tRNAscan-SE v.1.23 (April 2002) scan results (on host lowepub.cse.ucsc.edu)
Started: Sun May 18 10:45:34 PDT 2008

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Search Mode:                 Eukaryotic
Searching with:              tRNAscan + EufindtRNA -> Cove
Covariance model:            TRNA2-euk.cm
tRNAscan parameters:         Strict
EufindtRNA parameters:       Relaxed (Int Cutoff= -32.1)

Reporting HMM/2' structure score breakdown
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First-pass (tRNAscan/EufindtRNA) Stats:
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Sequences read:         52
Seqs w/at least 1 hit:  51
Bases read:             3350447512 (x2 for both strands)
Bases in tRNAs:         4042047
tRNAs predicted:        33310
Av. tRNA length:        121
Script CPU time:        629.96 s
Scan CPU time:          2066.24 s
Scan speed:             3243.0 Kbp/sec

First pass search(es) ended: Sun May 18 11:35:59 PDT 2008

Cove Stats:
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Candidate tRNAs read:     33310
Cove-confirmed tRNAs:     644
Bases scanned by covels:  4508387
% seq scanned by covels:  0.1 %
Script CPU time:          96.68 s
Cove CPU time:            5049.18 s
Scan speed:               892.9 bp/sec

Cove analysis of tRNAs ended: Sun May 18 13:44:17 PDT 2008

Summary
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Overall scan speed: 854481.5 bp/sec

tRNAs decoding Standard 20 AA:              525
Selenocysteine tRNAs (TCA):                 4
Possible suppressor tRNAs (CTA,TTA):        4
tRNAs with undetermined/unknown isotypes:   4
Predicted pseudogenes:                      107
                                            -------
Total tRNAs:                                644

tRNAs with introns:     	33

| Pro-AGG: 1 | Val-CAC: 1 | Val-TAC: 1 | Arg-TCT: 5 | Leu-CAA: 5 | Ile-TAT: 5 | Tyr-ATA: 1 | Tyr-GTA: 13 | Cys-ACA: 1 |

Isotype / Anticodon Counts:

Ala   : 46	  AGC: 32      GGC:         CGC: 5       TGC: 9     
Gly   : 31	  ACC:         GCC: 13      CCC: 11      TCC: 7     
Pro   : 23	  AGG: 11      GGG:         CGG: 5       TGG: 7     
Thr   : 20	  AGT: 10      GGT:         CGT: 4       TGT: 6     
Val   : 35	  AAC: 11      GAC:         CAC: 14      TAC: 10    
Ser   : 31	  AGA: 11      GGA:         CGA: 3       TGA: 5       ACT: 3       GCT: 9     
Arg   : 31	  ACG: 7       GCG: 1       CCG: 5       TCG: 6       CCT: 6       TCT: 6     
Leu   : 38	  AAG: 10      GAG:         CAG: 8       TAG: 3       CAA: 7       TAA: 10    
Phe   : 12	  AAA:         GAA: 12                              
Asn   : 35	  ATT: 2       GTT: 33                              
Lys   : 37	                            CTT: 19      TTT: 18    
Asp   : 17	  ATC: 1       GTC: 16                              
Glu   : 32	                            CTC: 14      TTC: 18    
His   : 10	  ATG:         GTG: 10                              
Gln   : 30	                            CTG: 19      TTG: 11    
Ile   : 23	  AAT: 16      GAT: 2                    TAT: 5     
Met   : 23	                            CAT: 23                 
Tyr   : 16	  ATA: 1       GTA: 15                              
Supres: 4	                            CTA: 2       TTA: 2     
Cys   : 28	  ACA: 1       GCA: 27                              
Trp   : 7	                            CCA: 7                  
SelCys: 4	                                         TCA: 4