tRNAscan-SE Run Options & Statistics

	
tRNAscan-SE v.2.0 (Jan 2016) scan results (on host hoag.soe.ucsc.edu)
Started: Sat Jan 30 15:03:28 PST 2016

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Search Mode:                 Eukaryotic
Searching with:              Infernal First Pass->Infernal
Mito isotype model scan: mammal
Covariance model:            TRNAinf-euk.cm
                             TRNAinf-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:         92
Seqs w/at least 1 hit:  32
Bases read:             3137144693 (x2 for both strands)
Bases in tRNAs:         77811
tRNAs predicted:        1051
Av. tRNA length:        74
Script CPU time:        458.15 s
Scan CPU time:          21958.25 s
Scan speed:             285.7 Kbp/sec

First pass search(es) ended: Sat Jan 30 15:25:46 PST 2016

Infernal Stats:
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Candidate tRNAs read:     1051
Infernal-confirmed tRNAs:     822
Bases scanned by Infernal:  98831
% seq scanned by Infernal:  0.0 %
Script CPU time:          7.32 s
Infernal CPU time:            1174.53 s
Scan speed:               84.1 bp/sec

Infernal analysis of tRNAs ended: Sat Jan 30 15:52:58 PST 2016

Overall scan speed: 265879.4 bp/sec

tRNAs decoding Standard 20 AA:              689
Selenocysteine tRNAs (TCA):                 3
Possible suppressor tRNAs (CTA,TTA):        4
tRNAs with undetermined/unknown isotypes:   6
Predicted pseudogenes:                      120
                                            -------
Total tRNAs:                                822

tRNAs with introns:     	45

| Pro-AGG: 1 | Thr-CGT: 1 | Arg-TCT: 5 | Leu-CAA: 15 | Ile-TAT: 6 | Tyr-ATA: 1 | Tyr-GTA: 13 | Supres-CTA: 1 | Cys-ACA: 1 | Cys-GCA: 1 |

Isotype / Anticodon Counts:

Ala   : 118	  AGC: 64      GGC: 1       CGC: 15      TGC: 38    
Gly   : 34	  ACC:         GCC: 15      CCC: 10      TCC: 9     
Pro   : 21	  AGG: 9       GGG: 1       CGG: 4       TGG: 7     
Thr   : 25	  AGT: 12      GGT:         CGT: 7       TGT: 6     
Val   : 39	  AAC: 17      GAC: 1       CAC: 14      TAC: 7     
Ser   : 29	  AGA: 10      GGA: 1       CGA: 4       TGA: 5       ACT:         GCT: 9     
Arg   : 41	  ACG: 7       GCG:         CCG: 16      TCG: 7       CCT: 5       TCT: 6     
Leu   : 59	  AAG: 20      GAG:         CAG: 10      TAG: 3       CAA: 19      TAA: 7     
Phe   : 54	  AAA:         GAA: 54                              
Asn   : 24	  ATT:         GTT: 24                              
Lys   : 43	                            CTT: 17      TTT: 26    
Asp   : 25	  ATC: 8       GTC: 17                              
Glu   : 25	                            CTC: 16      TTC: 9     
His   : 10	  ATG:         GTG: 10                              
Gln   : 27	                            CTG: 18      TTG: 9     
Ile   : 23	  AAT: 14      GAT: 3                    TAT: 6     
Met   : 30	                            CAT: 30                 
Tyr   : 23	  ATA: 2       GTA: 21                              
Supres: 4	                            CTA: 2       TTA: 2     
Cys   : 32	  ACA:         GCA: 32                              
Trp   : 7	                            CCA: 7                  
SelCys: 3	                                         TCA: 3