AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i011_CTP_synthase_hinf_reg_100.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

AATATTTGTCTCAACCAACACATCTCTTGA	1	19	1	TCAACCAACA	    0.995863	-282
ACTTAATTTATCATTCAACATTTGTAATGT	1	89	1	TCATTCAACA	    0.978784	-212
TAAAAAGGATTAAGCCAAAACTAGCATTGA	1	141	1	TAAGCCAAAA	    0.945093	-160
ACAGACAAAATCAACCAAAAGTGCGGTCAA	1	232	0	TCAACCAAAA	    0.990729	-69
TTATAGCTAATCATCCTACAGACAAAATCA	1	249	0	TCATCCTACA	    0.986517	-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

ATGCCACTACATACTTATTCAAGCAGTTAA	1	54	0	ATACTTATTC	    0.922169	-247
GTGGCATTTAATACTTAATTTATCATTCAA	1	77	1	ATACTTAATT	    0.968298	-224
GGATGGTAGTTTACCTGATTTGCGCAATGA	1	173	0	TTACCTGATT	     0.90947	-128
CCCGTCTTTGATAGCTAATTATCTTCGATT	1	201	1	ATAGCTAATT	    0.979273	-100
ATAAATGATTATAGCTAATCATCCTACAGA	1	257	0	ATAGCTAATC	    0.986718	-44
       AGGGAACCTAATCTGTATTGGAA	1	288	0	GAACCTAATC	    0.940459	-13
          **********

Masking position 6
Map Score:   3.42966

Number of sites scoring better than the average of aligned sites = 222
Number in coding regions = 193
Number in noncoding regions = 29
Number of orfs with sites within 600 bp upstream = 24
Fraction of orfs with sites within 600 bp upstream = 0.0038548


Motif number 3

CATATTTTAATATTTGTCTCAACCAACACA	1	11	1	TATTTGTCTC	    0.921039	-290
TCTCTTGATGTTTTTAACTGCTTGAATAAG	1	41	1	TTTTTAACTG	    0.969564	-260
GGCTTAATCCTTTTTATCCTTGGAAAGGAT	1	127	0	TTTTTATCCT	    0.925405	-174
TTATCTTCGATTTTTGACCGCACTTTTGGT	1	219	1	TTTTTGACCG	    0.987262	-82
CTTTTGGTTGATTTTGTCTGTAGGATGATT	1	241	1	ATTTTGTCTG	     0.96901	-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

TAAGTATTAAATGCCACTACATACTTATTCAAG	1	61	0	ATCCATACAA	    0.995774	-240
AGGATCCACAATCACATTACAAATGTTGAATGA	1	99	0	ATACATACAA	    0.993473	-202
ATTATAGCTAATCATCCTACAGACAAAATCAAC	1	247	0	ATATCTACAA	    0.957436	-54
AATCATTTATATTCCAATACAGATTAGGTTCCC	1	277	1	ATCCATACAA	    0.995769	-24
          ** *** **** *

Masking position 8
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

ATTTGTCTCAACCAACACATCTCTTGATGT	1	22	1	ACCAACACAT	    0.990365	-279
GAAAGGATCCACAATCACATTACAAATGTT	1	105	0	ACAATCACAT	    0.985177	-196
CAGGTAAACTACCATCCCGTCTTTGATAGC	1	186	1	ACCATCCCGT	    0.992176	-115
          **********

Masking position 4
Map Score:   0.807304

Number of sites scoring better than the average of aligned sites = 22
Number in coding regions = 19
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 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


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