tRNAscan-SE Run Options & Statistics

	
tRNAscan-SE v.2.0 (Sept 2015) scan results (on host hoag.soe.ucsc.edu)
Started: Fri Sep 25 10:08:51 PDT 2015

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Search Mode:                 Eukaryotic
Searching with:              Infernal First Pass->Infernal
Perform isotype specific model scan
Covariance model:            infernal-1.1/TRNAinf-euk.cm
Infernal first pass cutoff score: 0
Isotype specific

Reporting HMM/2' structure score breakdown
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First-pass (tRNAscan/EufindtRNA) Stats:
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Sequences read:         7
Seqs w/at least 1 hit:  6
Bases read:             100286070 (x2 for both strands)
Bases in tRNAs:         76579
tRNAs predicted:        1059
Av. tRNA length:        72
Script CPU time:        17.27 s
Scan CPU time:          55.92 s
Scan speed:             3586.8 Kbp/sec

First pass search(es) ended: Fri Sep 25 10:09:39 PDT 2015

Infernal Stats:
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Candidate tRNAs read:     1059
Infernal-confirmed tRNAs:     644
Bases scanned by Infernal:  97759
% seq scanned by Infernal:  0.0 %
Script CPU time:          9.90 s
Infernal CPU time:            1175.80 s
Scan speed:               83.1 bp/sec

Infernal analysis of tRNAs ended: Fri Sep 25 10:39:24 PDT 2015

Overall scan speed: 159324.6 bp/sec

tRNAs decoding Standard 20 AA:              602
Selenocysteine tRNAs (TCA):                 2
Possible suppressor tRNAs (CTA,TTA):        0
tRNAs with undetermined/unknown isotypes:   1
Predicted pseudogenes:                      39
                                            -------
Total tRNAs:                                644

tRNAs with introns:     	37

| Thr-GGT: 1 | Thr-TGT: 3 | Val-AAC: 1 | Leu-AAG: 2 | Leu-CAA: 7 | His-GTG: 1 | Ile-TAT: 3 | Tyr-GTA: 19 |

Isotype / Anticodon Counts:

Ala   : 35	  AGC: 22      GGC:         CGC: 4       TGC: 9     
Gly   : 55	  ACC:         GCC: 16      CCC: 3       TCC: 36    
Pro   : 41	  AGG: 6       GGG:         CGG: 4       TGG: 31    
Thr   : 35	  AGT: 17      GGT:         CGT: 7       TGT: 11    
Val   : 30	  AAC: 19      GAC:         CAC: 6       TAC: 5     
Ser   : 40	  AGA: 15      GGA:         CGA: 6       TGA: 9       ACT: 1       GCT: 9     
Arg   : 39	  ACG: 18      GCG:         CCG: 1       TCG: 8       CCT: 4       TCT: 8     
Leu   : 39	  AAG: 20      GAG:         CAG: 5       TAG: 3       CAA: 7       TAA: 4     
Phe   : 15	  AAA:         GAA: 15                              
Asn   : 20	  ATT:         GTT: 20                              
Lys   : 45	                            CTT: 30      TTT: 15    
Asp   : 27	  ATC:         GTC: 27                              
Glu   : 43	                            CTC: 24      TTC: 19    
His   : 19	  ATG:         GTG: 19                              
Gln   : 27	                            CTG: 7       TTG: 20    
Ile   : 29	  AAT: 22      GAT:                      TAT: 7     
Met   : 19	                            CAT: 19                 
Tyr   : 19	  ATA:         GTA: 19                              
Supres: 0	                            CTA:         TTA:       
Cys   : 13	  ACA:         GCA: 13                              
Trp   : 12	                            CCA: 12                 
SelCys: 2	                                         TCA: 2