.167492

Number of sites scoring better than the average of aligned sites = 100
Number in coding regions = 89
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 11
Fraction of orfs with sites within 600 bp upstream = 0.00176678


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


Motif number 8

          **********

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 9

          **********

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