tRNAscan-SE v.1.23 (April 2002) scan results (on host lowedev.cse.ucsc.edu)
Started: Thu Jul 17 21:58:53 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:         14
Seqs w/at least 1 hit:  14
Bases read:             19051922 (x2 for both strands)
Bases in tRNAs:         25835
tRNAs predicted:        238
Av. tRNA length:        108
Script CPU time:        2.63 s
Scan CPU time:          13.29 s
Scan speed:             2867.1 Kbp/sec

First pass search(es) ended: Thu Jul 17 21:59:11 PDT 2008

Cove Stats:
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Candidate tRNAs read:     238
Cove-confirmed tRNAs:     143
Bases scanned by covels:  29167
% seq scanned by covels:  0.1 %
Script CPU time:          0.72 s
Cove CPU time:            38.04 s
Scan speed:               766.7 bp/sec

Cove analysis of tRNAs ended: Thu Jul 17 22:00:06 PDT 2008

Summary
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Overall scan speed: 696851.6 bp/sec

tRNAs decoding Standard 20 AA:              141
Selenocysteine tRNAs (TCA):                 0
Possible suppressor tRNAs (CTA,TTA):        0
tRNAs with undetermined/unknown isotypes:   0
Predicted pseudogenes:                      2
                                            -------
Total tRNAs:                                143

tRNAs with introns:     	132

| Ala-AGC: 7 | Ala-CGC: 2 | Ala-TGC: 1 | Gly-GCC: 5 | Gly-CCC: 2 | Gly-TCC: 1 | Pro-AGG: 5 | Pro-CGG: 1 | Pro-TGG: 1 | Thr-AGT: 5 | Thr-CGT: 1 | Thr-TGT: 1 | Val-AAC: 7 | Val-CAC: 2 | Ser-AGA: 6 | Ser-CGA: 1 | Ser-TGA: 1 | Ser-GCT: 2 | Arg-ACG: 3 | Arg-CCG: 1 | Arg-TCG: 5 | Arg-CCT: 3 | Arg-TCT: 1 | Leu-AAG: 6 | Leu-CAG: 1 | Leu-CAA: 3 | Leu-TAA: 1 | Phe-GAA: 5 | Asn-GTT: 4 | Lys-CTT: 7 | Lys-TTT: 1 | Asp-GTC: 1 | Glu-CTC: 9 | Glu-TTC: 3 | His-GTG: 2 | Gln-TTG: 2 | Ile-AAT: 6 | Ile-TAT: 1 | Met-CAT: 6 | Tyr-GTA: 4 | Cys-GCA: 3 | Trp-CCA: 3 |

Isotype / Anticodon Counts:

Ala   : 10	  AGC: 7       GGC:         CGC: 2       TGC: 1     
Gly   : 14	  ACC:         GCC: 9       CCC: 2       TCC: 3     
Pro   : 7	  AGG: 5       GGG:         CGG: 1       TGG: 1     
Thr   : 7	  AGT: 5       GGT:         CGT: 1       TGT: 1     
Val   : 9	  AAC: 7       GAC:         CAC: 2       TAC:       
Ser   : 8	  AGA: 6       GGA:         CGA:         TGA: 1       ACT:         GCT: 1     
Arg   : 13	  ACG: 3       GCG:         CCG: 1       TCG: 5       CCT: 3       TCT: 1     
Leu   : 11	  AAG: 6       GAG:         CAG: 1       TAG:         CAA: 3       TAA: 1     
Phe   : 5	  AAA:         GAA: 5                               
Asn   : 4	  ATT:         GTT: 4                               
Lys   : 8	                            CTT: 7       TTT: 1     
Asp   : 1	  ATC:         GTC: 1                               
Glu   : 12	                            CTC: 9       TTC: 3     
His   : 4	  ATG:         GTG: 4                               
Gln   : 5	                            CTG: 3       TTG: 2     
Ile   : 7	  AAT: 6       GAT:                      TAT: 1     
Met   : 6	                            CAT: 6                  
Tyr   : 4	  ATA:         GTA: 4                               
Supres: 0	                            CTA:         TTA:       
Cys   : 3	  ACA:         GCA: 3                               
Trp   : 3	                            CCA: 3                  
SelCys: 0	                                         TCA: