tRNAscan-SE v.1.23 (April 2002) scan results (on host lowedev.cse.ucsc.edu)
Started: Tue Jan 27 09:47:46 PST 2009

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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:         16587
Seqs w/at least 1 hit:  14127
Bases read:             2796567085 (x2 for both strands)
Bases in tRNAs:         3655150
tRNAs predicted:        38515
Av. tRNA length:        94
Script CPU time:        327.30 s
Scan CPU time:          2039.42 s
Scan speed:             2742.5 Kbp/sec

First pass search(es) ended: Tue Jan 27 10:34:29 PST 2009

Cove Stats:
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Candidate tRNAs read:     38515
Cove-confirmed tRNAs:     2940
Bases scanned by covels:  4194355
% seq scanned by covels:  0.1 %
Script CPU time:          83.14 s
Cove CPU time:            3323.93 s
Scan speed:               1261.9 bp/sec

Cove analysis of tRNAs ended: Tue Jan 27 11:43:49 PST 2009

Summary
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Overall scan speed: 968711.0 bp/sec

tRNAs decoding Standard 20 AA:              1884
Selenocysteine tRNAs (TCA):                 6
Possible suppressor tRNAs (CTA,TTA):        11
tRNAs with undetermined/unknown isotypes:   17
Predicted pseudogenes:                      1022
                                            -------
Total tRNAs:                                2940

tRNAs with introns:     	64

| Thr-GGT: 1 | Val-AAC: 2 | Val-CAC: 1 | Val-TAC: 1 | Arg-TCT: 1 | Leu-TAA: 1 | Asn-ATT: 1 | Ile-AAT: 1 | Met-CAT: 31 | Tyr-ATA: 1 | Tyr-GTA: 22 | Cys-ACA: 1 |

Isotype / Anticodon Counts:

Ala   : 181	  AGC: 125     GGC:         CGC: 38      TGC: 18    
Gly   : 71	  ACC:         GCC: 42      CCC: 15      TCC: 14    
Pro   : 75	  AGG: 21      GGG: 1       CGG: 10      TGG: 43    
Thr   : 78	  AGT: 31      GGT: 14      CGT: 9       TGT: 24    
Val   : 75	  AAC: 34      GAC: 17      CAC: 19      TAC: 5     
Ser   : 87	  AGA: 16      GGA: 29      CGA: 9       TGA: 12      ACT:         GCT: 21    
Arg   : 105	  ACG: 50      GCG:         CCG: 10      TCG: 9       CCT: 13      TCT: 23    
Leu   : 96	  AAG: 42      GAG:         CAG: 17      TAG: 10      CAA: 20      TAA: 7     
Phe   : 35	  AAA: 2       GAA: 33                              
Asn   : 60	  ATT: 2       GTT: 58                              
Lys   : 468	                            CTT: 287     TTT: 181   
Asp   : 61	  ATC: 2       GTC: 59                              
Glu   : 72	                            CTC: 38      TTC: 34    
His   : 42	  ATG: 5       GTG: 37                              
Gln   : 47	                            CTG: 20      TTG: 27    
Ile   : 109	  AAT: 103     GAT:                      TAT: 6     
Met   : 105	                            CAT: 105                
Tyr   : 36	  ATA: 3       GTA: 33                              
Supres: 11	                            CTA: 9       TTA: 2     
Cys   : 42	  ACA: 2       GCA: 40                              
Trp   : 39	                            CCA: 39                 
SelCys: 6	                                         TCA: 6