AlignACE version 2.2  July 7, 1998
alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -inagC_rpxx_opreg_300.orf -g0.290 -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 =  	0.29
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	RP456	171	RIBOSOMAL PROTEIN L36 (rpmJ)
#2	RP581	114	unknown

Motif number 1

TATTAATTAAAATTAATTTATAAATTCTTAA    	1	7	0	AATAATTAAT	    0.987547	-165
AATTAATTTTAATTAATAGTTTAATACATTAAAAC	1	24	1	AATAAGTAAT	    0.969104	-148
GTATAGTTTTAATAGAATTAATAATTAATGCTATT	1	79	0	AATGATAAAT	    0.960605	-93
CTAATCAGTCAATTAAGTTCTGTATAGTTTTAATA	1	100	0	AATAATTTAT	    0.987617	-72
TGGGATTAATAATAAACATTTTTATCTAATCAGTC	1	125	0	AATAATTTAT	    0.986616	-47
TATTAATCCCAATTAATGTAATAAGTATATTGT  	1	149	1	AATAATAAAG	     0.96061	-23
AGCAACAAGTAATAAAGTTCAATATGTATATGTAT	2	12	0	AATAATATAT	     0.99152	-103
TGCTAGAAACAATAAAAATGACTATAACGTAACTT	2	43	1	AATAATATAT	    0.991518	-72
ATTTTAAATCAAGAAACTTTACTATTTTAATAAGT	2	74	0	AAGAATATAT	    0.960608	-41
CTTGATTTAAAATTAGCGGGATAATATAC      	2	96	1	AATAGGAAAT	    0.912907	-19
          *** **  * * ***

Masking position 2
Map Score:   17.2907

Number of sites scoring better than the average of aligned sites = 358
Number in coding regions = 211
Number in noncoding regions = 147
Number of orfs with sites within 600 bp upstream = 87
Fraction of orfs with sites within 600 bp upstream = 0.0139737


Motif number 2

AATTAATTTATAAATTCTTAA          	1	1	0	TAAATCTTAA	    0.833149	-171
GAATTTATAAATTAATTTTAATTAATAGTTT	1	15	1	ATTATTTTAA	    0.718441	-157
TTTAATGTATTAAACTATTAATTAAAATTAA	1	26	0	TAAATATTAA	     0.93177	-146
TCGGAATTAATAACGTTTTAATGTATTAAAC	1	42	0	TAACTTTTAA	    0.974391	-130
TTAAATAGCATTAATTATTAATTCTATTAAA	1	76	1	TTAATATTAA	    0.700203	-96
TTAAGTTCTGTATAGTTTTAATAGAATTAAT	1	92	0	TATATTTTAA	    0.836639	-80
GATTAATAATAAACATTTTTATCTAATCAGT	1	126	0	AAACTTTTTA	    0.785794	-46
     ACAATATACTTATTACATTAATTGGG	1	156	0	ATACTATTAC	    0.902543	-16
   AATACATATACATATTGAACTTTATTAC	2	8	1	ATACTATTGA	    0.912086	-107
TTGAACTTTATTACTTGTTGCTAGAAACAAT	2	25	1	TTACTGTTGC	    0.711792	-90
GACTATAACGTAACTTATTAAAATAGTAAAG	2	62	1	TAACTATTAA	    0.977372	-53
          **** ******

Masking position 6
Map Score:   9.07438

Number of sites scoring better than the average of aligned sites = 1078
Number in coding regions = 682
Number in noncoding regions = 396
Number of orfs with sites within 600 bp upstream = 191
Fraction of orfs with sites within 600 bp upstream = 0.0306778


Motif number 3

AAATTAATTTATAAATTCTTAA        	1	3	0	ATAAATTCTT	    0.811552	-169
GAATTTATAAATTAATTTTAATTAATAGTT	1	15	1	ATTAATTTTA	    0.963962	-157
TTAAAACGTTATTAATTCCGAGCTTTAAAT	1	52	1	ATTAATTCCG	    0.960377	-120
AGAATTAATAATTAATGCTATTTAAAGCTC	1	71	0	ATTAATGCTA	    0.987467	-101
AGCATTAATTATTAATTCTATTAAAACTAT	1	82	1	ATTAATTCTA	    0.991521	-90
AATGTTTATTATTAATCCCAATTAATGTAA	1	140	1	ATTAATCCCA	    0.966452	-32
ATTAATCCCAATTAATGTAATAAGTATATT	1	150	1	ATTAATGTAA	    0.816341	-22
AGTCATTTTTATTGTTTCTAGCAACAAGTA	2	36	0	ATTGTTTCTA	    0.847873	-79
          **********

Masking position 1
Map Score:   8.92986

Number of sites scoring better than the average of aligned sites = 488
Number in coding regions = 363
Number in noncoding regions = 125
Number of orfs with sites within 600 bp upstream = 54
Fraction of orfs with sites within 600 bp upstream = 0.00867331


Motif number 4

TTAATTAAAATTAATTTATAAATTCTTAA 	1	10	0	TTAATTTATA	    0.777378	-162
ATAAATTAATTTTAATTAATAGTTTAATAC	1	21	1	TTTAATTAAT	    0.762817	-151
TAATAACGTTTTAATGTATTAAACTATTAA	1	36	0	TTAATGTATT	    0.976133	-136
GAATTAATAATTAATGCTATTTAAAGCTCG	1	70	0	TTAATGCTAT	    0.931594	-102
GCATTAATTATTAATTCTATTAAAACTATA	1	83	1	TTAATTCTAT	    0.868292	-89
AATAAACATTTTTATCTAATCAGTCAATTA	1	120	0	TTTATCTAAT	    0.920354	-52
TTAATCCCAATTAATGTAATAAGTATATTG	1	151	1	TTAATGTAAT	    0.984819	-21
GTTCAATATGTATATGTATT          	2	1	0	TATATGTATT	    0.820591	-114
          **********

Masking position 4
Map Score:   4.86946

Number of sites scoring better than the average of aligned sites = 842
Number in coding regions = 540
Number in noncoding regions = 302
Number of orfs with sites within 600 bp upstream = 149
Fraction of orfs with sites within 600 bp upstream = 0.0239319


Motif number 5

          **********

No masking
Map Score:   1.09013e-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:   1.09013e-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:   1.09013e-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