GtRNAdb

tRNAscan-SE Analysis of Tetraodon nigroviridis (tetraodon) (Genoscope 8.0 Mar 2007)

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tRNAscan-SE Run Options & Statistics

tRNAscan-SE v.1.3 (March 2011) scan results (on host isla)
Started: Fri Dec 16 13:12:39 PST 2011

------------------------------------------------------------
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
------------------------------------------------------------

First-pass (tRNAscan/EufindtRNA) Stats:
---------------
Sequences read:         27
Seqs w/at least 1 hit:  27
Bases read:             358618246 (x2 for both strands)
Bases in tRNAs:         261001
tRNAs predicted:        2700
Av. tRNA length:        96
Script CPU time:        76.53 s
Scan CPU time:          194.37 s
Scan speed:             3690.1 Kbp/sec

First pass search(es) ended: Fri Dec 16 13:17:36 PST 2011

Cove Stats:
-----------
Candidate tRNAs read:     2700
Cove-confirmed tRNAs:     705
Bases scanned by Cove:  304201
% seq scanned by Cove:  0.0 %
Script CPU time:          11.18 s
Cove CPU time:            258.02 s
Scan speed:               1179.0 bp/sec

Cove analysis of tRNAs ended: Fri Dec 16 13:26:18 PST 2011

Summary
--------
Overall scan speed: 1327969.8 bp/sec

tRNAs decoding Standard 20 AA:              549
Selenocysteine tRNAs (TCA):                 1
Possible suppressor tRNAs (CTA,TTA):        0
tRNAs with undetermined/unknown isotypes:   9
Predicted pseudogenes:                      146
                                            -------
Total tRNAs:                                705

tRNAs with introns:     	39

| Ala-GGC: 1 | Thr-TGT: 1 | Ser-GGA: 2 | Ser-TGA: 1 | Arg-GCG: 1 | Arg-TCT: 8 | Leu-AAG: 1 | Leu-CAA: 6 | Leu-TAA: 1 | His-GTG: 1 | Ile-TAT: 5 | Tyr-GTA: 11 |

Isotype / Anticodon Counts:

Ala   : 31	  AGC: 19      GGC:         CGC: 2       TGC: 10    
Gly   : 35	  ACC:         GCC: 14      CCC: 6       TCC: 15    
Pro   : 30	  AGG: 12      GGG: 1       CGG: 4       TGG: 13    
Thr   : 52	  AGT: 27      GGT:         CGT: 13      TGT: 12    
Val   : 27	  AAC: 9       GAC:         CAC: 15      TAC: 3     
Ser   : 35	  AGA: 14      GGA:         CGA: 2       TGA: 7       ACT: 1       GCT: 11    
Arg   : 40	  ACG: 14      GCG:         CCG: 2       TCG: 6       CCT: 9       TCT: 9     
Leu   : 67	  AAG: 14      GAG:         CAG: 37      TAG: 6       CAA: 5       TAA: 5     
Phe   : 21	  AAA: 1       GAA: 20                              
Asn   : 17	  ATT:         GTT: 17                              
Lys   : 28	                            CTT: 18      TTT: 10    
Asp   : 19	  ATC:         GTC: 19                              
Glu   : 28	                            CTC: 13      TTC: 15    
His   : 13	  ATG:         GTG: 13                              
Gln   : 27	                            CTG: 18      TTG: 9     
Ile   : 22	  AAT: 17      GAT:                      TAT: 5     
Met   : 20	                            CAT: 20                 
Tyr   : 12	  ATA:         GTA: 12                              
Supres: 0	                            CTA:         TTA:       
Cys   : 16	  ACA:         GCA: 16                              
Trp   : 9	                            CCA: 9                  
SelCys: 1	                                         TCA: 1     


The Genomic tRNA Database is curated by Todd Lowe and Patricia Chan. Please email lowe@soe.ucsc.edu with any questions and comments. To submit corrections, please use our Bug and Request Tracking System.