tRNAscan-SE v.1.23 (April 2002) scan results (on host )
Started: Wed Dec 28 19:44:46 CET 2011

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Sequence file(s) to search:  /users/rg/didac/GENOMES/P.capsici/genome.fa
Search Mode:                 Eukaryotic
Results written to:          /users/rg/didac/STUDENTS_PROJECT/tRNA/P.capsici.txt
Output format:               Tabular
Searching with:              tRNAscan + EufindtRNA -> Cove
Covariance model:            TRNA2-euk.cm
tRNAscan parameters:         Strict
EufindtRNA parameters:       Relaxed (Int Cutoff= -32.1)
Search statistics saved in:  /users/rg/didac/STUDENTS_PROJECT/tRNA/P.capsici_summary.txt
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First-pass (tRNAscan/EufindtRNA) Stats:
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Sequences read:         917
Seqs w/at least 1 hit:  171
Bases read:             64023748 (x2 for both strands)
Bases in tRNAs:         110635
tRNAs predicted:        1149
Av. tRNA length:        96
Script CPU time:        7.50 s
Scan CPU time:          50.50 s
Scan speed:             2535.6 Kbp/sec

First pass search(es) ended: Wed Dec 28 19:45:50 CET 2011

Cove Stats:
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Candidate tRNAs read:     1149
Cove-confirmed tRNAs:     556
Bases scanned by covels:  126708
% seq scanned by covels:  0.1 %
Script CPU time:          2.15 s
Cove CPU time:            153.62 s
Scan speed:               824.8 bp/sec

Cove analysis of tRNAs ended: Wed Dec 28 19:48:31 CET 2011

Summary
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Overall scan speed: 598996.6 bp/sec

tRNAs decoding Standard 20 AA:              540
Selenocysteine tRNAs (TCA):                 0
Possible suppressor tRNAs (CTA,TTA):        0
tRNAs with undetermined/unknown isotypes:   7
Predicted pseudogenes:                      9
                                            -------
Total tRNAs:                                556

tRNAs with introns:     	11

| Tyr-GTA: 11 |

Isotype / Anticodon Counts:

Ala   : 72	  AGC: 28      GGC:         CGC: 18      TGC: 26    
Gly   : 13	  ACC: 1       GCC: 3       CCC: 4       TCC: 5     
Pro   : 30	  AGG: 6       GGG:         CGG: 5       TGG: 19    
Thr   : 41	  AGT: 17      GGT:         CGT: 14      TGT: 10    
Val   : 35	  AAC: 5       GAC:         CAC: 26      TAC: 4     
Ser   : 28	  AGA: 5       GGA:         CGA: 7       TGA: 3       ACT:         GCT: 13    
Arg   : 45	  ACG: 32      GCG:         CCG: 4       TCG: 5       CCT: 2       TCT: 2     
Leu   : 57	  AAG: 14      GAG:         CAG: 16      TAG: 5       CAA: 8       TAA: 14    
Phe   : 3	  AAA:         GAA: 3                               
Asn   : 15	  ATT:         GTT: 15                              
Lys   : 10	                            CTT: 3       TTT: 7     
Asp   : 9	  ATC:         GTC: 9                               
Glu   : 55	                            CTC: 41      TTC: 14    
His   : 15	  ATG: 1       GTG: 14                              
Gln   : 34	                            CTG: 17      TTG: 17    
Ile   : 21	  AAT: 17      GAT: 2                    TAT: 2     
Met   : 27	                            CAT: 27                 
Tyr   : 11	  ATA:         GTA: 11                              
Supres: 0	                            CTA:         TTA:       
Cys   : 6	  ACA:         GCA: 6                               
Trp   : 13	                            CCA: 13                 
SelCys: 0	                                         TCA: