AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i149_Thioredoxin_bsub_reg_100.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

TCTTCACTGTCATGTACTTTACCATGCCCTGC	1	49	0	CATTACTTAC	    0.955152	-252
CATAAGATCACATCTCCTCTTCACTGTCATGT	1	66	0	CATTCCTTTC	    0.997273	-235
AAAAAAAGAGCATATCCCATTCAACCATATAA	1	165	1	CATTCCCTTC	    0.998788	-136
TTTAGTATAGCATCTCCCATTCGTTCACGCTA	1	248	0	CATTCCCTTC	    0.998788	-53
TAAAAATCATCATTTCACATTGGAGGAATTCA	1	276	1	CATTCACTTG	    0.978179	-25
          *** **** ***

Masking position 5
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

      CATGCCGGCGCTCTTTTTCAGGTTTTA	1	5	1	CCGGGCCTTT	    0.989706	-296
CCATGCCCTGCCGGAGCTGTTTTAAAACCTGAA	1	27	0	CCGGGCGTTT	    0.989706	-274
GATCTTATGCTTCGTACCATTTTAATGATTATT	1	89	1	TTCGACATTT	    0.946552	-212
TTAATGATTATTGGGGCAATTGTAGTGATCGGG	1	110	1	TTGGGCATTT	    0.996919	-191
ATTGTAGTGATCGGGGCCATTATCAGATTTGTG	1	128	1	TCGGGCATTT	    0.997445	-173
CTCCCATTCGTTCACGCTATTTTAATGCTTACA	1	234	0	TTCAGCATTT	    0.946552	-67
TCATTTCACATTGGAGGAATTCAATA       	1	285	1	TTGGGGATTA	     0.92813	-16
          **** ** *** *

Masking position 10
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	    0.990594	-238
GGGCAATTGTAGTGATCGGGGCCATTATCA	1	123	1	AGTGATCGGG	    0.995632	-178
TATAAAAATGAGTAAACCGGCTGTGATCAG	1	192	1	AGTAAACCGG	     0.98355	-109
GTAAACCGGCTGTGATCAGGAAAAAATAAT	1	203	1	TGTGATCAGG	    0.988705	-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	    0.952206	-291
CAATTGCCCCAATAATCATTAAAATGGTAC	1	102	0	AATAATCATT	    0.850034	-199
TTGTGTTTTAAAAAAAGAGCATATCCCATT	1	156	1	AAAAAAGAGC	    0.981977	-145
TCAACCATATAAAAATGAGTAAACCGGCTG	1	185	1	AAAAATGAGT	    0.984698	-116
GTGATCAGGAAAAAATAATTTGTAAGCATT	1	214	1	AAAAATAATT	    0.910563	-87
ATGCTATACTAAAAATCATCATTTCACATT	1	267	1	AAAAATCATC	    0.977447	-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

        CATGCCGGCGCTCTTTTTCAGG	1	3	1	TGCCGGCGCT	    0.996911	-298
TACCATGCCCTGCCGGAGCTGTTTTAAAAC	1	32	0	TGCCGGAGCT	    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

ACCTGAAAAAGAGCGCCGGCATG       	1	4	0	GAGCGCCGGC	    0.997901	-297
GGTTTTAAAACAGCTCCGGCAGGGCATGGT	1	31	1	CAGCTCCGGC	    0.997826	-270
TTTTCCTGATCACAGCCGGTTTACTCATTT	1	197	0	CACAGCCGGT	    0.989053	-104
          **********

Masking position 2
Map Score:   1.20245

Number of sites scoring better than the average of aligned sites = 217
Number in coding regions = 203
Number in noncoding regions = 14
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


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