tRNAscan-SE Analysis of the Clostridium tetani E88 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 16:21:59 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:  2
Bases read:             2873333 (x2 for both strands)
Bases in tRNAs:         7178
tRNAs predicted:        79
Av. tRNA length:        90
Script CPU time:        0.44 s
Scan CPU time:          1.58 s
Scan speed:             3637.1 Kbp/sec

First pass search(es) ended: Sun Jul 27 16:22:01 PDT 2008

Cove Stats:
-----------
Candidate tRNAs read:     79
Cove-confirmed tRNAs:     54
Bases scanned by covels:  8284
% seq scanned by covels:  0.1 %
Script CPU time:          0.20 s
Cove CPU time:            9.58 s
Scan speed:               864.7 bp/sec

Cove analysis of tRNAs ended: Sun Jul 27 16:22:12 PDT 2008

Summary
--------
Overall scan speed: 487005.6 bp/sec

tRNAs decoding Standard 20 AA:              54
Selenocysteine tRNAs (TCA):                 0
Possible suppressor tRNAs (CTA,TTA):        0
tRNAs with undetermined/unknown isotypes:   0
Predicted pseudogenes:                      0
                                            -------
Total tRNAs:                                54

tRNAs with introns:     	0

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Isotype / Anticodon Counts:

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