tRNAscan-SE Analysis of the Lactococcus lactis 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 18:54:01 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:             2365589 (x2 for both strands)
Bases in tRNAs:         13224
tRNAs predicted:        141
Av. tRNA length:        93
Script CPU time:        0.38 s
Scan CPU time:          1.52 s
Scan speed:             3112.6 Kbp/sec

First pass search(es) ended: Sun Jul 27 18:54:03 PDT 2008

Cove Stats:
-----------
Candidate tRNAs read:     141
Cove-confirmed tRNAs:     62
Bases scanned by covels:  15198
% seq scanned by covels:  0.3 %
Script CPU time:          0.37 s
Cove CPU time:            15.26 s
Scan speed:               995.9 bp/sec

Cove analysis of tRNAs ended: Sun Jul 27 18:54:20 PDT 2008

Summary
--------
Overall scan speed: 269890.4 bp/sec

tRNAs decoding Standard 20 AA:              61
Selenocysteine tRNAs (TCA):                 0
Possible suppressor tRNAs (CTA,TTA):        0
tRNAs with undetermined/unknown isotypes:   1
Predicted pseudogenes:                      0
                                            -------
Total tRNAs:                                62

tRNAs with introns:     	0

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Isotype / Anticodon Counts:

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