tRNAscan-SE Analysis of the Clostridium perfringens 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 16:17:43 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:         2
Seqs w/at least 1 hit:  1
Bases read:             3085740 (x2 for both strands)
Bases in tRNAs:         12552
tRNAs predicted:        137
Av. tRNA length:        91
Script CPU time:        0.50 s
Scan CPU time:          1.72 s
Scan speed:             3588.1 Kbp/sec

First pass search(es) ended: Sun Jul 27 16:17:45 PDT 2008

Cove Stats:
-----------
Candidate tRNAs read:     137
Cove-confirmed tRNAs:     96
Bases scanned by covels:  14470
% seq scanned by covels:  0.2 %
Script CPU time:          0.39 s
Cove CPU time:            16.71 s
Scan speed:               865.9 bp/sec

Cove analysis of tRNAs ended: Sun Jul 27 16:18:04 PDT 2008

Summary
--------
Overall scan speed: 319434.8 bp/sec

tRNAs decoding Standard 20 AA:              95
Selenocysteine tRNAs (TCA):                 1
Possible suppressor tRNAs (CTA,TTA):        0
tRNAs with undetermined/unknown isotypes:   0
Predicted pseudogenes:                      0
                                            -------
Total tRNAs:                                96

tRNAs with introns:     	0

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Isotype / Anticodon Counts:

Ala   : 6	  AGC:         GGC:         CGC:         TGC: 6     
Gly   : 11	  ACC:         GCC: 4       CCC:         TCC: 7     
Pro   : 2	  AGG:         GGG:         CGG:         TGG: 2     
Thr   : 5	  AGT:         GGT: 1       CGT:         TGT: 4     
Val   : 4	  AAC:         GAC:         CAC:         TAC: 4     
Ser   : 6	  AGA:         GGA: 1       CGA:         TGA: 2       ACT:         GCT: 3     
Arg   : 6	  ACG: 1       GCG:         CCG:         TCG: 1       CCT: 1       TCT: 3     
Leu   : 9	  AAG:         GAG: 1       CAG:         TAG: 3       CAA: 1       TAA: 4     
Phe   : 4	  AAA:         GAA: 4                               
Asn   : 4	  ATT:         GTT: 4                               
Lys   : 9	                            CTT: 2       TTT: 7     
Asp   : 3	  ATC:         GTC: 3                               
Glu   : 3	                            CTC:         TTC: 3     
His   : 2	  ATG:         GTG: 2                               
Gln   : 2	                            CTG:         TTG: 2     
Ile   : 4	  AAT:         GAT: 4                    TAT:       
Met   : 8	                            CAT: 8                  
Tyr   : 3	  ATA:         GTA: 3                               
Supres: 0	                            CTA:         TTA:       
Cys   : 2	  ACA:         GCA: 2                               
Trp   : 2	                            CCA: 2                  
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.