AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i00480_hpyl_reg_100.orf -o00480_hpyl_100.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -0.39 -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 =  	0.38
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	HP0027	198	isocitrate dehydrogenase (icd)
#2	HP1101	65	glucose-6-phosphate dehydrogenase (g6pD)
#3	HP1118	210	gamma-glutamyltranspeptidase (ggt)

Motif number 1

AACGCAATGTTTTTAAAAGAAATCATTTAATTTTTTGGCTTAT	1	50	0	TTTTAATAAT	    0.978861	-149
AACATTGCGTTTTTTCAAGTTATTTCCAACCGCTACTTTTAAA	1	82	1	TTTTAATTAC	    0.971623	-117
TAAAAATCTTTTTTTGAATGCGTGTTTAAAAGTAGCGGTTGGA	1	106	0	TTTTAATTAT	    0.993159	-93
AAAAAAAGATTTTTAAGGGTTATATAGTATTTTTGCGCTAGTA	1	134	1	TTTTGGTTAT	    0.943619	-65
TGTTTATCCTTTTTCTAAAGTTTGAGTAACTATACTAGCGCAA	1	166	0	TTTTAATAAT	    0.978862	-33
TTTTAGAGTGTTTTTGAGTTATTATTATATATTAAATCTTAAT	2	24	0	TTTTAGTTAT	     0.98623	-42
CAAATAAGCCTTATTTAACTTATTTTTTAAACTCTATCTATTT	3	35	1	TTATAATTAT	    0.958501	-176
ACTCTATCTATTTTAAAACTCATTTTTGAGCCTTTTTTATAGC	3	65	1	TTTTAATTAT	    0.993222	-146
CGAGAGAGTGTTTTGTAAAGCTTGTGTTATAATAACAAAGAAA	3	147	1	TTTTAATTAT	    0.993222	-64
          ****  **    * *   *   *

Masking position 13
Map Score:   13.4799

Number of sites scoring better than the average of aligned sites = 310
Number in coding regions = 249
Number in noncoding regions = 61
Number of orfs with sites within 600 bp upstream = 50
Fraction of orfs with sites within 600 bp upstream = 0.00803084


Motif number 2

CCTAATTATAAGCCAAAAAATTAAATGATT	1	43	1	AGCCAAAAAA	    0.885719	-156
TTAAATGATTTCTTTTAAAAACATTGCGTT	1	63	1	TCTTTTAAAA	    0.772819	-136
GTTGGAAATAACTTGAAAAAACGCAATGTT	1	82	0	ACTTGAAAAA	    0.898319	-117
TCCAACCGCTACTTTTAAACACGCATTCAA	1	106	1	ACTTTTAAAC	    0.918757	-93
TTAAACACGCATTCAAAAAAAGATTTTTAA	1	120	1	ATTCAAAAAA	    0.725353	-79
ATACTATATAACCCTTAAAAATCTTTTTTT	1	134	0	ACCCTTAAAA	    0.961851	-65
AGTTACTCAAACTTTAGAAAAAGGATAAAC	1	178	1	ACTTTAGAAA	    0.856091	-21
TATAATAATAACTCAAAAACACTCTAAAAG	2	38	1	ACTCAAAAAC	     0.90376	-28
ACTCAAAAACACTCTAAAAGGGTTATTG  	2	48	1	ACTCTAAAAG	    0.907734	-18
AAATAGATAGAGTTTAAAAAATAAGTTAAA	3	48	0	AGTTTAAAAA	    0.950591	-163
CTCAAAAATGAGTTTTAAAATAGATAGAGT	3	65	0	AGTTTTAAAA	    0.943369	-146
TTTGAGCGCTAGCTATAAAAAAGGCTCAAA	3	89	0	AGCTATAAAA	    0.828834	-122
TCAATCAGTTACGCTTAAAATTTCTTTGTT	3	180	0	ACGCTTAAAA	    0.903898	-31
          **********

Masking position 8
Map Score:   12.069

Number of sites scoring better than the average of aligned sites = 1534
Number in coding regions = 1266
Number in noncoding regions = 268
Number of orfs with sites within 600 bp upstream = 194
Fraction of orfs with sites within 600 bp upstream = 0.0311597


Motif number 3

CTTAAGTTTTGATAGCATTCAACTCCTAAT	1	19	1	GATAGCATTC	    0.947681	-180
CTTTTAAAAACATTGCGTTTTTTCAAGTTA	1	74	1	CATTGCGTTT	    0.930231	-125
TTAAGGGTTATATAGTATTTTTGCGCTAGT	1	146	1	TATAGTATTT	    0.841951	-53
ATAACCCTTTTAGAGTGTTTTTGAGTTATT	2	44	0	TAGAGTGTTT	    0.929522	-22
GTTTTCTACCCATAGCGTTTTGATCAAATA	3	11	1	CATAGCGTTT	    0.986738	-200
TTTTAAAATAGATAGAGTTTAAAAAATAAG	3	53	0	GATAGAGTTT	    0.964638	-158
CTTTTTTATAGCTAGCGCTCAAACCATTAA	3	96	1	GCTAGCGCTC	    0.850376	-115
TTATAAGCGAGAGAGTGTTTTGTAAAGCTT	3	140	1	GAGAGTGTTT	    0.975018	-71
          **********

Masking position 9
Map Score:   5.72112

Number of sites scoring better than the average of aligned sites = 913
Number in coding regions = 831
Number in noncoding regions = 82
Number of orfs with sites within 600 bp upstream = 54
Fraction of orfs with sites within 600 bp upstream = 0.00867331


Motif number 4

CATTTAATTTTTTGGCTTATAATTAGGAGT	1	40	0	TTTGGCTTAT	    0.829395	-159
       TGTTTATCCTTTTTCTAAAGTTT	1	186	0	TTATCCTTTT	    0.974822	-13
       CAATAACCCTTTTAGAGTGTTTT	2	53	0	TAACCCTTTT	    0.940651	-13
TTTGATCAAATAAGCCTTATTTAACTTATT	3	29	1	TAAGCCTTAT	    0.948672	-182
AACTCATTTTTGAGCCTTTTTTATAGCTAG	3	81	1	TGAGCCTTTT	    0.985012	-130
ATAACTTACATGATGCTATTAATGGTTTGA	3	114	0	TGATGCTATT	    0.785476	-97
       CTGTTTTCCTTTCAATCAGTTAC	3	198	0	TTTTCCTTTC	     0.83826	-13
          **********

Masking position 7
Map Score:   1.67923

Number of sites scoring better than the average of aligned sites = 778
Number in coding regions = 670
Number in noncoding regions = 108
Number of orfs with sites within 600 bp upstream = 114
Fraction of orfs with sites within 600 bp upstream = 0.0183103


Motif number 5

          **********

No masking
Map Score:   1.09013e-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:   1.09013e-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:   1.09013e-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