AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i149_Thioredoxin_hpyl_reg_300.orf -o149_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	RHP00236	132	AE000511
#2	RHP00241	68	AE000511
#3	RHP00243	173	AE000511
#4	RHP00247	88	AE000511

Motif number 1

TTATTGTTGGTTGAGATGAGTTTGATGAAAGGAAA	1	14	0	TTGAAGTTTA	    0.918395	-119
TTTGACTAGAATAGCGCTTCTATTATTGTTGGTTG	1	36	0	ATAGGTTATA	    0.682014	-97
TAGCGCAAAAATAAGGCGATTTTGACTAGAATAGC	1	56	0	ATAAGGTTTA	    0.988027	-77
ATTTTCAATAATAATGACTTTTTAAAACTAGTTTG	1	93	1	ATAAGCTTTA	    0.879416	-40
TAAAACTAGTTTGAAGGGAGTTTGGAGT       	1	115	1	TTGAGGTTTG	    0.943289	-18
AAGGCATTCTTTAATGTTGGTTGCAGG        	2	3	0	TTAAGTTTGA	    0.929928	-66
ACTTATTTGGATAAAGGGGTTTTAAAATGCTAAAG	2	35	0	ATAAGGTTTA	    0.821795	-34
        TTTTAAGGCTGATTTAAAAATTCTGGC	3	3	1	TTAAGTTTTA	    0.975754	-171
CGTGGTGCTGTTGGTGGGCGTTTGCATAGAAGAAT	3	37	1	TTGGGGTTTC	    0.938005	-137
CATAGAAGAATTAGAGCTGTTTGAAGTTTTTTTAG	3	61	1	TTAGGTTTGA	    0.923267	-113
TGAAGTTTTTTTAGCGGGTTTTTCATTGAATGGAG	3	82	1	TTAGGGTTTA	    0.992509	-92
TTTTCATTGAATGGAGGGGCTTTATAACCGCAAGC	3	101	1	ATGGGGTTTT	    0.852747	-73
 AAACTGATCTTAACATGCTTTTTAGCGCTTGTAG	3	150	0	TTAAAGTTTA	     0.94339	-24
ATGATTTTGATTAACGAGAATTATATTAGCTTAAG	4	47	0	TTAAGGTTAA	    0.944214	-42
          **** * *  *** *

Masking position 11
Map Score:   17.2245

Number of sites scoring better than the average of aligned sites = 2138
Number in coding regions = 1912
Number in noncoding regions = 226
Number of orfs with sites within 600 bp upstream = 158
Fraction of orfs with sites within 600 bp upstream = 0.0253774


Motif number 2

   GATTTTCCTTTCATCAAACTCATCTCA	1	8	1	CTTTCATCAA	    0.946866	-125
ATAATAGAAGCGCTATTCTAGTCAAAATCG	1	45	1	CGCTATTCTA	    0.868348	-88
  ACTCCAAACTCCCTTCAAACTAGTTTTA	1	115	0	CTCCCTTCAA	    0.983159	-18
         CCTGCAACCAACATTAAAGAA	2	2	1	CTGCAACCAA	    0.943116	-67
TTTAAAACCCCTTTATCCAAATAAGTTTGG	2	44	1	CTTTATCCAA	    0.946865	-25
TCTATGCAAACGCCCACCAACAGCACCACG	3	37	0	CGCCCACCAA	    0.982483	-137
TATAAAGCCCCTCCATTCAATGAAAAACCC	3	97	0	CTCCATTCAA	    0.983487	-77
ATATAATTCTCGTTAATCAAAATCATATAT	4	56	1	CGTTAATCAA	    0.946866	-33
          **********

Masking position 10
Map Score:   9.29726

Number of sites scoring better than the average of aligned sites = 361
Number in coding regions = 331
Number in noncoding regions = 30
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 3

TCAATAATAATGACTTTTTAAAACTAGTTT	1	97	1	TGACTTTTTA	    0.821741	-36
GAATGCCTTTAGCATTTTAAAACCCCTTTA	2	29	1	AGCATTTTAA	    0.946808	-40
TATCCAAATAAGTTTGGTTATA        	2	57	1	AGTTTGGTTA	    0.878244	-12
GCACCACGCCAGAATTTTTAAATCAGCCTT	3	15	0	AGAATTTTTA	    0.971784	-159
AGCTGTTTGAAGTTTTTTTAGCGGGTTTTT	3	75	1	AGTTTTTTTA	    0.889267	-99
ACCGCAAGCTTGAATGGTTATTGCTACAAG	3	127	1	TGAATGGTTA	    0.918852	-47
AGCGCTAAAAAGCATGTTAAGATCAGTTT 	3	155	1	AGCATGTTAA	    0.965792	-19
TATTAGCTTAAGAATGTTAATGAAATCGCA	4	29	0	AGAATGTTAA	    0.971472	-60
          **********

Masking position 10
Map Score:   5.6727

Number of sites scoring better than the average of aligned sites = 378
Number in coding regions = 316
Number in noncoding regions = 62
Number of orfs with sites within 600 bp upstream = 55
Fraction of orfs with sites within 600 bp upstream = 0.00883392


Motif number 4

TTTTGACTAGAATAGCGCTTCTATTATTGT	1	42	0	AATAGCGCTT	     0.95455	-91
ATCGCCTTATTTTTGCGCTATGATTTTCAA	1	71	1	TTTTGCGCTA	    0.911818	-62
         TTTTAAGGCTGATTTAAAAAT	3	2	1	TTTAAGGCTG	    0.921246	-172
GCATAGAAGAATTAGAGCTGTTTGAAGTTT	3	60	1	ATTAGAGCTG	    0.976296	-114
AGCAATAACCATTCAAGCTTGCGGTTATAA	3	122	0	ATTCAAGCTT	    0.853109	-52
TAACATGCTTTTTAGCGCTTGTAGCAATAA	3	144	0	TTTAGCGCTT	    0.988493	-30
          **********

Masking position 3
Map Score:   1.15094

Number of sites scoring better than the average of aligned sites = 879
Number in coding regions = 817
Number in noncoding regions = 62
Number of orfs with sites within 600 bp upstream = 51
Fraction of orfs with sites within 600 bp upstream = 0.00819146


Motif number 5

          **********

No masking
Map Score:   -5.58897e-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:   -5.58897e-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:   -5.58897e-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