AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i142_Cytochrome_Oxidase_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	ctaC	239	cytochrome caa3 oxidase (subunit II)
#2	ctaD	32	cytochrome caa3 oxidase (subunit I)

Motif number 1

TGAAGCGATAAAACAAGCATCATATCTATT	1	13	0	AAACAAGCAT	    0.842042	-227
CCGCCTGATTAAACAAGAGGTCAAGGCGGC	1	68	0	AAACAAGAGG	    0.985264	-172
CCTCTTGTTTAATCAGGCGGCTTTACTTTT	1	78	1	AATCAGGCGG	    0.974206	-162
TCATAATTTAAGAGAAGAGGAAATGTAAGT	1	138	1	AGAGAAGAGG	    0.975138	-102
TCTGGTCAATACAAAGGCGGAAAGCGGATC	1	204	0	ACAAAGGCGG	    0.985479	-36
TGTATTGACCAGAAAAGGGGTTGGGTGAA 	1	221	1	AGAAAAGGGG	    0.990424	-19
       GGAAGAAAGGGAGATATTGGGGG	2	4	1	AGAAAGGGAG	    0.971487	-29
          **********

Masking position 5
Map Score:   6.4464

Number of sites scoring better than the average of aligned sites = 1801
Number in coding regions = 1425
Number in noncoding regions = 376
Number of orfs with sites within 600 bp upstream = 403
Fraction of orfs with sites within 600 bp upstream = 0.0647286


Motif number 2

GACAACTAGTAAATGCCGCCTTGACCTCTT	1	54	1	AAATGCCGCC	    0.996106	-186
TGTATAAAAGTAAAGCCGCCTGATTAAACA	1	83	0	TAAAGCCGCC	    0.993157	-157
TTTTTACTCAAAATGCCATCTATGTATAAA	1	105	0	AAATGCCATC	    0.990533	-135
GATCGAAATCTATCGCCATCCAACCTATCA	1	178	0	TATCGCCATC	    0.971155	-62
          **********

Masking position 2
Map Score:   3.22928

Number of sites scoring better than the average of aligned sites = 272
Number in coding regions = 247
Number in noncoding regions = 25
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 3

      AAAATAGATATGATGCTTGTTTTA	1	5	1	TAGATATGAT	     0.80215	-235
CGGCATTTACTAGTTGTCATCGTTTATTTT	1	42	0	TAGTTGTCAT	    0.958116	-198
ACAAGAGGTCAAGGCGGCATTTACTAGTTG	1	56	0	AAGGCGGCAT	    0.983329	-184
CTTGTTTAATCAGGCGGCTTTACTTTTATA	1	81	1	CAGGCGGCTT	    0.959221	-159
CTTTTATACATAGATGGCATTTTGAGTAAA	1	103	1	TAGATGGCAT	    0.991569	-137
TTATTGGTGATAGGTTGGATGGCGATAGAT	1	171	1	TAGGTTGGAT	    0.964337	-69
          **********

Masking position 2
Map Score:   2.35171

Number of sites scoring better than the average of aligned sites = 714
Number in coding regions = 621
Number in noncoding regions = 93
Number of orfs with sites within 600 bp upstream = 80
Fraction of orfs with sites within 600 bp upstream = 0.0128493


Motif number 4

AAATCTATCGCCATCCAACCTATCACCAAT	1	173	0	CCATCCAACC	    0.991216	-67
         TTCACCCAACCCCTTTTCTGG	1	229	0	TCACCCAACC	    0.997277	-11
  ATGTGACCTCCCCCAATATCTCCCTTTC	2	15	0	TCCCCCAATA	    0.976399	-18
          **********

Masking position 7
Map Score:   0.0190475

Number of sites scoring better than the average of aligned sites = 39
Number in coding regions = 28
Number in noncoding regions = 11
Number of orfs with sites within 600 bp upstream = 12
Fraction of orfs with sites within 600 bp upstream = 0.0019274


Motif number 5

          **********

No masking
Map Score:   -3.31523e-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:   -3.31523e-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:   -3.31523e-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