AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i111_Amino_Acid_Transport_2_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	HI1549	146	ABC transporter, ATP-binding protein
#2	HI1556	59	2-hydroxyacid dehydrogenase
#3	HI1560	22	H. influenzae predicted coding region HI1560
#4	HI1561	106	peptide chain release factor 1 (prfA)

Motif number 1

GCACGAGTCTATCACACTTTTCCTTGAGCT	1	75	0	ATCACACTTT	    0.988571	-72
ACTCGTTTTAACCGCACTTTAGCGGCAGAT	1	122	0	ACCGCACTTT	    0.999206	-25
GTCAAAATTAACCGCACTTTTGATGAAAT 	2	10	0	ACCGCACTTT	    0.999206	-50
GTTAATTTTGACCGCACTTTGTATATAAAA	2	28	1	ACCGCACTTT	    0.999206	-32
          **********

Masking position 6
Map Score:   12.972

Number of sites scoring better than the average of aligned sites = 1115
Number in coding regions = 700
Number in noncoding regions = 415
Number of orfs with sites within 600 bp upstream = 285
Fraction of orfs with sites within 600 bp upstream = 0.0457758


Motif number 2

GATTTGAATACTTTAGGTGTATTGAAATTTAAG	1	44	1	CTTTAGTGTT	    0.979794	-103
TCTATCACACTTTTCCTTGAGCTTAAATTTCAA	1	65	0	TTTTCCTGAT	    0.986776	-82
CTCGTGCAAGTTTTTGATGGTGTTATCTGCCGC	1	98	1	TTTTTGTGGT	    0.948671	-49
         TTTTTACTCGTTTTAACCGCACTT	1	133	0	TTTTACCGTT	    0.894095	-14
ATTAACCGCACTTTTGATGAAAT          	2	1	0	CTTTTGTGAT	    0.971117	-59
ATCTCAGACGCTTTATTTGTGATTTACCCA   	4	8	0	CTTTATTGTT	    0.882376	-99
CTTAATTTCCTTTTCGCTGTCAATTTTCCCTAA	4	42	1	TTTTCGTGTA	    0.950177	-65
TCGCTGTCAATTTTCCCTAAAATCGGCTAGAAT	4	55	1	TTTTCCTAAT	    0.879372	-52
GCCGATTTTATTTTCGGTGACTTACAA      	4	90	1	TTTTCGTGAT	    0.991822	-17
          ****** ***  *

Masking position 4
Map Score:   7.32472

Number of sites scoring better than the average of aligned sites = 597
Number in coding regions = 492
Number in noncoding regions = 105
Number of orfs with sites within 600 bp upstream = 92
Fraction of orfs with sites within 600 bp upstream = 0.0147767


Motif number 3

GTATTCAAATCCTGTTTCAGGAAAATGTTT	1	25	0	CCTGTTTCAG	    0.981357	-122
  TAATTGCTCCTTTTTTATATACAAAGTG	2	42	0	CCTTTTTTAT	    0.935814	-18
ATAGGGACATCTGATTTCAG          	3	13	1	CTGATTTCAG	    0.901644	-10
CGTATTCTAGCCGATTTTAGGGAAAATTGA	4	61	0	CCGATTTTAG	    0.995291	-46
ATAAAATCGGCGTATTCTAGCCGATTTTAG	4	71	0	CGTATTCTAG	    0.936467	-36
CTAGAATACGCCGATTTTATTTTCGGTGAC	4	81	1	CCGATTTTAT	    0.986908	-26
          **********

Masking position 5
Map Score:   5.72242

Number of sites scoring better than the average of aligned sites = 210
Number in coding regions = 181
Number in noncoding regions = 29
Number of orfs with sites within 600 bp upstream = 31
Fraction of orfs with sites within 600 bp upstream = 0.00497912


Motif number 4

ACTTTTCCTTGAGCTTAAATTTCAATACAC	1	60	0	GAGCTTAAAT	    0.944743	-87
CCGCTAAAGTGCGGTTAAAACGAGTAAAAA	1	127	1	GCGGTTAAAA	    0.986314	-20
CATCAAAAGTGCGGTTAATTTTGACCGCAC	2	15	1	GCGGTTAATT	    0.994538	-45
TTTCCTTTTCGCTGTCAATTTTCCCTAAAA	4	47	1	GCTGTCAATT	    0.964137	-60
          **********

Masking position 5
Map Score:   1.19729

Number of sites scoring better than the average of aligned sites = 696
Number in coding regions = 454
Number in noncoding regions = 242
Number of orfs with sites within 600 bp upstream = 170
Fraction of orfs with sites within 600 bp upstream = 0.0273049


Motif number 5

     AACGTTATCTTGAAAAACATTTTCC	1	6	1	TATCTTGAAA	    0.872384	-141
TGAAAAACATTTTCCTGAAACAGGATTTGA	1	21	1	TTTCCTGAAA	    0.683727	-126
ATACACCTAAAGTATTCAAATCCTGTTTCA	1	36	0	AGTATTCAAA	    0.895458	-111
ATACTTTAGGTGTATTGAAATTTAAGCTCA	1	51	1	TGTATTGAAA	    0.964598	-96
         ATTTCATCAAAAGTGCGGTTA	2	2	1	TTTCATCAAA	    0.664675	-58
GCTCCTTTTTTATATACAAAGTGCGGTCAA	2	35	0	TATATACAAA	    0.845784	-25
          **********

Masking position 3
Map Score:   1.94395

Number of sites scoring better than the average of aligned sites = 331
Number in coding regions = 260
Number in noncoding regions = 71
Number of orfs with sites within 600 bp upstream = 79
Fraction of orfs with sites within 600 bp upstream = 0.0126887


Motif number 6

          **********

No masking
Map Score:   -3.24418e-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:   -3.24418e-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:   -3.24418e-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