tRNAscan-SE Analysis of the Campylobacter jejuni RM1221 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 15:27:23 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:         1
Seqs w/at least 1 hit:  1
Bases read:             1777831 (x2 for both strands)
Bases in tRNAs:         7688
tRNAs predicted:        77
Av. tRNA length:        99
Script CPU time:        0.27 s
Scan CPU time:          1.03 s
Scan speed:             3452.1 Kbp/sec

First pass search(es) ended: Sun Jul 27 15:27:25 PDT 2008

Cove Stats:
-----------
Candidate tRNAs read:     77
Cove-confirmed tRNAs:     44
Bases scanned by covels:  8766
% seq scanned by covels:  0.2 %
Script CPU time:          0.19 s
Cove CPU time:            10.35 s
Scan speed:               847.0 bp/sec

Cove analysis of tRNAs ended: Sun Jul 27 15:27:36 PDT 2008

Summary
--------
Overall scan speed: 300309.3 bp/sec

tRNAs decoding Standard 20 AA:              43
Selenocysteine tRNAs (TCA):                 1
Possible suppressor tRNAs (CTA,TTA):        0
tRNAs with undetermined/unknown isotypes:   0
Predicted pseudogenes:                      0
                                            -------
Total tRNAs:                                44

tRNAs with introns:     	0

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Isotype / Anticodon Counts:

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