tRNAscan-SE Run Options & Statistics

	
tRNAscan-SE v.2.0rc1 (March 2016) scan results (on host hoag.soe.ucsc.edu)
Started: Sat Mar 12 15:15:07 PST 2016

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Search Mode:                 Eukaryotic
Searching with:              Infernal First Pass->Infernal
Mito isotype model scan: Yes
Covariance model:            euk.cm
                             euk-SeC.cm
Infernal first pass cutoff score: 10

Temporary directory:         /tmp

Reporting HMM/2' structure score breakdown
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First-pass Stats:
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Sequences read:         17
Seqs w/at least 1 hit:  17
Bases read:             12157105 (x2 for both strands)
Bases in tRNAs:         22976
tRNAs predicted:        289
Av. tRNA length:        79
Script CPU time:        1.91 s
Scan CPU time:          54.52 s
Scan speed:             446.0 Kbp/sec

First pass search(es) ended: Sat Mar 12 15:15:26 PST 2016

Infernal Stats:
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Candidate tRNAs read:     289
Infernal-confirmed tRNAs:     289
Bases scanned by Infernal:  28756
% seq scanned by Infernal:  0.1 %
Script CPU time:          2.14 s
Infernal CPU time:            151.09 s
Scan speed:               190.3 bp/sec

Infernal analysis of tRNAs ended: Sat Mar 12 15:19:41 PST 2016

Overall scan speed: 115969.7 bp/sec

tRNAs decoding Standard 20 AA:              287
Selenocysteine tRNAs (TCA):                 1
Possible suppressor tRNAs (CTA,TTA):        0
tRNAs with undetermined/unknown isotypes:   0
Predicted pseudogenes:                      1
                                            -------
Total tRNAs:                                289

tRNAs with introns:     	61

| Pro-TGG: 10 | Ser-CGA: 1 | Ser-GCT: 4 | Leu-TAG: 3 | Leu-CAA: 10 | Phe-GAA: 10 | Lys-TTT: 7 | Ile-TAT: 2 | Tyr-GTA: 8 | Trp-CCA: 6 |

Isotype / Anticodon Counts:

Ala   : 17	  AGC: 11      GGC:         CGC:         TGC: 6     
Gly   : 21	  ACC:         GCC: 16      CCC: 2       TCC: 3     
Pro   : 12	  AGG: 2       GGG:         CGG:         TGG: 10    
Thr   : 17	  AGT: 11      GGT:         CGT: 1       TGT: 5     
Val   : 19	  AAC: 14      GAC:         CAC: 2       TAC: 3     
Ser   : 20	  AGA: 11      GGA:         CGA: 1       TGA: 4       ACT:         GCT: 4     
Arg   : 20	  ACG: 6       GCG:         CCG: 1       TCG:         CCT: 1       TCT: 12    
Leu   : 22	  AAG:         GAG: 1       CAG:         TAG: 3       CAA: 10      TAA: 8     
Phe   : 11	  AAA:         GAA: 11                              
Asn   : 11	  ATT:         GTT: 11                              
Lys   : 22	                            CTT: 14      TTT: 8     
Asp   : 16	  ATC:         GTC: 16                              
Glu   : 16	                            CTC: 2       TTC: 14    
His   : 8	  ATG:         GTG: 8                               
Gln   : 10	                            CTG: 1       TTG: 9     
Ile   : 16	  AAT: 13      GAT: 1                    TAT: 2     
Met   : 11	                            CAT: 11                 
Tyr   : 8	  ATA:         GTA: 8                               
Supres: 0	                            CTA:         TTA:       
Cys   : 4	  ACA:         GCA: 4                               
Trp   : 6	                            CCA: 6                  
SelCys: 1	                                         TCA: 1