tRNAscan-SE v.1.23 (April 2002) scan results (on host lowepub.cse.ucsc.edu)
Started: Mon May 19 10:14:37 PDT 2008

------------------------------------------------------------
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
------------------------------------------------------------

First-pass (tRNAscan/EufindtRNA) Stats:
---------------
Sequences read:         34
Seqs w/at least 1 hit:  34
Bases read:             2462493800 (x2 for both strands)
Bases in tRNAs:         17530494
tRNAs predicted:        213756
Av. tRNA length:        82
Script CPU time:        2989.49 s
Scan CPU time:          1577.82 s
Scan speed:             3121.4 Kbp/sec

First pass search(es) ended: Mon May 19 11:34:36 PDT 2008

Cove Stats:
-----------
Candidate tRNAs read:     213756
Cove-confirmed tRNAs:     2667
Bases scanned by covels:  20523078
% seq scanned by covels:  0.4 %
Script CPU time:          605.29 s
Cove CPU time:            12728.66 s
Scan speed:               1612.4 bp/sec

Cove analysis of tRNAs ended: Mon May 19 19:48:39 PDT 2008

Summary
--------
Overall scan speed: 275119.6 bp/sec

tRNAs decoding Standard 20 AA:              885
Selenocysteine tRNAs (TCA):                 19
Possible suppressor tRNAs (CTA,TTA):        7
tRNAs with undetermined/unknown isotypes:   23
Predicted pseudogenes:                      1733
                                            -------
Total tRNAs:                                2667

tRNAs with introns:     	53

| Ala-CGC: 1 | Gly-CCC: 1 | Thr-CGT: 1 | Ser-GGA: 1 | Ser-GCT: 1 | Arg-TCT: 8 | Leu-CAA: 6 | Lys-CTT: 1 | Lys-TTT: 1 | Glu-CTC: 5 | Gln-CTG: 6 | Ile-TAT: 4 | Tyr-ATA: 1 | Tyr-GTA: 14 | Supres-CTA: 1 | Trp-CCA: 1 |

Isotype / Anticodon Counts:

Ala   : 47	  AGC: 28      GGC:         CGC: 9       TGC: 10    
Gly   : 31	  ACC:         GCC: 11      CCC: 14      TCC: 6     
Pro   : 21	  AGG: 10      GGG:         CGG: 3       TGG: 8     
Thr   : 20	  AGT: 9       GGT:         CGT: 4       TGT: 7     
Val   : 42	  AAC: 15      GAC: 3       CAC: 18      TAC: 6     
Ser   : 36	  AGA: 12      GGA:         CGA: 7       TGA: 4       ACT:         GCT: 13    
Arg   : 41	  ACG: 10      GCG: 1       CCG: 6       TCG: 5       CCT: 9       TCT: 10    
Leu   : 30	  AAG: 8       GAG:         CAG: 4       TAG: 6       CAA: 7       TAA: 5     
Phe   : 13	  AAA:         GAA: 13                              
Asn   : 22	  ATT: 1       GTT: 21                              
Lys   : 69	                            CTT: 51      TTT: 18    
Asp   : 21	  ATC: 6       GTC: 15                              
Glu   : 337	                            CTC: 308     TTC: 29    
His   : 14	  ATG: 1       GTG: 13                              
Gln   : 36	                            CTG: 23      TTG: 13    
Ile   : 26	  AAT: 22      GAT:                      TAT: 4     
Met   : 26	                            CAT: 26                 
Tyr   : 16	  ATA: 1       GTA: 15                              
Supres: 7	                            CTA: 6       TTA: 1     
Cys   : 28	  ACA: 1       GCA: 27                              
Trp   : 9	                            CCA: 9                  
SelCys: 19	                                         TCA: 19