AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -icoldbox_mthe_opreg_100.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

GAGAGCAGCCAAAAACACCGGAAACAAAAG	1	25	1	AAAAACACCG	    0.988523	-276
GGAAACAAAAGAATACACCACCCAGACAAC	1	44	1	GAATACACCA	    0.995125	-257
ACACCACCCAGACAACAGCGACCAGCCCCA	1	58	1	GACAACAGCG	    0.953814	-243
ACCAGCCCCAAAAAACACCACAAACAAAAG	1	78	1	AAAAACACCA	    0.992248	-223
ACAAACAAAAGAATACACCACCCAGACAAC	1	97	1	GAATACACCA	    0.995125	-204
ACACCACCCAGACAACTCCAGGAACACCTC	1	111	1	GACAACTCCA	    0.985483	-190
CCTCACGGATGAAAAAACCAACAGTTTAAA	1	137	1	GAAAAAACCA	    0.973381	-164
CCAACAGTTTAAATACTCCCGGGTACAATA	1	154	1	AAATACTCCC	    0.914387	-147
          **********

Masking position 5
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	    0.987598	-269
AAAGAATACACCACCCAGACAACAGCGACCA	1	51	1	CCACCAGACA	    0.988712	-250
ACAACAGCGACCAGCCCCAAAAAACACCACA	1	69	1	CCAGCCCAAA	    0.988935	-232
CCAAAAAACACCACAAACAAAAGAATACACC	1	85	1	CCACAACAAA	     0.98823	-216
AAAGAATACACCACCCAGACAACTCCAGGAA	1	104	1	CCACCAGACA	    0.988712	-197
CCAGACAACTCCAGGAACACCTCACGGATGA	1	118	1	CCAGAACACC	    0.976966	-183
TTAAATACTCCCGGGTACAATAGAGTAGCTG	1	162	1	CCGGTACAAT	    0.908756	-139
CAGGATTCTGCCAGGCACAGATAATTAAAAA	1	201	0	CCAGCACAGA	    0.991936	-100
TCCTGAACTTCCAGTTTGAAAATGGTCTGCC	1	227	1	CCAGTTGAAA	    0.913046	-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

CAGCCAAAAACACCGGAAACAAAAGAATAC	1	30	1	CACCGGAAAC	    0.914216	-271
CAAAAGAATACACCACCCAGACAACAGCGA	1	49	1	CACCACCCAG	    0.998006	-252
ACCCAGACAACAGCGACCAGCCCCAAAAAA	1	63	1	CAGCGACCAG	    0.974984	-238
CCCCAAAAAACACCACAAACAAAAGAATAC	1	83	1	CACCACAAAC	    0.968218	-218
CAAAAGAATACACCACCCAGACAACTCCAG	1	102	1	CACCACCCAG	    0.998006	-199
ACTCCAGGAACACCTCACGGATGAAAAAAC	1	125	1	CACCTCACGG	     0.97822	-176
AATTAAAAATCAGTACACAGCTACTCTATT	1	180	0	CAGTACACAG	    0.954887	-121
TATCAATTATCAGCTGCCATCTGGCAGACC	1	250	0	CAGCTGCCAT	    0.915013	-51
          **********

Masking position 2
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

 ATACAGCACCGCTCGAGAGCAGCCAAAAA	1	10	1	CGCTCGAGAG	    0.875117	-291
TGGTCGCTGTTGTCTGGGTGGTGTATTCTT	1	52	0	TGTCTGGGTG	    0.990182	-249
TTCCTGGAGTTGTCTGGGTGGTGTATTCTT	1	105	0	TGTCTGGGTG	    0.990182	-196
TTGGTTTTTTCATCCGTGAGGTGTTCCTGG	1	128	0	CATCCGTGAG	    0.954316	-173
TACTCTATTGTACCCGGGAGTATTTAAACT	1	159	0	TACCCGGGAG	    0.842555	-142
TAATTATCTGTGCCTGGCAGAATCCTGAAC	1	205	1	TGCCTGGCAG	    0.991818	-96
TATCAGCTGCCATCTGGCAGACCATTTTCA	1	243	0	CATCTGGCAG	     0.98287	-58
          **********

Masking position 6
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