tRNAscan-SE Analysis of the Lactobacillus plantarum Genome

[Main Overview] [Secondary Structures] [Analysis Notes]
[tRNAs by Isotype] [tRNAs by Locus]       [Run Options/Stats]
[tRNA Alignments][FASTA Seqs] [Genome DB] [Genome Seq]
[BLAST] [Download] [Bugs/Requests] [Citation] [Legend]
[GtRNAdb Home] [tRNAscan-SE Server] [Lowe Lab] [Other Links]
tRNAscan-SE Run Options & Statistics 

tRNAscan-SE v.1.23 (April 2002) scan results (on host lowedev.cse.ucsc.edu)
Started: Sun Jul 27 18:56:20 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:         4
Seqs w/at least 1 hit:  2
Bases read:             3348625 (x2 for both strands)
Bases in tRNAs:         27107
tRNAs predicted:        241
Av. tRNA length:        112
Script CPU time:        0.59 s
Scan CPU time:          2.36 s
Scan speed:             2837.8 Kbp/sec

First pass search(es) ended: Sun Jul 27 18:56:23 PDT 2008

Cove Stats:
-----------
Candidate tRNAs read:     241
Cove-confirmed tRNAs:     72
Bases scanned by covels:  30480
% seq scanned by covels:  0.5 %
Script CPU time:          0.63 s
Cove CPU time:            33.52 s
Scan speed:               909.3 bp/sec

Cove analysis of tRNAs ended: Sun Jul 27 18:57:00 PDT 2008

Summary
--------
Overall scan speed: 180518.9 bp/sec

tRNAs decoding Standard 20 AA:              70
Selenocysteine tRNAs (TCA):                 0
Possible suppressor tRNAs (CTA,TTA):        0
tRNAs with undetermined/unknown isotypes:   2
Predicted pseudogenes:                      0
                                            -------
Total tRNAs:                                72

tRNAs with introns:     	0

|

Isotype / Anticodon Counts:

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