AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i226_Glycyl_TRNA_synthase_hinf_reg_100.orf -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -g0.38 -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 =  	0.38
 maxlen =  	30
 weight =  	0.8
 exclude = 	0

Input sequences:
#1	HI0924	300	glycyl-tRNA synthetase, beta chain (glyS)
#2	HI0927	265	glycyl-tRNA synthetase, alpha chain (glyQ)

Motif number 1

CCCTCTTTAGCAAAGAGGGGTAGGGGAGAT	1	61	0	CAAAGAGGGG	    0.998956	-240
CCCTCTTTGCTAAAGAGGGGAATTCTTGAA	1	72	1	TAAAGAGGGG	    0.998386	-229
CCCTCTTTGCTAAAGAGGGGATTGGATCTT	1	204	0	TAAAGAGGGG	    0.998386	-97
CCCTCTTTAGCAAAGAGGGGTAGGGGCGAT	1	215	1	CAAAGAGGGG	    0.998956	-86
          **********

Masking position 6
Map Score:   13.5752

Number of sites scoring better than the average of aligned sites = 5
Number in coding regions = 1
Number in noncoding regions = 4
Number of orfs with sites within 600 bp upstream = 3
Fraction of orfs with sites within 600 bp upstream = 0.00048185


Motif number 2

CTCATTTACATTTTAATTTCAATAGAGATTAAATTA	1	120	1	TTTAATCTAA	    0.981767	-181
ATTATCTGCTTTCAAAAAACGTTAAAGTAGAACATA	1	152	1	TTAAAACTAA	    0.955353	-149
TTTCTCTTATTTAAAAATTCTGTAGATTTAAATTCT	1	271	0	TTAAATCTAA	    0.990009	-30
TGTAGACTCCTTGTAAAGTTAATAAATTTAGTTAGG	2	11	1	TTTAATTTAA	    0.936484	-255
AAGAAATTCATTTCAACCTAACTAAATTTATTAACT	2	27	0	TTCAATATAA	    0.925332	-239
ATTTCGATTGTTTAAACCTTTCTATATGATACGCAA	2	61	0	TTAAATTTAA	    0.965492	-205
TATTAAATTAATCAAAAAAAACTATACTAAAATAAA	2	98	1	ATAAAAATAA	    0.719593	-168
AAAATAAAACTTAAAATCTACCTAAATATTCAAAAT	2	126	1	TTAAATATAA	    0.975724	-140
AATTACTTACTTGATATATCTTTATAAAGCCTGATT	2	159	1	TTATATCTAA	    0.903801	-107
ATACCAACATTTTTAATCACATTAGATCAACGATT 	2	241	1	TTTAAACTAA	    0.960701	-25
          ** ***  **  ** *

Masking position 6
Map Score:   9.99804

Number of sites scoring better than the average of aligned sites = 137
Number in coding regions = 83
Number in noncoding regions = 54
Number of orfs with sites within 600 bp upstream = 42
Fraction of orfs with sites within 600 bp upstream = 0.0067459


Motif number 3

TGAACGTTGCTTTAGCAACGGCACGAAGTG	1	15	1	TTTAGCAACG	    0.987253	-286
AATTCCCCTCTTTAGCAAAGAGGGGTAGGG	1	66	0	TTTAGCAAAG	    0.990156	-235
CAATCCCCTCTTTAGCAAAGAGGGGTAGGG	1	210	1	TTTAGCAAAG	    0.990156	-91
AGTTAATAAATTTAGTTAGGTTGAAATGAA	2	27	1	TTTAGTTAGG	    0.940334	-239
TTGCGTATCATATAGAAAGGTTTAAACAAT	2	61	1	TATAGAAAGG	    0.899506	-205
TAAGTTTTATTTTAGTATAGTTTTTTTTGA	2	109	0	TTTAGTATAG	    0.935981	-157
          **********

Masking position 4
Map Score:   6.541

Number of sites scoring better than the average of aligned sites = 77
Number in coding regions = 56
Number in noncoding regions = 21
Number of orfs with sites within 600 bp upstream = 13
Fraction of orfs with sites within 600 bp upstream = 0.00208802


Motif number 4

CTAAAGAGGGGAATTCTTGAATAAATTGATAGTAACT	1	81	1	GATTTAATTT	     0.91926	-220
ACTGGCTCATTTACATTTTAATTTCAATAGAGATTAA	1	115	1	TAATTAATAA	    0.815038	-186
TTTTGAAAGCAGATAATTTAATCTCTATTGAAATTAA	1	132	0	AAATTAATTA	    0.942045	-169
TTGGATCTTTGGAGAGTTAAATATTTATGTTCTACTT	1	176	0	GAATTAATTA	    0.991622	-125
TAAAAATTCTGTAGATTTAAATTCTTATTTTCTCGTT	1	259	0	GAATTAATTA	      0.9851	-42
AGTTTTTTTTGATTAATTTAATAGATTTCGATTGTTT	2	84	0	GTATTAATTT	    0.835206	-182
GAATATTTAGGTAGATTTTAAGTTTTATTTTAGTATA	2	120	0	GAATTAAGTA	    0.960393	-146
TATCAAGTAAGTAATTTTGAATATTTAGGTAGATTTT	2	138	0	GATTTAATTA	    0.973379	-128
AATGTTGGTATTATACTTGAATCCGTAAAAGGGATAA	2	215	0	TAATTAATTA	    0.964967	-51
          * * * ** ***   **

Masking position 8
Map Score:   8.25405

Number of sites scoring better than the average of aligned sites = 146
Number in coding regions = 122
Number in noncoding regions = 24
Number of orfs with sites within 600 bp upstream = 22
Fraction of orfs with sites within 600 bp upstream = 0.00353357


Motif number 5

GAGTAAATCTCCCCTACCCCTCTTTGCTAA	1	55	1	CCCCTACCCC	    0.998934	-246
TGCCAAATCGCCCCTACCCCTCTTTGCTAA	1	221	0	CCCCTACCCC	    0.998934	-80
GCATTTTTCGCCTTTATCCCTTTTACGGAT	2	202	1	CCTTTATCCC	    0.978821	-64
          **********

Masking position 6
Map Score:   3.32721

Number of sites scoring better than the average of aligned sites = 6
Number in coding regions = 3
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 6

          **********

No masking
Map Score:   -1.28365e-12

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:   -1.28365e-12

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:   -1.28365e-12

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