AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i129_Transmembrane_Transport_3_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	HI1692	173	molybdenum ABC transporter, permease protein (modB)
#2	HI1693	137	molybdenum ABC transporter, periplasmic-binding protein (modA)

Motif number 1

GCCCTTTTGTTATTATAGAGCATCTTACCTC	1	48	1	TATATAGAGC	    0.892204	-126
ATGAATCCTTATCTAAATAGCCTCTCTTTAA	1	113	0	ATTAAATAGC	     0.92773	-61
TTATTTAGTAAAATATATAACGCTTAGGCTT	2	40	0	AATATATAAC	    0.986501	-98
TTATATATTTTACTAAATAATTTTTCTTTTG	2	51	1	TATAAATAAT	    0.879105	-87
AATAAATAACAATCATATAGCAAAAGAAAAA	2	71	0	AACATATAGC	    0.950065	-67
TTATATATTGAAATAAATAACAATCATATAG	2	82	0	AATAAATAAC	    0.986501	-56
TTATTTATTTCAATATATAATCAAGTAAATA	2	93	1	CATATATAAT	    0.859391	-45
ATATATAATCAAGTAAATAACGTTTAATCGT	2	105	1	AATAAATAAC	    0.986501	-33
          ** ********

Masking position 5
Map Score:   8.44576

Number of sites scoring better than the average of aligned sites = 189
Number in coding regions = 147
Number in noncoding regions = 42
Number of orfs with sites within 600 bp upstream = 26
Fraction of orfs with sites within 600 bp upstream = 0.00417604


Motif number 2

CTTAGGATTACTTAGGAACAGCAAA     	2	6	0	CTTAGGAACA	    0.981716	-132
AGGCTTACCACTTAGGATTACTTAGGAACA	2	16	0	CTTAGGATTA	    0.995695	-122
ATATATAACGCTTAGGCTTACCACTTAGGA	2	29	0	CTTAGGCTTA	    0.992683	-109
 AAATCATCTCCTACGATTAAACGTTATTT	2	119	0	CCTACGATTA	    0.980624	-19
          **********

Masking position 4
Map Score:   3.82552

Number of sites scoring better than the average of aligned sites = 21
Number in coding regions = 18
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 3

GCAGAAATATCCGCCCTTCATGACTATTAA	1	20	0	CCGCCCTTCA	    0.996993	-154
GCGGATATTTCTGCCCTTTTGTTATTATAG	1	36	1	CTGCCCTTTT	    0.955255	-138
GAGCATCTTACCTCTCATCAATGTGGGATA	1	65	1	CCTCTCATCA	     0.98209	-109
ATCTAAATAGCCTCTCTTTAAATCCCTTGT	1	104	0	CCTCTCTTTA	    0.988959	-70
          **********

Masking position 8
Map Score:   2.21845

Number of sites scoring better than the average of aligned sites = 96
Number in coding regions = 63
Number in noncoding regions = 33
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 4

TAGATAAGGATTCATTTTGCTTACCCAATT	1	129	1	TTCATTTTGC	    0.992961	-45
CCCAATTTTTTTCATTTTTCAATCTGACGC	1	152	1	TTCATTTTTC	    0.981029	-22
CTAAGCGTTATATATTTTACTAAATAATTT	2	44	1	TATATTTTAC	    0.929735	-94
CTAAATAATTTTTCTTTTGCTATATGATTG	2	63	1	TTTCTTTTGC	     0.98165	-75
          **********

Masking position 5
Map Score:   2.29297

Number of sites scoring better than the average of aligned sites = 123
Number in coding regions = 103
Number in noncoding regions = 20
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 5

         GATAGAATCTTAATAGTCATG	1	2	1	ATAGAATCTT	    0.964214	-172
TTGTTATTATAGAGCATCTTACCTCTCATC	1	54	1	AGAGCATCTT	    0.989008	-120
CCTTATCTAAATAGCCTCTCTTTAAATCCC	1	108	0	ATAGCCTCTC	    0.989809	-66
          AAATCATCTCCTACGATTAA	2	128	0	AAATCATCTC	    0.959407	-10
          **********

Masking position 7
Map Score:   1.19072

Number of sites scoring better than the average of aligned sites = 44
Number in coding regions = 37
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 6

          **********

No masking
Map Score:   2.58227e-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:   2.58227e-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:   2.58227e-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