tRNAscan-SE v.1.23 (April 2002) scan results (on host lowepub.cse.ucsc.edu)
Started: Sun May 18 03:53:41 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:         49
Seqs w/at least 1 hit:  46
Bases read:             3107677273 (x2 for both strands)
Bases in tRNAs:         3462654
tRNAs predicted:        28619
Av. tRNA length:        120
Script CPU time:        563.49 s
Scan CPU time:          1931.70 s
Scan speed:             3217.6 Kbp/sec

First pass search(es) ended: Sun May 18 04:39:48 PDT 2008

Cove Stats:
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Candidate tRNAs read:     28619
Cove-confirmed tRNAs:     697
Bases scanned by covels:  3863320
% seq scanned by covels:  0.1 %
Script CPU time:          78.23 s
Cove CPU time:            4341.24 s
Scan speed:               889.9 bp/sec

Cove analysis of tRNAs ended: Sun May 18 06:26:41 PDT 2008

Summary
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Overall scan speed: 898866.3 bp/sec

tRNAs decoding Standard 20 AA:              574
Selenocysteine tRNAs (TCA):                 3
Possible suppressor tRNAs (CTA,TTA):        3
tRNAs with undetermined/unknown isotypes:   3
Predicted pseudogenes:                      114
                                            -------
Total tRNAs:                                697

tRNAs with introns:     	36

| Pro-AGG: 1 | Arg-TCT: 5 | Leu-CAA: 9 | Ile-TAT: 5 | Tyr-ATA: 1 | Tyr-GTA: 13 | Cys-ACA: 1 | Trp-CCA: 1 |

Isotype / Anticodon Counts:

Ala   : 67	  AGC: 42      GGC:         CGC: 8       TGC: 17    
Gly   : 31	  ACC:         GCC: 15      CCC: 7       TCC: 9     
Pro   : 21	  AGG: 10      GGG:         CGG: 4       TGG: 7     
Thr   : 24	  AGT: 11      GGT:         CGT: 7       TGT: 6     
Val   : 32	  AAC: 11      GAC:         CAC: 16      TAC: 5     
Ser   : 29	  AGA: 11      GGA:         CGA: 4       TGA: 5       ACT:         GCT: 9     
Arg   : 32	  ACG: 7       GCG:         CCG: 8       TCG: 6       CCT: 5       TCT: 6     
Leu   : 48	  AAG: 16      GAG:         CAG: 10      TAG: 3       CAA: 11      TAA: 8     
Phe   : 22	  AAA:         GAA: 22                              
Asn   : 33	  ATT: 1       GTT: 32                              
Lys   : 37	                            CTT: 17      TTT: 20    
Asp   : 19	  ATC:         GTC: 19                              
Glu   : 28	                            CTC: 15      TTC: 13    
His   : 11	  ATG:         GTG: 11                              
Gln   : 35	                            CTG: 23      TTG: 12    
Ile   : 27	  AAT: 14      GAT: 8                    TAT: 5     
Met   : 24	                            CAT: 24                 
Tyr   : 15	  ATA: 1       GTA: 14                              
Supres: 3	                            CTA: 1       TTA: 2     
Cys   : 30	  ACA:         GCA: 30                              
Trp   : 9	                            CCA: 9                  
SelCys: 3	                                         TCA: 3