GtRNAdb

tRNAscan-SE Analysis of Arabidopsis thaliana (Feb 2004)

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tRNAscan-SE Run Options & Statistics

tRNAscan-SE v.1.23 (April 2002) scan results (on host lowedev.cse.ucsc.edu)
Started: Fri Aug  8 20:45:21 PDT 2008

------------------------------------------------------------
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:         5
Seqs w/at least 1 hit:  5
Bases read:             119186497 (x2 for both strands)
Bases in tRNAs:         145783
tRNAs predicted:        1561
Av. tRNA length:        93
Script CPU time:        17.21 s
Scan CPU time:          78.39 s
Scan speed:             3040.9 Kbp/sec

First pass search(es) ended: Fri Aug  8 20:47:03 PDT 2008

Cove Stats:
-----------
Candidate tRNAs read:     1561
Cove-confirmed tRNAs:     639
Bases scanned by covels:  167637
% seq scanned by covels:  0.1 %
Script CPU time:          4.00 s
Cove CPU time:            164.09 s
Scan speed:               1021.6 bp/sec

Cove analysis of tRNAs ended: Fri Aug  8 20:51:27 PDT 2008

Summary
--------
Overall scan speed: 903989.5 bp/sec

tRNAs decoding Standard 20 AA:              630
Selenocysteine tRNAs (TCA):                 0
Possible suppressor tRNAs (CTA,TTA):        0
tRNAs with undetermined/unknown isotypes:   1
Predicted pseudogenes:                      8
                                            -------
Total tRNAs:                                639

tRNAs with introns:     	83

| Ser-GCT: 2 | Met-CAT: 11 | Tyr-GTA: 70 |

Isotype / Anticodon Counts:

Ala   : 33	  AGC: 16      GGC:         CGC: 7       TGC: 10    
Gly   : 41	  ACC: 1       GCC: 23      CCC: 5       TCC: 12    
Pro   : 66	  AGG: 16      GGG:         CGG: 5       TGG: 45    
Thr   : 24	  AGT: 10      GGT:         CGT: 6       TGT: 8     
Val   : 30	  AAC: 15      GAC:         CAC: 8       TAC: 7     
Ser   : 64	  AGA: 37      GGA: 1       CGA: 4       TGA: 9       ACT:         GCT: 13    
Arg   : 36	  ACG: 9       GCG:         CCG: 4       TCG: 6       CCT: 8       TCT: 9     
Leu   : 42	  AAG: 12      GAG: 1       CAG: 3       TAG: 10      CAA: 10      TAA: 6     
Phe   : 16	  AAA:         GAA: 16                              
Asn   : 16	  ATT:         GTT: 16                              
Lys   : 31	                            CTT: 18      TTT: 13    
Asp   : 26	  ATC:         GTC: 26                              
Glu   : 25	                            CTC: 13      TTC: 12    
His   : 10	  ATG:         GTG: 10                              
Gln   : 17	                            CTG: 9       TTG: 8     
Ile   : 24	  AAT: 19      GAT:                      TAT: 5     
Met   : 24	                            CAT: 24                 
Tyr   : 76	  ATA:         GTA: 76                              
Supres: 0	                            CTA:         TTA:       
Cys   : 15	  ACA:         GCA: 15                              
Trp   : 14	                            CCA: 14                 
SelCys: 0	                                         TCA:       


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.