AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i321_mixed6_hpyl_reg_300.orf -o321_hpyl_300.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -g0.39 -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 =  	0.39
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RHP00864	26	AE000511
#2	RHP00871	104	AE000511
#3	RHP00872	138	AE000511
#4	RHP00951	74	AE000511

Motif number 1

AATCTCAGAATTTTAACATAAAAGATTAAG	2	43	0	TTTTAACATA	      0.9906	-62
       AACTTTAAACCTAAAACCTAACG	2	92	0	TTTAAACCTA	    0.963803	-13
AATGAGCCATTTTTATCAAACAACGCTTTT	3	53	1	TTTTATCAAA	    0.931603	-86
AGTGGTCTTATTCTATCCAATTAGCCCTTG	3	94	0	TTCTATCCAA	    0.971199	-45
TAATCAAACATTCTAACATAAGGAGAATAA	4	20	0	TTCTAACATA	    0.988776	-55
TGTTTGATTATTGTAACATACTAAATAAAA	4	40	1	TTGTAACATA	     0.97945	-35
        GCTTTTATCCTATGGTTTTATT	4	63	0	TTTTATCCTA	    0.989089	-12
          **********

Masking position 5
Map Score:   12.3416

Number of sites scoring better than the average of aligned sites = 138
Number in coding regions = 110
Number in noncoding regions = 28
Number of orfs with sites within 600 bp upstream = 30
Fraction of orfs with sites within 600 bp upstream = 0.0048185


Motif number 2

    AGACAAGCCATGAAAAAAGAAAAGTC	1	7	1	GCCATGAAAA	    0.954653	-20
TAAAAATCAAGCCTTCAAAAACC       	2	4	0	GCCTTCAAAA	    0.979748	-101
TTAAGCCTAACTTTTAAAAATCAAGCCTTC	2	18	0	CTTTTAAAAA	    0.901241	-87
TTTAAAGAGAGTTTTAAAAA          	3	1	0	GTTTTAAAAA	    0.907547	-138
TTTTAAAACTCTCTTTAAAATTTTACTTTA	3	12	1	CTCTTTAAAA	    0.973497	-127
CCTTGAGCCACTCTTAAAAAGCGTTGTTTG	3	69	0	CTCTTAAAAA	    0.988342	-70
       ATCGTCATAAAAACCTTGTTCTA	3	126	0	GTCATAAAAA	    0.985657	-13
          **********

Masking position 7
Map Score:   10.4698

Number of sites scoring better than the average of aligned sites = 629
Number in coding regions = 545
Number in noncoding regions = 84
Number of orfs with sites within 600 bp upstream = 64
Fraction of orfs with sites within 600 bp upstream = 0.0102795


Motif number 3

  GGTTTTTGAAGGCTTGATTTTTAAAAGTT	2	9	1	AAGGCTTATT	    0.970971	-96
GTTTGATAAAAATGGCTCATTATATGGTATC	3	43	0	AATGGCTATT	    0.965419	-96
CTTAAAAAGCGTTGTTTGATAAAAATGGCTC	3	56	0	GTTGTTTATA	    0.794162	-83
AGAGTGGCTCAAGGGCTAATTGGATAGAATA	3	85	1	AAGGGCTATT	    0.986721	-54
TGTTCTAATAGTGGTCTTATTCTATCCAATT	3	102	0	GTGGTCTATT	    0.978881	-37
CTTATGTTAGAATGTTTGATTATTGTAACAT	4	28	1	AATGTTTATT	    0.972742	-47
CTTTTATCCTATGGTTTTATTTAGTATGTTA	4	53	0	ATGGTTTATT	     0.98277	-22
          ******* ***

Masking position 9
Map Score:   6.87844

Number of sites scoring better than the average of aligned sites = 230
Number in coding regions = 189
Number in noncoding regions = 41
Number of orfs with sites within 600 bp upstream = 36
Fraction of orfs with sites within 600 bp upstream = 0.0057822


Motif number 4

          **********

No masking
Map Score:   3.36387e-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 5

AACTTTTAAAAATCAAGCCTTCAAAAACC  	2	9	0	AATCAGCCTT	    0.913413	-96
TGATTTTTAAAAGTTAGGCTTAATCTTTTAT	2	25	1	AAGTAGGCTT	    0.942948	-80
TAAAATTTTAAAGAGAGTTTTAAAAA     	3	6	0	AAGAAGTTTT	    0.799063	-133
ACCATATAATGAGCCATTTTTATCAAACAAC	3	46	1	GAGCATTTTT	    0.902397	-93
CATTTTTATCAAACAACGCTTTTTAAGAGTG	3	60	1	AAACACGCTT	    0.704729	-79
ATTAGCCCTTGAGCCACTCTTAAAAAGCGTT	3	74	0	GAGCACTCTT	    0.945653	-65
ACCACTATTAGAACAAGGTTTTTATGACGAT	3	118	1	GAACAGGTTT	    0.959488	-21
          **** ******

Masking position 6
Map Score:   1.10117

Number of sites scoring better than the average of aligned sites = 871
Number in coding regions = 802
Number in noncoding regions = 69
Number of orfs with sites within 600 bp upstream = 53
Fraction of orfs with sites within 600 bp upstream = 0.00851269


Motif number 6

          **********

No masking
Map Score:   3.36387e-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:   3.36387e-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:   3.36387e-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