tRNAscan-SE Analysis of the Bacillus thuringiensis konkukian 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 14:01:13 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:             5314794 (x2 for both strands)
Bases in tRNAs:         26270
tRNAs predicted:        261
Av. tRNA length:        100
Script CPU time:        0.94 s
Scan CPU time:          3.28 s
Scan speed:             3240.7 Kbp/sec

First pass search(es) ended: Sun Jul 27 14:01:18 PDT 2008

Cove Stats:
-----------
Candidate tRNAs read:     261
Cove-confirmed tRNAs:     105
Bases scanned by covels:  29924
% seq scanned by covels:  0.3 %
Script CPU time:          0.67 s
Cove CPU time:            31.58 s
Scan speed:               947.6 bp/sec

Cove analysis of tRNAs ended: Sun Jul 27 14:01:53 PDT 2008

Summary
--------
Overall scan speed: 291461.1 bp/sec

tRNAs decoding Standard 20 AA:              105
Selenocysteine tRNAs (TCA):                 0
Possible suppressor tRNAs (CTA,TTA):        0
tRNAs with undetermined/unknown isotypes:   0
Predicted pseudogenes:                      0
                                            -------
Total tRNAs:                                105

tRNAs with introns:     	0

|

Isotype / Anticodon Counts:

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