GtRNAdb

tRNAscan-SE Analysis of Mus musculus (mm9 July 2007)

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tRNAscan-SE Run Options & Statistics

tRNAscan-SE v.1.23 (April 2002) scan results (on host lowepub.cse.ucsc.edu)
Started: Sun May 18 19:19:49 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:         34
Seqs w/at least 1 hit:  33
Bases read:             2725749182 (x2 for both strands)
Bases in tRNAs:         12889413
tRNAs predicted:        159626
Av. tRNA length:        80
Script CPU time:        2028.54 s
Scan CPU time:          1724.23 s
Scan speed:             3161.7 Kbp/sec

First pass search(es) ended: Sun May 18 20:27:04 PDT 2008

Cove Stats:
-----------
Candidate tRNAs read:     159626
Cove-confirmed tRNAs:     26264
Bases scanned by covels:  15124177
% seq scanned by covels:  0.3 %
Script CPU time:          473.15 s
Cove CPU time:            11164.51 s
Scan speed:               1354.7 bp/sec

Cove analysis of tRNAs ended: Mon May 19 03:47:42 PDT 2008

Summary
--------
Overall scan speed: 354213.5 bp/sec

tRNAs decoding Standard 20 AA:              2856
Selenocysteine tRNAs (TCA):                 5
Possible suppressor tRNAs (CTA,TTA):        2
tRNAs with undetermined/unknown isotypes:   425
Predicted pseudogenes:                      22976
                                            -------
Total tRNAs:                                26264

tRNAs with introns:     	128

| Ala-AGC: 15 | Ala-GGC: 2 | Ala-CGC: 1 | Ala-TGC: 2 | Gly-CCC: 2 | Gly-TCC: 2 | Pro-AGG: 1 | Pro-GGG: 4 | Pro-TGG: 1 | Thr-AGT: 6 | Thr-GGT: 1 | Thr-TGT: 1 | Val-AAC: 3 | Val-TAC: 2 | Ser-AGA: 15 | Ser-GGA: 1 | Ser-CGA: 1 | Ser-TGA: 1 | Ser-ACT: 1 | Ser-GCT: 4 | Arg-TCT: 5 | Leu-GAG: 4 | Leu-CAG: 4 | Leu-CAA: 5 | Phe-GAA: 1 | Asn-ATT: 1 | Asn-GTT: 2 | Lys-CTT: 1 | Lys-TTT: 5 | Glu-CTC: 1 | His-ATG: 1 | His-GTG: 1 | Gln-CTG: 2 | Gln-TTG: 1 | Ile-AAT: 1 | Ile-GAT: 1 | Ile-TAT: 4 | Met-CAT: 2 | Tyr-ATA: 2 | Tyr-GTA: 13 | Supres-CTA: 1 | Supres-TTA: 1 | Cys-GCA: 3 |

Isotype / Anticodon Counts:

Ala   : 462	  AGC: 328     GGC: 63      CGC: 17      TGC: 54    
Gly   : 94	  ACC: 24      GCC: 43      CCC: 12      TCC: 15    
Pro   : 39	  AGG: 21      GGG: 3       CGG: 5       TGG: 10    
Thr   : 119	  AGT: 55      GGT: 31      CGT: 7       TGT: 26    
Val   : 118	  AAC: 56      GAC: 12      CAC: 37      TAC: 13    
Ser   : 1302	  AGA: 39      GGA: 7       CGA: 7       TGA: 10      ACT: 71      GCT: 1168  
Arg   : 73	  ACG: 6       GCG: 2       CCG: 3       TCG: 5       CCT: 27      TCT: 30    
Leu   : 52	  AAG: 12      GAG: 4       CAG: 15      TAG: 6       CAA: 10      TAA: 5     
Phe   : 13	  AAA: 4       GAA: 9                               
Asn   : 197	  ATT: 22      GTT: 175                             
Lys   : 66	                            CTT: 41      TTT: 25    
Asp   : 41	  ATC: 17      GTC: 24                              
Glu   : 41	                            CTC: 29      TTC: 12    
His   : 14	  ATG: 3       GTG: 11                              
Gln   : 22	                            CTG: 12      TTG: 10    
Ile   : 75	  AAT: 26      GAT: 42                   TAT: 7     
Met   : 26	                            CAT: 26                 
Tyr   : 18	  ATA: 4       GTA: 14                              
Supres: 2	                            CTA: 1       TTA: 1     
Cys   : 76	  ACA: 6       GCA: 70                              
Trp   : 8	                            CCA: 8                  
SelCys: 5	                                         TCA: 5     


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.