AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -icspA_bsub_opreg_100.orf -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	gyrA	210	DNA gyrase (subunit A)

Motif number 1

TTTCTTATTGGAAATAAGGCTTTTTATGA 	1	10	0	GAAATAAGGC	    0.981445	-201
TTTCCAATAAGAAATAAGGCTTTTTTCTGA	1	26	1	GAAATAAGGC	    0.981445	-185
TAAGTTTATTGATATAATGGAGAATAGTGA	1	120	1	GATATAATGG	    0.983275	-91
CGTATTGAAGGTCATAATGGACAATCTACT	1	153	1	GTCATAATGG	    0.963401	-58
AGTATCACATGAAATATGTGGGAGTAGATT	1	175	0	GAAATATGTG	    0.854779	-36
          **********

Masking position 5
Map Score:   6.02849

Number of sites scoring better than the average of aligned sites = 204
Number in coding regions = 161
Number in noncoding regions = 43
Number of orfs with sites within 600 bp upstream = 41
Fraction of orfs with sites within 600 bp upstream = 0.00658529


Motif number 2

TATTGGAAATAAGGCTTTTTATGA      	1	5	0	AAGGCTTTTT	    0.997382	-206
AATAAGAAATAAGGCTTTTTTCTGAACAAG	1	31	1	AAGGCTTTTT	    0.997382	-180
ATACTTCAGGGAGGTTTTTTA         	1	200	1	GAGGTTTTTT	    0.991863	-11
          **********

Masking position 2
Map Score:   5.14474

Number of sites scoring better than the average of aligned sites = 77
Number in coding regions = 54
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 16
Fraction of orfs with sites within 600 bp upstream = 0.00256987


Motif number 3

TGCAGCGATGCCTGCAATACCTATATATTC	1	67	1	CCTGCAATAC	    0.997446	-144
TCCATTATGACCTTCAATACGATTTCACTA	1	144	0	CCTTCAATAC	    0.989929	-67
TGAAGTATCACATGAAATATGTGGGAGTAG	1	178	0	CATGAAATAT	    0.976238	-33
AAAAAACCTCCCTGAAGTATCACATGAAAT	1	190	0	CCTGAAGTAT	    0.989664	-21
          **********

Masking position 6
Map Score:   4.57387

Number of sites scoring better than the average of aligned sites = 117
Number in coding regions = 110
Number in noncoding regions = 7
Number of orfs with sites within 600 bp upstream = 5
Fraction of orfs with sites within 600 bp upstream = 0.000803084


Motif number 4

TTATTGATATAATGGAGAATAGTGAAATCG	1	125	1	AATGGAGAAT	    0.991424	-86
TGAAGGTCATAATGGACAATCTACTCCCAC	1	158	1	AATGGACAAT	    0.956697	-53
          **********

Masking position 6
Map Score:   0.487675

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 5

          **********

No masking
Map Score:   3.71914e-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:   3.71914e-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:   3.71914e-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