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tRNA Search Results

tRNA search developed by the Washington University Department of Genetics. Processing for tRNA is provided by the BCM Search Launcher,Human Genome Sequencing Center, Baylor College of Medicine. 

tRNAscan-SE v.1.11 (Nov 97) - scan sequences for transfer RNAs

  Please cite: 
	Lowe, T.M. & Eddy, S.R. (1997) "tRNAscan-SE: A program for
	improved detection of transfer RNA genes in genomic sequence"
	Nucl. Acids Res. 25: 955-964.

  This program uses a modified, optimized version of tRNAscan v1.3
  (Fichant & Burks, J. Mol. Biol. 1991, 220: 659-671),
  a new implementation of a multistep weight matrix algorithm
  for identification of eukaryotic tRNA promoter regions
  (Pavesi et al., Nucl. Acids Res. 1994, 22: 1247-1256),
  as well as the RNA covariance analysis package Cove v.2.4.2
  (Eddy & Durbin, Nucl. Acids Res. 1994, 22: 2079-2088W.
Run Statistics:


------------------------------------------------------------
Sequence file(s) to search:  /tmp/tRNA.13234.fa
Search Mode:                 Eukaryotic
Results written to:          Standard output
Output format:               Tabular
Searching with:              tRNAscan + EufindtRNA -> Cove
Covariance model:            TRNA2.cm
tRNAscan parameters:         Strict
EufindtRNA parameters:       Relaxed (Int Cutoff= -32.1)
tRNA secondary structure
    predictions saved to:    /tmp/tRNA.13234.out
------------------------------------------------------------


Phase I: Searching for tRNAs with tRNAscan and/or EufindtRNA

Scanned seqs: 0 (at query_seq)

1 seqs scanned, 1 seqs had at least one hit.
1 total tRNAs predicted in first pass scans


Phase II: Cove verification of candidate tRNAs detected
with tRNAscan and/or EufindtRNA

Results:



Sequence		tRNA Bounds	tRNA	Anti	Intron Bounds	Cove
Name     	tRNA #	Begin	End	Type	Codon	Begin	End	Score
--------	------	-----	---	----	-----	-----	-----	-----
query_seq	1	782	854	Gly	GCC	0	0	77.65

Predicted tRNA Secondary Structure:

query_seq.trna1 (782-854)	Length: 73 bp
Type: Gly	Anticodon: GCC at 34-36 (815-817)	Score: 77.65
         *    |    *    |    *    |    *    |    *    |    *    |    *    |  
Seq: GCGGGAATAGCTCAGTTGGTAGAGCACGACCTTGCCAAGGTCGGGGtCGCGAGTTCGAGTCTCGTTTCCCGCT
Str: >>>>>>>..>>>>........<<<<.>>>>>.......<<<<<.....>>>>>.......<<<<<<<<<<<<.