tRNAscan-SE v.1.23 (April 2002) scan results (on host lowepub.cse.ucsc.edu)
Started: Mon May 19 20:57:21 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:         22
Seqs w/at least 1 hit:  22
Bases read:             2864106071 (x2 for both strands)
Bases in tRNAs:         3566074
tRNAs predicted:        29029
Av. tRNA length:        122
Script CPU time:        534.02 s
Scan CPU time:          1798.14 s
Scan speed:             3185.6 Kbp/sec

First pass search(es) ended: Mon May 19 21:40:15 PDT 2008

Cove Stats:
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Candidate tRNAs read:     29029
Cove-confirmed tRNAs:     521
Bases scanned by covels:  3972480
% seq scanned by covels:  0.1 %
Script CPU time:          79.40 s
Cove CPU time:            4464.82 s
Scan speed:               889.7 bp/sec

Cove analysis of tRNAs ended: Mon May 19 23:26:29 PDT 2008

Summary
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Overall scan speed: 833027.3 bp/sec

tRNAs decoding Standard 20 AA:              421
Selenocysteine tRNAs (TCA):                 2
Possible suppressor tRNAs (CTA,TTA):        1
tRNAs with undetermined/unknown isotypes:   1
Predicted pseudogenes:                      96
                                            -------
Total tRNAs:                                521

tRNAs with introns:     	28

| Arg-TCT: 4 | Leu-CAA: 3 | Ile-TAT: 5 | Tyr-ATA: 1 | Tyr-GTA: 14 | Cys-GCA: 1 |

Isotype / Anticodon Counts:

Ala   : 31	  AGC: 16      GGC: 1       CGC: 5       TGC: 9     
Gly   : 26	  ACC:         GCC: 13      CCC: 8       TCC: 5     
Pro   : 18	  AGG: 9       GGG:         CGG: 4       TGG: 5     
Thr   : 18	  AGT: 8       GGT:         CGT: 4       TGT: 6     
Val   : 29	  AAC: 7       GAC: 1       CAC: 14      TAC: 7     
Ser   : 26	  AGA: 9       GGA:         CGA: 4       TGA: 5       ACT:         GCT: 8     
Arg   : 26	  ACG: 7       GCG:         CCG: 4       TCG: 5       CCT: 5       TCT: 5     
Leu   : 27	  AAG: 9       GAG:         CAG: 6       TAG: 4       CAA: 3       TAA: 5     
Phe   : 10	  AAA: 1       GAA: 9                               
Asn   : 23	  ATT: 1       GTT: 22                              
Lys   : 30	                            CTT: 13      TTT: 17    
Asp   : 16	  ATC:         GTC: 16                              
Glu   : 21	                            CTC: 7       TTC: 14    
His   : 11	  ATG:         GTG: 11                              
Gln   : 21	                            CTG: 11      TTG: 10    
Ile   : 21	  AAT: 12      GAT: 4                    TAT: 5     
Met   : 18	                            CAT: 18                 
Tyr   : 15	  ATA: 1       GTA: 14                              
Supres: 1	                            CTA:         TTA: 1     
Cys   : 27	  ACA: 1       GCA: 26                              
Trp   : 7	                            CCA: 7                  
SelCys: 2	                                         TCA: 2