tRNAscan-SE v.1.23 (April 2002) scan results (on host lowedev.cse.ucsc.edu)
Started: Tue Jun 16 22:50:29 PDT 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:         9
Seqs w/at least 1 hit:  9
Bases read:             321041031 (x2 for both strands)
Bases in tRNAs:         1066551
tRNAs predicted:        12726
Av. tRNA length:        83
Script CPU time:        69.80 s
Scan CPU time:          183.93 s
Scan speed:             3490.9 Kbp/sec

First pass search(es) ended: Tue Jun 16 22:54:55 PDT 2009

Cove Stats:
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Candidate tRNAs read:     12726
Cove-confirmed tRNAs:     726
Bases scanned by covels:  1244715
% seq scanned by covels:  0.2 %
Script CPU time:          31.09 s
Cove CPU time:            858.32 s
Scan speed:               1450.2 bp/sec

Cove analysis of tRNAs ended: Tue Jun 16 23:13:50 PDT 2009

Summary
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Overall scan speed: 561682.8 bp/sec

tRNAs decoding Standard 20 AA:              581
Selenocysteine tRNAs (TCA):                 1
Possible suppressor tRNAs (CTA,TTA):        5
tRNAs with undetermined/unknown isotypes:   7
Predicted pseudogenes:                      132
                                            -------
Total tRNAs:                                726

tRNAs with introns:     	40

| Ala-TGC: 1 | Ser-GCT: 1 | Leu-TAA: 2 | Asn-ATT: 1 | Lys-TTT: 2 | Glu-TTC: 3 | Gln-TTG: 2 | Ile-TAT: 4 | Met-CAT: 13 | Tyr-ATA: 1 | Tyr-GTA: 9 | SelCys-TCA: 1 |

Isotype / Anticodon Counts:

Ala   : 44	  AGC: 25      GGC:         CGC: 3       TGC: 16    
Gly   : 42	  ACC: 1       GCC: 23      CCC: 3       TCC: 15    
Pro   : 19	  AGG: 7       GGG:         CGG: 1       TGG: 11    
Thr   : 25	  AGT: 10      GGT: 4       CGT: 1       TGT: 10    
Val   : 34	  AAC: 17      GAC: 3       CAC: 7       TAC: 7     
Ser   : 39	  AGA: 12      GGA: 2       CGA: 2       TGA: 8       ACT:         GCT: 15    
Arg   : 34	  ACG: 12      GCG:         CCG: 3       TCG: 5       CCT: 6       TCT: 8     
Leu   : 44	  AAG: 9       GAG:         CAG: 4       TAG: 10      CAA: 14      TAA: 7     
Phe   : 26	  AAA:         GAA: 26                              
Asn   : 37	  ATT: 9       GTT: 28                              
Lys   : 34	                            CTT: 16      TTT: 18    
Asp   : 28	  ATC:         GTC: 28                              
Glu   : 30	                            CTC: 11      TTC: 19    
His   : 17	  ATG:         GTG: 17                              
Gln   : 22	                            CTG: 5       TTG: 17    
Ile   : 29	  AAT: 19      GAT:                      TAT: 10    
Met   : 40	                            CAT: 40                 
Tyr   : 13	  ATA: 1       GTA: 12                              
Supres: 5	                            CTA:         TTA: 5     
Cys   : 10	  ACA:         GCA: 10                              
Trp   : 14	                            CCA: 14                 
SelCys: 1	                                         TCA: 1