tRNAscan-SE Run Options & Statistics

	
tRNAscan-SE v.2.0 (Sept 2015) scan results (on host hoag.soe.ucsc.edu)
Started: Fri Sep 25 11:19:04 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:         1870
Seqs w/at least 1 hit:  5
Bases read:             143726002 (x2 for both strands)
Bases in tRNAs:         22710
tRNAs predicted:        300
Av. tRNA length:        75
Script CPU time:        23.81 s
Scan CPU time:          171.34 s
Scan speed:             1677.7 Kbp/sec

First pass search(es) ended: Fri Sep 25 11:24:20 PDT 2015

Infernal Stats:
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Candidate tRNAs read:     300
Infernal-confirmed tRNAs:     295
Bases scanned by Infernal:  28710
% seq scanned by Infernal:  0.0 %
Script CPU time:          3.74 s
Infernal CPU time:            506.99 s
Scan speed:               56.6 bp/sec

Infernal analysis of tRNAs ended: Fri Sep 25 11:36:29 PDT 2015

Overall scan speed: 407225.0 bp/sec

tRNAs decoding Standard 20 AA:              288
Selenocysteine tRNAs (TCA):                 1
Possible suppressor tRNAs (CTA,TTA):        0
tRNAs with undetermined/unknown isotypes:   2
Predicted pseudogenes:                      4
                                            -------
Total tRNAs:                                295

tRNAs with introns:     	15

| Leu-CAA: 4 | Ile-TAT: 2 | Tyr-GTA: 9 |

Isotype / Anticodon Counts:

Ala   : 17	  AGC: 12      GGC:         CGC: 3       TGC: 2     
Gly   : 20	  ACC:         GCC: 14      CCC:         TCC: 6     
Pro   : 17	  AGG: 7       GGG:         CGG: 5       TGG: 5     
Thr   : 17	  AGT: 8       GGT:         CGT: 3       TGT: 6     
Val   : 15	  AAC: 6       GAC:         CAC: 7       TAC: 2     
Ser   : 20	  AGA: 8       GGA:         CGA: 4       TGA: 2       ACT:         GCT: 6     
Arg   : 26	  ACG: 10      GCG:         CCG:         TCG: 10      CCT: 3       TCT: 3     
Leu   : 22	  AAG: 4       GAG:         CAG: 8       TAG: 2       CAA: 4       TAA: 4     
Phe   : 8	  AAA:         GAA: 8                               
Asn   : 10	  ATT:         GTT: 10                              
Lys   : 19	                            CTT: 13      TTT: 6     
Asp   : 14	  ATC:         GTC: 14                              
Glu   : 19	                            CTC: 13      TTC: 6     
His   : 5	  ATG:         GTG: 5                               
Gln   : 12	                            CTG: 8       TTG: 4     
Ile   : 11	  AAT: 9       GAT:                      TAT: 2     
Met   : 12	                            CAT: 12                 
Tyr   : 9	  ATA:         GTA: 9                               
Supres: 0	                            CTA:         TTA:       
Cys   : 7	  ACA:         GCA: 7                               
Trp   : 8	                            CCA: 8                  
SelCys: 1	                                         TCA: 1