AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i149_Thioredoxin_bsub_reg_300.orf -aORF_bsub.txt -zbsub.fna -g0.435 -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 =  	0.435
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	trxA	300	thioredoxin

Motif number 1

GCAGGGCATGGTAAAGTACATGACAGTGAAGA	1	49	1	GTAAGTAATG	    0.952807	-252
ACATGACAGTGAAGAGGAGATGTGATCTTATG	1	66	1	GAAAGGAATG	    0.997123	-235
TTATATGGTTGAATGGGATATGCTCTTTTTTT	1	165	0	GAAGGGAATG	    0.998721	-136
TAGCGTGAACGAATGGGAGATGCTATACTAAA	1	248	1	GAAGGGAATG	    0.998721	-53
TGAATTCCTCCAATGTGAAATGATGATTTTTA	1	276	0	CAAGTGAATG	    0.977009	-25
          *** **** ***

Masking position 8
Map Score:   7.60724

Number of sites scoring better than the average of aligned sites = 135
Number in coding regions = 113
Number in noncoding regions = 22
Number of orfs with sites within 600 bp upstream = 24
Fraction of orfs with sites within 600 bp upstream = 0.0038548


Motif number 2

TAAAACCTGAAAAAGAGCGCCGGCATG      	1	5	0	AAAGGCCCGG	    0.989741	-296
TTCAGGTTTTAAAACAGCTCCGGCAGGGCATGG	1	27	1	AAACGCCCGG	    0.989741	-274
AATAATCATTAAAATGGTACGAAGCATAAGATC	1	89	0	AAATGTCGAA	    0.946727	-212
CCCGATCACTACAATTGCCCCAATAATCATTAA	1	110	0	AAATGCCCAA	     0.99693	-191
CACAAATCTGATAATGGCCCCGATCACTACAAT	1	128	0	AAATGCCCGA	    0.997454	-173
TGTAAGCATTAAAATAGCGTGAACGAATGGGAG	1	234	1	AAATGCTGAA	    0.946727	-67
       TATTGAATTCCTCCAATGTGAAATGA	1	285	0	TAATCCCCAA	    0.928362	-16
          * *** ** ****

Masking position 4
Map Score:   6.53498

Number of sites scoring better than the average of aligned sites = 501
Number in coding regions = 469
Number in noncoding regions = 32
Number of orfs with sites within 600 bp upstream = 23
Fraction of orfs with sites within 600 bp upstream = 0.00369419


Motif number 3

AGTACATGACAGTGAAGAGGAGATGTGATC	1	63	1	AGTGAAGAGG	    0.990985	-238
GGGCAATTGTAGTGATCGGGGCCATTATCA	1	123	1	AGTGATCGGG	    0.995799	-178
TATAAAAATGAGTAAACCGGCTGTGATCAG	1	192	1	AGTAAACCGG	     0.98423	-109
GTAAACCGGCTGTGATCAGGAAAAAATAAT	1	203	1	TGTGATCAGG	    0.988967	-98
          **********

Masking position 5
Map Score:   3.37598

Number of sites scoring better than the average of aligned sites = 142
Number in coding regions = 122
Number in noncoding regions = 20
Number of orfs with sites within 600 bp upstream = 9
Fraction of orfs with sites within 600 bp upstream = 0.00144555


Motif number 4

TTTAAAACCTGAAAAAGAGCGCCGGCATG 	1	10	0	GAAAAAGAGC	    0.948401	-291
CAATTGCCCCAATAATCATTAAAATGGTAC	1	102	0	AATAATCATT	    0.842941	-199
TTGTGTTTTAAAAAAAGAGCATATCCCATT	1	156	1	AAAAAAGAGC	    0.980494	-145
TCAACCATATAAAAATGAGTAAACCGGCTG	1	185	1	AAAAATGAGT	    0.983447	-116
GTGATCAGGAAAAAATAATTTGTAAGCATT	1	214	1	AAAAATAATT	    0.903979	-87
ATGCTATACTAAAAATCATCATTTCACATT	1	267	1	AAAAATCATC	    0.975682	-34
          **********

Masking position 5
Map Score:   4.07857

Number of sites scoring better than the average of aligned sites = 1093
Number in coding regions = 884
Number in noncoding regions = 209
Number of orfs with sites within 600 bp upstream = 222
Fraction of orfs with sites within 600 bp upstream = 0.0356569


Motif number 5

CCTGAAAAAGAGCGCCGGCATG        	1	3	0	AGCGCCGGCA	    0.996911	-298
GTTTTAAAACAGCTCCGGCAGGGCATGGTA	1	32	1	AGCTCCGGCA	    0.996515	-269
          **********

Masking position 1
Map Score:   1.68854

Number of sites scoring better than the average of aligned sites = 22
Number in coding regions = 20
Number in noncoding regions = 2
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


Motif number 6

TGAAAAAGAGCGCCGGCATG          	1	1	0	CGCCGGCATG	     0.99828	-300
TTTAAAACAGCTCCGGCAGGGCATGGTAAA	1	34	1	CTCCGGCAGG	    0.996982	-267
ATCTCCTCTTCACTGTCATGTACTTTACCA	1	57	0	CACTGTCATG	    0.981377	-244
          **********

Masking position 8
Map Score:   1.41892

Number of sites scoring better than the average of aligned sites = 95
Number in coding regions = 92
Number in noncoding regions = 3
Number of orfs with sites within 600 bp upstream = 2
Fraction of orfs with sites within 600 bp upstream = 0.000321234


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


Motif number 8

          **********

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 9

          **********

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