tRNAscan-SE Analysis of the Helicobacter pylori J99 Genome

[Main Overview] [Secondary Structures]	[Analysis Notes]
[tRNAs by Isotype] [tRNAs by Locus]	[Run Options/Stats]
[tRNA Alignments][FASTA Seqs]	[Genome DB] [Genome Seq]

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Predicted tRNA Secondary Structures

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chr.trna29 (258464-258389)	Length: 76 bp
Type: Ala	Anticodon: GGC at 34-36 (258431-258429)	Score: 83.42
Seq: GGGGTGTTAGCTCAGTTGGGAGAGCGCAACGCTGGCAGCGTTGAGGtCAGGGGTTCGAACCCCCTACACTCCACCA
Str: >>>>>>>..>>>>........<<<<.>>>>>.......<<<<<.....>>>>>.......<<<<<<<<<<<<....

chr.trna9 (1132494-1132569)	Length: 76 bp
Type: Ala	Anticodon: TGC at 34-36 (1132527-1132529)	Score: 92.67
Seq: GGGGAATTAGCTCAGCTGGGAGAGCACCTGCTTTGCACGCAGGAGGtCAGCGGTTCGATCCCGCTATTCTCCACCA
Str: >>>>>>>..>>>>........<<<<.>>>>>.......<<<<<.....>>>>>.......<<<<<<<<<<<<....

chr.trna3 (852570-852646)	Length: 77 bp
Type: Arg	Anticodon: CCT at 35-37 (852604-852606)	Score: 82.70
Seq: GTCCTTGTAGCTCAGCTGGAtAGAGCGTATGATTCCTAATCGTAAGGtCGTGGGTTCGAATCCCGCCAAGGACACCA
Str: >>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<.....>>>>>.......<<<<<<<<<<<<....

chr.trna2 (341122-341198)	Length: 77 bp
Type: Arg	Anticodon: GCG at 35-37 (341156-341158)	Score: 69.51
Seq: GTGCTCGTAGCTCAGCTGAAtAGAGCAACAGGTTGCGGTCCTGTAGGtCGGGGGTTTGAATCCCTCCGAGCACACCA
Str: >>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<.....>>>>>.......<<<<<<<<<<<<....

chr.trna22 (1076872-1076796)	Length: 77 bp
Type: Arg	Anticodon: TCG at 35-37 (1076838-1076836)	Score: 79.58
Seq: GCGTTCGTAGCTCAATTGGAtAGAGCACCAGACTTCGGATCTGGGGGtTAGGGGTTCGACTCCCTTCGGGCGTACCA
Str: >>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<.....>>>>>.......<<<<<<<<<<<<....

chr.trna23 (1076774-1076698)	Length: 77 bp
Type: Arg	Anticodon: TCT at 35-37 (1076740-1076738)	Score: 92.26
Seq: GCGCTTGTAGCTCAGCTGGAtAGAGCAACAGCCTTCTAAGCCGTAGGtCGCAGGTTCGAGTCCTGCCAAGCGCACCA
Str: >>>>>>>..>>>>.........<<<<.>>.>>.......<<.<<.....>>>>>.......<<<<<<<<<<<<....

chr.trna30 (235409-235335)	Length: 75 bp
Type: Asn	Anticodon: GTT at 33-35 (235377-235375)	Score: 73.96
Seq: TCCAGATTAGCTCAGCGGTAGAGTAGGCGGCTGTTAACCGCTTGGtCGTAGGTTCCAATCCTACATCTGGAACCA
Str: >>>>>>>..>>>>.......<<<<.>>>>>.......<<<<<.....>>>>>.......<<<<<<<<<<<<....

chr.trna35 (4290-4214)	Length: 77 bp
Type: Asp	Anticodon: GTC at 35-37 (4256-4254)	Score: 91.95
Seq: GGAGCGGTAGTTCAGCTGGTtAGAATATCTGCCTGTCACGCAGGGGGtCGCGGGTTCGAGTCCCGTCCGCTCCGCCA
Str: >>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<.....>>>>>.......<<<<<<<<<<<<....

chr.trna6 (974816-974890)	Length: 75 bp
Type: Cys	Anticodon: GCA at 33-35 (974848-974850)	Score: 69.98
Seq: GGCGACATAGCCAAGTGGTAAGGCATGAGTCTGCAAAACTTTGATcCCCCGGTTCGAATCCGGGTGTCGCCTCCA
Str: >>>>>>>..>>>.........<<<..>>>>.......<<<<......>>>>>.......<<<<<<<<<<<<....

chr.trna24 (915582-915508)	Length: 75 bp
Type: Gln	Anticodon: TTG at 33-35 (915550-915548)	Score: 72.57
Seq: TGGGGTGTCGCCAAGCGGTAAGGCACCAGGTTTTGGTCCTGGCATtCCGAGGTTCGAATCCTTGCACCCCAGCCA
Str: >>>>>>>..>>>.........<<<.>>>>>.......<<<<<.....>>>>>.......<<<<<<<<<<<<....

chr.trna36 (4154-4079)	Length: 76 bp
Type: Glu	Anticodon: TTC at 35-37 (4120-4118)	Score: 52.89
Seq: GACCCTTTCATCTAGTGGCcaAGGATACCACCCTTTCACGGTGGAAACGGAAGTTCAAATCTTTCAAGGGTCGCCA
Str: >>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<....>>>>>.......<<<<<<<<<<<<....

chr.trna33 (4528-4454)	Length: 75 bp
Type: Glu	Anticodon: TTC at 34-36 (4495-4493)	Score: 63.09
Seq: GGCTCCTTCATCTAGTGGTtAGGATACCACCCTTTCACGGTGGTTACAGGGGTTCAAATCCCCTAGGAGTCACCA
Str: >>>>>>>..>>>>........<<<<.>>>>>.......<<<<<....>>>>>.......<<<<<<<<<<<<....

chr.trna4 (974561-974636)	Length: 76 bp
Type: Gly	Anticodon: GCC at 34-36 (974594-974596)	Score: 75.95
Seq: GCGGGAATAGCTCAGTGGTaGAAGCACGACCTTGCCAAGGTCGGGGcCGCGGGTTCGATCCCCGTTTCCCGCTCCA
Str: >>>>>>>..>>>..........<<<.>>>>>.......<<<<<.....>>>>>.......<<<<<<<<<<<<....

chr.trna15 (1260531-1260455)	Length: 77 bp
Type: Gly	Anticodon: TCC at 35-37 (1260497-1260495)	Score: 99.75
Seq: GCGGGAATAGCTCAGTTGGCtAGAGCATCAGCCTTCCAAGCTGAGGGtCGCGGGTTCGAGTCCCGTTTCCCGCTCCA
Str: >>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<.....>>>>>.......<<<<<<<<<<<<....

chr.trna21 (1077008-1076932)	Length: 77 bp
Type: His	Anticodon: GTG at 35-37 (1076974-1076972)	Score: 77.54
Seq: GTGGGAGTAGCTCAGTCGGTtAGAGCATCAGATTGTGGTCCTGAGGGtCGTGGGTTCGATTCCCATCTTCCACCCCA
Str: >>>>>>>..>>>>.........<<<<.>>>>.........<<<<.....>>>>>.......<<<<<<<<<<<<....

chr.trna8 (1132400-1132476)	Length: 77 bp
Type: Ile	Anticodon: GAT at 35-37 (1132434-1132436)	Score: 90.80
Seq: GGGCTTATAGCTCAGGTGGTtAGAGCGCACCCCTGATAAGGGTGAGGtCGGAGGTTCAACTCCTCCTAAGCCCACCA
Str: >>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<.....>>>>>.......<<<<<<<<<<<<....

chr.trna12 (1266155-1266069)	Length: 87 bp
Type: Leu	Anticodon: CAA at 35-37 (1266121-1266119)	Score: 76.32
Seq: GCCGAAGTGGTGGAATTGGTaGACACGCTAGACTCAAAATCTGGTGGGAGCAATCCCGTGTCGGTTCGAGTCCGACCTTCGGCACCA
Str: >>>>>>>..>>>...........<<<.>>>>>.......<<<<<.>>>>....<<<<..>>>>>.......<<<<<<<<<<<<....

chr.trna11 (1266295-1266209)	Length: 87 bp
Type: Leu	Anticodon: GAG at 35-37 (1266261-1266259)	Score: 57.27
Seq: GCACTGGTGGTGGAATTGGTaGACACGCCATCTTGAGGGGGTGGTGGGAGCAATCTCGTGCGAGTTCGAGTCTCGCCCAGTGCACCA
Str: >>>>>>>..>>>...........<<<.>>>>>.......<<<<<.>>>>....<<<<..>>>>>.......<<<<<<<<<<<<....

chr.trna5 (974676-974762)	Length: 87 bp
Type: Leu	Anticodon: TAA at 35-37 (974710-974712)	Score: 69.17
Seq: GCCCAGGTGGTGGAATTGGTaGACACAAGGGACTTAAAATCCCTCGGTAGCAATACCGTGCCGGTTCAAGTCCGGCTTTGGGCACCA
Str: >>>>>>>..>>>...........<<<.>>>>>.......<<<<<.>>>>....<<<<..>>>>>.......<<<<<<<<<<<<....

chr.trna19 (1127608-1127524)	Length: 85 bp
Type: Leu	Anticodon: TAG at 35-37 (1127574-1127572)	Score: 79.22
Seq: GCGGAAGTGGCGAAATTGGTaGACGCACTAGACTTAGGATCTAGCGCCGCAAGGCATGAAGGTTCGATTCCTTTCTTCCGCACCA
Str: >>>>>>>..>>>...........<<<.>>>>>.......<<<<<.>>>....<<<..>>>>>.......<<<<<<<<<<<<....

chr.trna32 (4616-4541)	Length: 76 bp
Type: Lys	Anticodon: TTT at 34-36 (4583-4581)	Score: 87.72
Seq: GACCCGTTAGCTCAGCTGGTAGAGCAATTCCCTTTTAAGGAATGGGcCGTTGGTTCAAATCCAACACGGGTCACCA
Str: >>>>>>>..>>>>........<<<<.>>>>>.......<<<<<.....>>>>>.......<<<<<<<<<<<<....

chr.trna18 (1230308-1230231)	Length: 78 bp
Type: Met	Anticodon: CAT at 36-38 (1230273-1230271)	Score: 82.06
Seq: GTCAAGGTAGCTCAGCTGGTttAGAGCGCTGGTCTCATAAGCCGGAGGtCGGGGGTTCAAGTCCCCCTCTTGACACCA
Str: >>>>>>>..>>>>..........<<<<.>>>>>.......<<<<<.....>>>>>.......<<<<<<<<<<<<....

chr.trna25 (915475-915399)	Length: 77 bp
Type: Met	Anticodon: CAT at 35-37 (915441-915439)	Score: 84.27
Seq: CGCGGAGTAGAGCAGTCcGGTAGCTCGTTGGGCTCATAACCCAAAGGtCAGTGGTTCAAATCCATTCTCCGCAACCA
Str: .>>>>>>..>>>>.........<<<<.>>>>>.......<<<<<.....>>>>>.......<<<<<<<<<<<.....

chr.trna26 (760112-760036)	Length: 77 bp
Type: Met	Anticodon: CAT at 35-37 (760078-760076)	Score: 85.21
Seq: GGATTCTTAGCTCAGCTGGTcAGAGCGCTCGGCTCATAACCGATTGGtCGTAGGTTCAAGTCCTACAGAATCCACCA
Str: >>>>>>>..>>>>.........<<<<..>>>>.......<<<<......>>>>>.......<<<<<<<<<<<<....

chr.trna10 (1556051-1556126)	Length: 76 bp
Type: Phe	Anticodon: GAA at 34-36 (1556084-1556086)	Score: 84.96
Seq: GGCTTGATAGCTCAGTCGGTAGAGCAGAAGACTGAAAATCTTCGTGtCGGTGGTTCGATTCCGCCTCAAGCCACCA
Str: >>>>>>>..>>>>........<<<<.>>>>>.......<<<<<.....>>>>>.......<<<<<<<<<<<<....

chr.trna27 (442411-442334)	Length: 78 bp
Type: Pro	Anticodon: GGG at 36-38 (442376-442374)	Score: 66.35
Seq: CGGAGTATGGCGCAGCCtGATtAGCGCGCACCCTTGGGGTGGGTGAGGtCGTGGGTTTGAATCCCGCTACTCCGACCA
Str: >>>>>>>..>>>>..........<<<<.>>>>>.......<<<<<.....>>>>>.......<<<<<<<<<<<<....

chr.trna20 (1077152-1077075)	Length: 78 bp
Type: Pro	Anticodon: TGG at 36-38 (1077117-1077115)	Score: 92.94
Seq: CGGGGCGTAGCGCAGTCtGGTtAGCGCACTTGGTTTGGGACCAAGGGGtCGAAGGTTCGAATCCTTTCGCCCCGACCA
Str: >>>>>>>..>>>>..........<<<<.>>>>>.......<<<<<.....>>>>>.......<<<<<<<<<<<<....

chr.trna1 (93161-93252)	Length: 92 bp
Type: Ser	Anticodon: GCT at 36-38 (93196-93198)	Score: 69.60
Seq: GGACAGGTGGGTGAGTTGGCtgAAACCACATCCCTGCTAAGGATGCGTAGCCGTCAAGGTTAcCGAGGGTTCGAATCCCTCCCTGTCCGCCA
Str: >>>>>>>..>>>............<<<.>>>>>.......<<<<<...>.>......<.<....>>>>>.......<<<<<<<<<<<<....

chr.trna28 (391097-391010)	Length: 88 bp
Type: Ser	Anticodon: GGA at 35-37 (391063-391061)	Score: 70.08
Seq: GGGGAGATGTCCGAGTGGTtgAAGGAGCACGCCTGGAACGCGTGTAAGGTGCAAGCCTTCGAGGGTTCGAATCCCTCTCTCTCCGCCA
Str: >>>>>>>..>>>...........<<<.>>>>>.......<<<<<..>>>>....<<<<..>>>>>.......<<<<<<<<<<<<....

chr.trna7 (974940-975027)	Length: 88 bp
Type: Ser	Anticodon: TGA at 35-37 (974974-974976)	Score: 71.62
Seq: CGGGAGATGGCTGAGTGGTtgAAAGCGGCGGTCTTGAAAACCGTTGAGGGTCATACCTCCGGGGGTTCGAATCCCTCTCTCCCGGCCA
Str: >>>>>>>..>>>...........<<<.>>>>>.......<<<<<..>>>......<<<..>>>>>.......<<<<<<<<<<<<....

chr.trna16 (1260424-1260350)	Length: 75 bp
Type: Thr	Anticodon: GGT at 33-35 (1260392-1260390)	Score: 85.16
Seq: GCCTATATAGCTCAGAGGCAGAGCACTTCCTTGGTAAGGAAGAGGtCGGCGGTTCAATTCCGCTTATAGGCTCCA
Str: >>>>>>>..>>>>.......<<<<.>>>>>.......<<<<<.....>>>>>.......<<<<<<<<<<<<....

chr.trna13 (1260735-1260660)	Length: 76 bp
Type: Thr	Anticodon: TGT at 34-36 (1260702-1260700)	Score: 96.71
Seq: GCTGGCTTAGCTCAGTTGGTAGAGCAGCTGCCTTGTAAGCAGCAGGtCGGGGGTTCAAGTCCCTTAGCCAGCTCCA
Str: >>>>>>>..>>>>........<<<<.>>>>>.......<<<<<.....>>>>>.......<<<<<<<<<<<<....

chr.trna17 (1258778-1258703)	Length: 76 bp
Type: Trp	Anticodon: CCA at 34-36 (1258745-1258743)	Score: 70.15
Seq: AGGTCAGTAGCTCCAATGGTAGAGCGTCGGTCTCCAAAACCGGTTGtTGGGGGTTCGAGTCCCTCCTGGCCTGCCA
Str: >>>>>>>..>>>>........<<<<.>>>>>.......<<<<<.....>>>>>.......<<<<<<<<<<<<....

chr.trna14 (1260632-1260548)	Length: 85 bp
Type: Tyr	Anticodon: GTA at 35-37 (1260598-1260596)	Score: 59.67
Seq: GGTGAGATACTCAAGTGGCcaACGAGGGCAGACTGTAAATCTGCTGACTATGTCTtCCGTGGTTCGAATCCACGTCTCACCACCA
Str: >>>>>>>..>>>...........<<<.>>>>>.......<<<<<....>><<.....>>>>>.......<<<<<<<<<<<<....

chr.trna31 (75803-75728)	Length: 76 bp
Type: Val	Anticodon: GAC at 34-36 (75770-75768)	Score: 82.34
Seq: GGTCGCGTAGCTCAGTTGGTAGAGCACTACCTTGACATGGTAGTGGcCGCTGGTTCAAGTCCAGTCGTGGCCACCA
Str: >>>>>>>..>>>>........<<<<.>>>>>.......<<<<<.....>>>>>.......<<<<<<<<<<<<....

chr.trna34 (4416-4341)	Length: 76 bp
Type: Val	Anticodon: TAC at 34-36 (4383-4381)	Score: 92.56
Seq: GGTCGCTTAGCTCAGTTGGTAGAGCGCTACCCTTACAAGGTAGATGtCATAAGTTCGAGTCTTATAGCGACCACCA
Str: >>>>>>>..>>>>........<<<<.>>>>>.......<<<<<.....>>>>>.......<<<<<<<<<<<<....

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.