tRNAscan-SE Analysis of the Desulfotalea psychrophila LSv54 Genome

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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: Sun Jul 27 16:56:00 PDT 2008

------------------------------------------------------------
Search Mode:                 Bacterial
Searching with:              tRNAscan + EufindtRNA -> Cove
Covariance model:            TRNA2-bact.cm
tRNAscan parameters:         Strict
EufindtRNA parameters:       Relaxed (Int Cutoff= -36)

Reporting HMM/2' structure score breakdown
------------------------------------------------------------

First-pass (tRNAscan/EufindtRNA) Stats:
---------------
Sequences read:         3
Seqs w/at least 1 hit:  2
Bases read:             3659634 (x2 for both strands)
Bases in tRNAs:         20885
tRNAs predicted:        189
Av. tRNA length:        110
Script CPU time:        0.62 s
Scan CPU time:          2.50 s
Scan speed:             2927.7 Kbp/sec

First pass search(es) ended: Sun Jul 27 16:56:04 PDT 2008

Cove Stats:
-----------
Candidate tRNAs read:     189
Cove-confirmed tRNAs:     64
Bases scanned by covels:  23531
% seq scanned by covels:  0.3 %
Script CPU time:          0.51 s
Cove CPU time:            26.04 s
Scan speed:               903.6 bp/sec

Cove analysis of tRNAs ended: Sun Jul 27 16:56:32 PDT 2008

Summary
--------
Overall scan speed: 246689.2 bp/sec

tRNAs decoding Standard 20 AA:              63
Selenocysteine tRNAs (TCA):                 1
Possible suppressor tRNAs (CTA,TTA):        0
tRNAs with undetermined/unknown isotypes:   0
Predicted pseudogenes:                      0
                                            -------
Total tRNAs:                                64

tRNAs with introns:     	0

|

Isotype / Anticodon Counts:

Ala   : 3	  AGC:         GGC: 1       CGC:         TGC: 2     
Gly   : 3	  ACC:         GCC: 2       CCC:         TCC: 1     
Pro   : 2	  AGG:         GGG: 1       CGG:         TGG: 1     
Thr   : 4	  AGT:         GGT: 2       CGT: 1       TGT: 1     
Val   : 7	  AAC:         GAC: 1       CAC:         TAC: 6     
Ser   : 3	  AGA:         GGA: 1       CGA:         TGA: 1       ACT:         GCT: 1     
Arg   : 5	  ACG: 2       GCG:         CCG:         TCG: 1       CCT: 1       TCT: 1     
Leu   : 6	  AAG:         GAG: 2       CAG: 1       TAG: 1       CAA: 1       TAA: 1     
Phe   : 2	  AAA:         GAA: 2                               
Asn   : 1	  ATT:         GTT: 1                               
Lys   : 2	                            CTT:         TTT: 2     
Asp   : 6	  ATC:         GTC: 6                               
Glu   : 4	                            CTC: 2       TTC: 2     
His   : 2	  ATG:         GTG: 2                               
Gln   : 2	                            CTG:         TTG: 2     
Ile   : 2	  AAT:         GAT: 2                    TAT:       
Met   : 5	                            CAT: 5                  
Tyr   : 2	  ATA:         GTA: 2                               
Supres: 0	                            CTA:         TTA:       
Cys   : 1	  ACA:         GCA: 1                               
Trp   : 1	                            CCA: 1                  
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.