tRNAscan-SE v.2.0 (December 2017) - scan sequences for transfer RNAs
Copyright (C) 2017 Patricia Chan and Todd Lowe
                   University of California Santa Cruz
Freely distributed under the GNU General Public License (GPLv3)

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Sequence file(s) to search:        /usr/share/doc/trnascan-se/examples/Example1.fa
Search Mode:                       Eukaryotic
Results written to:                trnascan-se_sample.output
Output format:                     Tabular
Searching with:                    Infernal First Pass->Infernal
Isotype-specific model scan:       Yes
Covariance model:                  /usr/share/trnascan-se/models/TRNAinf-euk.cm
                                   /usr/share/trnascan-se/models/TRNAinf-euk-SeC.cm
Infernal first pass cutoff score:  10

Temporary directory:               /tmp
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Status: Phase I: Searching for tRNAs with HMM-enabled Infernal
Status: Phase I: Searching for tRNAs with HMM-enabled Infernal
Scanned seqs: 0 (at CELF22B7)
/usr/bin/cmsearch -g --mid --notrunc -T 10 /usr/share/trnascan-se/models/TRNAinf-euk.cm /tmp/tscan26061.fa > /tmp/tscan26061_fp_cm_Domain.out
/usr/bin/cmsearch -g --mid --notrunc -T 10 /usr/share/trnascan-se/models/TRNAinf-euk-SeC.cm /tmp/tscan26061.fa > /tmp/tscan26061_fp_cm_SeC.out

1 seqs scanned, 1 seqs had at least one hit.
5 total tRNAs predicted in first pass scans
Status: Phase II: Infernal verification of candidate tRNAs detected with first-pass scan
Status: Phase II: Infernal verification of candidate tRNAs detected with first-pass scan
Scanning CELF22B7
/usr/bin/cmsearch -g --nohmm --toponly --notrunc /usr/share/trnascan-se/models/TRNAinf-euk.cm /tmp/tscan26061.trna > /tmp/tscan26061_cm_Domain.out
/usr/bin/cmsearch -g --nohmm --toponly --notrunc /usr/share/trnascan-se/models/TRNAinf-euk-SeC.cm /tmp/tscan26061.trna > /tmp/tscan26061_cm_SeC.out
/usr/bin/cmsearch -g --toponly --notextw /usr/share/trnascan-se/models/TRNAinf-euk.cm /tmp/tscan26061.trna > /tmp/tscan26061_trunc_cm_Domain.out
/usr/bin/cmscan -g --mid --toponly --notrunc --fmt 2 --tblout /tmp/tscan26061_iso_cm.tab -o /tmp/tscan26061_iso_cm.out /usr/share/trnascan-se/models/TRNAinf-euk-iso /tmp/tscan26061.trna
CELF22B7.tRNA1-LeuCAA:  Infernal type= Leu	 Score= 74.2
CELF22B7.tRNA2-SerAGA:  Infernal type= Ser	 Score= 81.6
CELF22B7.tRNA3-PheGAA:  Infernal type= Phe	 Score= 82.5
CELF22B7.tRNA4-PheGAA:  Infernal type= Phe	 Score= 82.5
CELF22B7.tRNA5-ProCGG:  Infernal type= Pro	 Score= 71.5

End Time: Tue Mar 27 23:02:00 2018
Sequence 		tRNA 	Bounds	tRNA	Anti	Intron Bounds	Inf	Hit	      
Name     	tRNA #	Begin	End  	Type	Codon	Begin	End	Score	Origin	Note
-------- 	------	-----	------	----	-----	-----	----	------	------	------
CELF22B7 	1	12619	12738	Leu	CAA	12657	12692	74.2	Inf	
CELF22B7 	2	19480	19561	Ser	AGA	0	0	81.6	Inf	
CELF22B7 	3	26367	26439	Phe	GAA	0	0	82.5	Inf	
CELF22B7 	4	26992	26920	Phe	GAA	0	0	82.5	Inf	
CELF22B7 	5	23765	23694	Pro	CGG	0	0	71.5	Inf	
