AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i150_ATP_synthase_1_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	HI0478	29	ATP synthase F1, subunit epsilon (atpC)
#2	HI0483	49	ATP synthase F0, subunit b (atpF)
#3	HI0484	55	ATP synthase F0, subunit c (atpE)
#4	HI0485	36	ATP synthase F0, subunit a (atpB)
#5	HI0485.1	125	H. influenzae predicted coding region HI0485.1

Motif number 1

AGCCCTAGAGCCGGTTAATAAAAAACGA       	3	4	0	CCTTAAAAAA	    0.990255	-52
AACTTAACTTCTATTGGAGAAAATT          	3	41	1	CTTGAAAAAT	    0.919572	-15
TTGGGTTATTCTTCTTCAGAACAAAGGATCGATT 	4	13	1	CTTTAAACAA	    0.989783	-24
ATATAAATCACACTTTTAGAAAATAATTTATCTAT	5	21	0	CATTAAAAAA	    0.993746	-105
GCTTTAGATTCAACTTAAAAACACATAAAAAGTGT	5	57	0	CATTAAACAA	      0.9934	-69
          CACTTTTACAAAATAATTTTAGCCC	5	111	0	CATTAAAAAA	    0.993746	-15
          **  ** * **** *

Masking position 8
Map Score:   7.04817

Number of sites scoring better than the average of aligned sites = 114
Number in coding regions = 73
Number in noncoding regions = 41
Number of orfs with sites within 600 bp upstream = 41
Fraction of orfs with sites within 600 bp upstream = 0.00658529


Motif number 2

ACACTTTTAGAAAATAATTTATCTATTTGTT	5	16	0	AAATAATTTA	     0.82047	-110
TGTTATATAAATCACACTTTTAGAAAATAAT	5	29	0	ATACACTTTT	    0.988727	-97
TGTGATTTATATAACACTTTTTATGTGTTTT	5	44	1	ATACACTTTT	     0.98772	-82
TAGCCCGCCGATTATACCTTTGCTGGCTTTA	5	86	0	ATATACCTTT	    0.973524	-40
 CACTTTTACAAAATAATTTTAGCCCGCCGA	5	106	0	AAATAATTTT	    0.607838	-20
          ** ********

Masking position 6
Map Score:   3.04046

Number of sites scoring better than the average of aligned sites = 80
Number in coding regions = 58
Number in noncoding regions = 22
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 3

       TCACCTTATTTGCTTATCAACGTAAAA	2	4	1	CCTTTTGTTT	    0.988661	-46
 AACGTCCTCCTTACTATGCTTGTTTTACGTTGA	2	27	0	CTTATTGTTT	    0.962889	-23
          CTTTGGGTTATTCTTCTTCAGAAC	4	1	1	CTTTGTTTTT	    0.967174	-36
AATAATTTATCTATTTGTTACTTT          	5	1	0	CTATTTTCTT	    0.904441	-125
TTATATAACACTTTTTATGTGTTTTTAAGTTGAA	5	50	1	CTTTTTGGTT	     0.98405	-76
GCCGATTATACCTTTGCTGGCTTTAGATTCAACT	5	77	0	CCTTGTGCTT	    0.987347	-49
          **** * ** ** *

Masking position 8
Map Score:   1.87181

Number of sites scoring better than the average of aligned sites = 120
Number in coding regions = 97
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


Motif number 4

       TTTGTTCTCCTTCAAATGACTTG	1	17	0	GTTCTCCTTC	    0.995296	-13
       AACGTCCTCCTTACTATGCTTGT	2	37	0	GTCCTCCTTA	     0.98769	-13
 CTTTGGGTTATTCTTCTTCAGAACAAAGG	4	10	1	ATTCTTCTTC	    0.980449	-27
CTGGCTTTAGATTCAACTTAAAAACACATA	5	65	0	ATTCAACTTA	      0.9277	-61
          **********

Masking position 8
Map Score:   1.69136

Number of sites scoring better than the average of aligned sites = 54
Number in coding regions = 46
Number in noncoding regions = 8
Number of orfs with sites within 600 bp upstream = 7
Fraction of orfs with sites within 600 bp upstream = 0.00112432


Motif number 5

TAGAAGTTAAGTTTTAGCCCTAGAGCCGGT	3	24	0	GTTTTAGCCC	      0.9948	-32
         AATTTTCTCCAATAGAAGTTA	3	45	0	ATTTTCTCCA	    0.962906	-11
TTACAAAATAATTTTAGCCCGCCGATTATA	5	101	0	ATTTTAGCCC	    0.995663	-25
          **********

Masking position 5
Map Score:   0.853792

Number of sites scoring better than the average of aligned sites = 32
Number in coding regions = 28
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 4
Fraction of orfs with sites within 600 bp upstream = 0.000642467


Motif number 6

          **********

No masking
Map Score:   3.15071e-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:   3.15071e-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:   3.15071e-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