tRNAscan-SE v.1.23 (April 2002) scan results (on host )
Started: Wed Dec 28 17:23:05 CET 2011

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Sequence file(s) to search:  /users/rg/didac/GENOMES/G.niphandrodes/genome.fa
Search Mode:                 Eukaryotic
Results written to:          G.niphandrodes.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:  G.niphandrodes_summary.txt
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First-pass (tRNAscan/EufindtRNA) Stats:
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Sequences read:         3680
Seqs w/at least 1 hit:  1724
Bases read:             15362869 (x2 for both strands)
Bases in tRNAs:         366512
tRNAs predicted:        4353
Av. tRNA length:        84
Script CPU time:        4.15 s
Scan CPU time:          22.04 s
Scan speed:             1394.1 Kbp/sec

First pass search(es) ended: Wed Dec 28 17:23:51 CET 2011

Cove Stats:
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Candidate tRNAs read:     4353
Cove-confirmed tRNAs:     2791
Bases scanned by covels:  427096
% seq scanned by covels:  1.4 %
Script CPU time:          5.34 s
Cove CPU time:            626.52 s
Scan speed:               681.7 bp/sec

Cove analysis of tRNAs ended: Wed Dec 28 17:35:22 CET 2011

Summary
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Overall scan speed: 46692.1 bp/sec

tRNAs decoding Standard 20 AA:              2350
Selenocysteine tRNAs (TCA):                 7
Possible suppressor tRNAs (CTA,TTA):        8
tRNAs with undetermined/unknown isotypes:   33
Predicted pseudogenes:                      393
                                            -------
Total tRNAs:                                2791

tRNAs with introns:     	141

| Ala-AGC: 1 | Ala-CGC: 1 | Thr-AGT: 1 | Val-AAC: 3 | Ser-TGA: 1 | Arg-CCG: 2 | Arg-TCG: 1 | Leu-CAG: 2 | Leu-CAA: 4 | Leu-TAA: 37 | Asn-GTT: 1 | Lys-CTT: 20 | Lys-TTT: 1 | Glu-CTC: 1 | Gln-CTG: 1 | Ile-AAT: 5 | Met-CAT: 1 | Tyr-ATA: 2 | Tyr-GTA: 47 | Supres-TTA: 6 | Cys-GCA: 2 | Trp-CCA: 1 |

Isotype / Anticodon Counts:

Ala   : 103	  AGC: 46      GGC: 4       CGC: 42      TGC: 11    
Gly   : 180	  ACC: 1       GCC: 120     CCC: 21      TCC: 38    
Pro   : 243	  AGG: 141     GGG: 9       CGG: 62      TGG: 31    
Thr   : 175	  AGT: 100     GGT: 3       CGT: 40      TGT: 32    
Val   : 115	  AAC: 60      GAC: 3       CAC: 52      TAC:       
Ser   : 125	  AGA: 37      GGA: 5       CGA: 23      TGA: 21      ACT: 8       GCT: 31    
Arg   : 131	  ACG: 26      GCG:         CCG: 32      TCG: 33      CCT: 19      TCT: 21    
Leu   : 214	  AAG: 30      GAG: 2       CAG: 56      TAG:         CAA: 69      TAA: 57    
Phe   : 27	  AAA: 9       GAA: 18                              
Asn   : 98	  ATT: 4       GTT: 94                              
Lys   : 177	                            CTT: 141     TTT: 36    
Asp   : 94	  ATC: 2       GTC: 92                              
Glu   : 154	                            CTC: 83      TTC: 71    
His   : 32	  ATG: 1       GTG: 31                              
Gln   : 156	                            CTG: 154     TTG: 2     
Ile   : 72	  AAT: 58      GAT:                      TAT: 14    
Met   : 72	                            CAT: 72                 
Tyr   : 43	  ATA: 2       GTA: 41                              
Supres: 8	                            CTA: 3       TTA: 5     
Cys   : 67	  ACA: 1       GCA: 66                              
Trp   : 72	                            CCA: 72                 
SelCys: 7	                                         TCA: 7