tRNAscan-SE v.1.23 (April 2002) scan results (on host lowepub.cse.ucsc.edu)
Started: Sun May 18 04:37:28 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:         1
Seqs w/at least 1 hit:  1
Bases read:             161944676 (x2 for both strands)
Bases in tRNAs:         349101
tRNAs predicted:        4130
Av. tRNA length:        84
Script CPU time:        44.52 s
Scan CPU time:          105.93 s
Scan speed:             3057.6 Kbp/sec

First pass search(es) ended: Sun May 18 04:40:14 PDT 2008

Cove Stats:
-----------
Candidate tRNAs read:     4130
Cove-confirmed tRNAs:     971
Bases scanned by covels:  406921
% seq scanned by covels:  0.1 %
Script CPU time:          12.16 s
Cove CPU time:            331.04 s
Scan speed:               1229.2 bp/sec

Cove analysis of tRNAs ended: Sun May 18 04:54:59 PDT 2008

Summary
--------
Overall scan speed: 656111.3 bp/sec

tRNAs decoding Standard 20 AA:              782
Selenocysteine tRNAs (TCA):                 1
Possible suppressor tRNAs (CTA,TTA):        2
tRNAs with undetermined/unknown isotypes:   9
Predicted pseudogenes:                      177
                                            -------
Total tRNAs:                                971

tRNAs with introns:     	55

| Ala-GGC: 1 | Gly-ACC: 4 | Pro-AGG: 10 | Leu-CAA: 12 | Ile-TAT: 4 | Tyr-GTA: 24 |

Isotype / Anticodon Counts:

Ala   : 46	  AGC: 26      GGC: 1       CGC: 6       TGC: 13    
Gly   : 73	  ACC:         GCC: 23      CCC: 6       TCC: 44    
Pro   : 54	  AGG: 8       GGG: 4       CGG: 6       TGG: 36    
Thr   : 38	  AGT: 20      GGT: 1       CGT: 6       TGT: 11    
Val   : 40	  AAC: 27      GAC:         CAC: 9       TAC: 4     
Ser   : 46	  AGA: 17      GGA:         CGA: 7       TGA: 11      ACT: 1       GCT: 10    
Arg   : 60	  ACG: 28      GCG:         CCG: 2       TCG: 12      CCT: 4       TCT: 14    
Leu   : 54	  AAG: 22      GAG: 1       CAG: 5       TAG: 8       CAA: 12      TAA: 6     
Phe   : 18	  AAA:         GAA: 18                              
Asn   : 23	  ATT: 1       GTT: 22                              
Lys   : 69	                            CTT: 48      TTT: 21    
Asp   : 39	  ATC:         GTC: 39                              
Glu   : 46	                            CTC: 22      TTC: 24    
His   : 22	  ATG: 1       GTG: 21                              
Gln   : 32	                            CTG: 10      TTG: 22    
Ile   : 40	  AAT: 26      GAT: 1                    TAT: 13    
Met   : 27	                            CAT: 27                 
Tyr   : 23	  ATA:         GTA: 23                              
Supres: 2	                            CTA:         TTA: 2     
Cys   : 15	  ACA:         GCA: 15                              
Trp   : 17	                            CCA: 17                 
SelCys: 1	                                         TCA: 1