AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -icoldbox_mthe_opreg_300.orf -g0.495 -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 =  	0.495
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	MTH203	300	ATP-dependent RNA helicase, eIF-4A family 

Motif number 1

CTTTTGTTTCCGGTGTTTTTGGCTGCTCTC	1	25	0	CGGTGTTTTT	    0.990612	-276
GTTGTCTGGGTGGTGTATTCTTTTGTTTCC	1	44	0	TGGTGTATTC	    0.996017	-257
TGGGGCTGGTCGCTGTTGTCTGGGTGGTGT	1	58	0	CGCTGTTGTC	    0.961978	-243
CTTTTGTTTGTGGTGTTTTTTGGGGCTGGT	1	78	0	TGGTGTTTTT	    0.993663	-223
GTTGTCTGGGTGGTGTATTCTTTTGTTTGT	1	97	0	TGGTGTATTC	    0.996017	-204
GAGGTGTTCCTGGAGTTGTCTGGGTGGTGT	1	111	0	TGGAGTTGTC	    0.988119	-190
TTTAAACTGTTGGTTTTTTCATCCGTGAGG	1	137	0	TGGTTTTTTC	    0.978166	-164
TATTGTACCCGGGAGTATTTAAACTGTTGG	1	154	0	GGGAGTATTT	    0.929001	-147
          **********

Masking position 6
Map Score:   17.312

Number of sites scoring better than the average of aligned sites = 204
Number in coding regions = 183
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 14
Fraction of orfs with sites within 600 bp upstream = 0.00224863


Motif number 2

GCCAAAAACACCGGAAACAAAAGAATACACC	1	32	1	CCGGAACAAA	     0.98643	-269
AAAGAATACACCACCCAGACAACAGCGACCA	1	51	1	CCACCAGACA	    0.987648	-250
ACAACAGCGACCAGCCCCAAAAAACACCACA	1	69	1	CCAGCCCAAA	    0.987891	-232
CCAAAAAACACCACAAACAAAAGAATACACC	1	85	1	CCACAACAAA	     0.98712	-216
AAAGAATACACCACCCAGACAACTCCAGGAA	1	104	1	CCACCAGACA	    0.987648	-197
CCAGACAACTCCAGGAACACCTCACGGATGA	1	118	1	CCAGAACACC	    0.974822	-183
TTAAATACTCCCGGGTACAATAGAGTAGCTG	1	162	1	CCGGTACAAT	    0.900907	-139
CAGGATTCTGCCAGGCACAGATAATTAAAAA	1	201	0	CCAGCACAGA	    0.991173	-100
TCCTGAACTTCCAGTTTGAAAATGGTCTGCC	1	227	1	CCAGTTGAAA	    0.905529	-74
          **** ******

Masking position 9
Map Score:   13.1403

Number of sites scoring better than the average of aligned sites = 292
Number in coding regions = 263
Number in noncoding regions = 29
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 3

GTATTCTTTTGTTTCCGGTGTTTTTGGCTG	1	30	0	GTTTCCGGTG	    0.914216	-271
TCGCTGTTGTCTGGGTGGTGTATTCTTTTG	1	49	0	CTGGGTGGTG	    0.998006	-252
TTTTTTGGGGCTGGTCGCTGTTGTCTGGGT	1	63	0	CTGGTCGCTG	    0.974984	-238
GTATTCTTTTGTTTGTGGTGTTTTTTGGGG	1	83	0	GTTTGTGGTG	    0.968218	-218
CTGGAGTTGTCTGGGTGGTGTATTCTTTTG	1	102	0	CTGGGTGGTG	    0.998006	-199
GTTTTTTCATCCGTGAGGTGTTCCTGGAGT	1	125	0	CCGTGAGGTG	     0.97822	-176
AATAGAGTAGCTGTGTACTGATTTTTAATT	1	180	1	CTGTGTACTG	    0.954887	-121
GGTCTGCCAGATGGCAGCTGATAATTGATA	1	250	1	ATGGCAGCTG	    0.915013	-51
          **********

Masking position 9
Map Score:   10.9653

Number of sites scoring better than the average of aligned sites = 869
Number in coding regions = 813
Number in noncoding regions = 56
Number of orfs with sites within 600 bp upstream = 51
Fraction of orfs with sites within 600 bp upstream = 0.00819146


Motif number 4

TTTTTGGCTGCTCTCGAGCGGTGCTGTAT 	1	10	0	CTCTCGAGCG	    0.881763	-291
AAGAATACACCACCCAGACAACAGCGACCA	1	52	1	CACCCAGACA	    0.991007	-249
AAGAATACACCACCCAGACAACTCCAGGAA	1	105	1	CACCCAGACA	    0.991007	-196
CCAGGAACACCTCACGGATGAAAAAACCAA	1	128	1	CTCACGGATG	    0.956653	-173
AGTTTAAATACTCCCGGGTACAATAGAGTA	1	159	1	CTCCCGGGTA	    0.832796	-142
GTTCAGGATTCTGCCAGGCACAGATAATTA	1	205	0	CTGCCAGGCA	    0.992546	-96
TGAAAATGGTCTGCCAGATGGCAGCTGATA	1	243	1	CTGCCAGATG	    0.984311	-58
          **********

Masking position 5
Map Score:   10.7288

Number of sites scoring better than the average of aligned sites = 626
Number in coding regions = 597
Number in noncoding regions = 29
Number of orfs with sites within 600 bp upstream = 21
Fraction of orfs with sites within 600 bp upstream = 0.00337295


Motif number 5

          **********

No masking
Map Score:   7.91135e-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:   7.91135e-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:   7.91135e-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