tRNAscan-SE v.1.23 (April 2002) scan results (on host lowedev.cse.ucsc.edu)
Started: Thu Aug 14 01:19:37 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:         114222
Seqs w/at least 1 hit:  12933
Bases read:             907070087 (x2 for both strands)
Bases in tRNAs:         3010448
tRNAs predicted:        37576
Av. tRNA length:        80
Script CPU time:        155.70 s
Scan CPU time:          629.28 s
Scan speed:             2882.9 Kbp/sec

First pass search(es) ended: Thu Aug 14 02:29:41 PDT 2008

Cove Stats:
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Candidate tRNAs read:     37576
Cove-confirmed tRNAs:     13842
Bases scanned by covels:  3535675
% seq scanned by covels:  0.2 %
Script CPU time:          68.86 s
Cove CPU time:            2943.02 s
Scan speed:               1201.4 bp/sec

Cove analysis of tRNAs ended: Thu Aug 14 04:02:42 PDT 2008

Summary
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Overall scan speed: 477800.1 bp/sec

tRNAs decoding Standard 20 AA:              2045
Selenocysteine tRNAs (TCA):                 32
Possible suppressor tRNAs (CTA,TTA):        7
tRNAs with undetermined/unknown isotypes:   23
Predicted pseudogenes:                      11735
                                            -------
Total tRNAs:                                13842

tRNAs with introns:     	93

| Gly-CCC: 1 | Pro-CGG: 3 | Pro-TGG: 4 | Thr-AGT: 1 | Thr-CGT: 5 | Thr-TGT: 1 | Val-AAC: 1 | Val-CAC: 4 | Ser-GGA: 1 | Ser-TGA: 3 | Ser-ACT: 1 | Arg-CCG: 1 | Leu-AAG: 3 | Leu-TAG: 1 | Leu-CAA: 1 | Asn-GTT: 1 | Asp-GTC: 1 | Glu-CTC: 3 | His-GTG: 4 | Gln-CTG: 1 | Ile-TAT: 14 | Met-CAT: 3 | Tyr-GTA: 30 | Supres-TTA: 1 | Cys-GCA: 1 | Trp-CCA: 2 |

Isotype / Anticodon Counts:

Ala   : 228	  AGC: 49      GGC: 144     CGC: 12      TGC: 23    
Gly   : 90	  ACC:         GCC: 46      CCC: 9       TCC: 35    
Pro   : 59	  AGG: 21      GGG: 3       CGG: 10      TGG: 25    
Thr   : 91	  AGT: 30      GGT: 3       CGT: 32      TGT: 26    
Val   : 75	  AAC: 21      GAC: 3       CAC: 37      TAC: 14    
Ser   : 127	  AGA: 28      GGA: 18      CGA: 10      TGA: 50      ACT: 3       GCT: 18    
Arg   : 102	  ACG: 30      GCG: 1       CCG: 1       TCG: 22      CCT: 25      TCT: 23    
Leu   : 67	  AAG: 21      GAG: 3       CAG: 6       TAG: 11      CAA: 7       TAA: 19    
Phe   : 15	  AAA: 5       GAA: 10                              
Asn   : 44	  ATT:         GTT: 44                              
Lys   : 119	                            CTT: 59      TTT: 60    
Asp   : 101	  ATC: 3       GTC: 98                              
Glu   : 135	                            CTC: 99      TTC: 36    
His   : 80	  ATG: 10      GTG: 70                              
Gln   : 44	                            CTG: 25      TTG: 19    
Ile   : 108	  AAT: 74      GAT: 6                    TAT: 28    
Met   : 460	                            CAT: 460                
Tyr   : 33	  ATA:         GTA: 33                              
Supres: 7	                            CTA: 2       TTA: 5     
Cys   : 49	  ACA: 1       GCA: 48                              
Trp   : 18	                            CCA: 18                 
SelCys: 32	                                         TCA: 32