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tRNAscan-SE Analysis of Kluyveromyces lactis NRRL Y-1140

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

tRNAs Sorted by tRNA Isoacceptor Type plain text version [Ala] [Arg] [Asn] [Asp] [Cys] [Gln] [Glu] [Gly] [His] [Ile] [Leu] [Lys] [Met] [Phe] [Pro] [Ser] [Thr] [Trp] [Tyr] [Val] [Selenocysteine] [Possible pseudogene] [Undetermined] Sequence Name tRNA # tRNA Bounds tRNA Isotype Anticodon Upstream Region Downstream Region Intron Bounds Scores First-Pass Scanner Begin End Begin End Total (Cove) HMM 2' Str chrA 19 752414 752342 Ala AGC caagaattac ttttcttttt 0 0 68.13 47.33 20.80 Both chrB 5 588418 588490 Ala AGC catattaatt taattttttg 0 0 68.13 47.33 20.80 Both chrC 5 816018 816090 Ala AGC tgattaatac aaatttttat 0 0 68.13 47.33 20.80 Both chrD 24 953980 953908 Ala AGC taagaaatta atctttttat 0 0 68.13 47.33 20.80 Both chrE 10 1401022 1401094 Ala AGC aacgtattac ttttcttttt 0 0 68.13 47.33 20.80 Both chrE 20 342648 342576 Ala AGC aaaatacatt ttttcttttt 0 0 68.13 47.33 20.80 Both chrE 9 1330784 1330856 Ala AGC cagaaattac ttttcttttt 0 0 68.13 47.33 20.80 Both chrMT 19 5850 5778 Ala TGC ataatatgta ttatatataa 0 0 45.42 15.64 29.78 tRNAscan chrA 10 785915 785987 Ala TGC cagaaaattt tgactttttc 0 0 76.57 52.31 24.26 Both chrB 16 749078 749006 Ala TGC cgacttctgt taactttttc 0 0 76.57 52.31 24.26 Both chrF 12 1583941 1584013 Ala TGC aatcgtgtcg cttatttttt 0 0 76.57 52.31 24.26 Both   chrD 34 106366 106277 Arg ACG cgaaatctta attttgtttt 106329 106313 65.75 43.81 21.94 Both chrF 34 1064322 1064233 Arg ACG cgttttctta atttcgtatc 1064285 1064269 65.75 43.81 21.94 Both chrF 8 1297753 1297842 Arg ACG caagttctta aacttttttt 1297790 1297806 65.75 43.81 21.94 Both chrB 25 518415 518344 Arg CCG gctttttaca cctctgattt 0 0 55.51 36.42 19.09 Both chrA 7 719495 719566 Arg CCT acttaagacg aaattttttt 0 0 68.09 50.16 17.93 Both chrMT 12 7738 7666 Arg TCT ataattatta ttatattata 0 0 59.85 27.17 32.68 Both chrA 4 420025 420096 Arg TCT caaaaaaaaa cttttatttt 0 0 64.75 51.14 13.61 Both chrA 18 754419 754348 Arg TCT aattcattaa ctttattttt 0 0 69.00 50.75 18.25 Both chrB 20 605932 605861 Arg TCT aaattaatat ctttctttgg 0 0 69.00 50.75 18.25 Both chrC 7 1032177 1032248 Arg TCT atcattattg ttttcttttt 0 0 69.00 50.75 18.25 Both chrD 11 1212660 1212731 Arg TCT caattaatat ctttattttt 0 0 69.00 50.75 18.25 Both chrE 6 1035777 1035848 Arg TCT cataacagtt ctttattttt 0 0 69.00 50.75 18.25 Both chrF 28 2001628 2001557 Arg TCT gaattaaata ctttatttca 0 0 69.00 50.75 18.25 Both   chrMT 18 5942 5871 Asn GTT caaatatata taattattgt 0 0 62.34 38.27 24.07 Both chrB 19 636018 635945 Asn GTT cgaaaaacac tttatttttt 0 0 77.01 50.19 26.82 Both chrB 8 762452 762525 Asn GTT acaacaacat tttatttttt 0 0 77.01 50.19 26.82 Both chrD 2 228254 228327 Asn GTT ccagcaagta ttttttttgg 0 0 77.01 50.19 26.82 Both chrE 18 1062464 1062391 Asn GTT ccacaaatac tttaattttt 0 0 77.01 50.19 26.82 Both chrF 24 2283336 2283263 Asn GTT taacaagtta tttttttttt 0 0 77.01 50.19 26.82 Both chrF 35 1020230 1020157 Asn GTT ccagaaacgt ttttcttttt 0 0 77.01 50.19 26.82 Both   chrB 21 605839 605768 Asp GTC ttttaccaca aatttttatt 0 0 65.00 38.80 26.20 Both chrB 22 555075 555004 Asp GTC acagaaatcg aatttttatt 0 0 65.00 38.80 26.20 Both chrB 24 537399 537328 Asp GTC aaatatctat aagctttttt 0 0 65.00 38.80 26.20 Both chrD 13 1215538 1215609 Asp GTC aatttactat gaattttttt 0 0 65.00 38.80 26.20 Both chrD 7 403068 403139 Asp GTC ttacaaagcg gactagcttt 0 0 65.00 38.80 26.20 Both chrE 7 1062834 1062905 Asp GTC caagtacaga tatatttttt 0 0 65.00 38.80 26.20 Both chrF 29 2001543 2001472 Asp GTC tatttcaaaa atcttttttc 0 0 65.00 38.80 26.20 Both chrF 37 393978 393907 Asp GTC tagaaagttg tgatttttta 0 0 65.00 38.80 26.20 Both   chrMT 5 14762 14690 Cys GCA ataagttaga atatatatac 0 0 32.23 10.64 21.59 Eufind chrB 14 835831 835760 Cys GCA caagaaacca gttatttttt 0 0 75.04 50.16 24.88 Both chrB 17 643228 643157 Cys GCA tactagtttt gaaacttttt 0 0 75.04 50.16 24.88 Both chrD 8 561671 561742 Cys GCA ttgaaagtca attttctttt 0 0 75.04 50.16 24.88 Both   chrA 22 249975 249870 Gln CTG ataagttgac ttctttttgg 249938 249905 58.73 35.48 23.25 Both chrA 8 732629 732700 Gln TTG atgcaatctc accttttttt 0 0 69.31 44.87 24.44 Both chrD 20 1492013 1492084 Gln TTG tttattattt actttttttc 0 0 69.31 44.87 24.44 Both chrD 27 743333 743262 Gln TTG catgataact acttttttgt 0 0 69.31 44.87 24.44 Both chrD 9 745312 745383 Gln TTG catgatagct acttttttgt 0 0 69.31 44.87 24.44 Both chrC 14 1592204 1592133 Gln TTG taagaatttc ctttttttag 0 0 70.23 46.39 23.84 Both chrE 16 1993950 1993879 Gln TTG catgaatttc aattttttac 0 0 71.46 46.25 25.21 Both   chrB 23 548669 548598 Glu CTC cgttttatat gagaaagcga 0 0 69.05 40.62 28.43 Both chrF 1 544290 544361 Glu CTC aaattagtaa aaaaaattat 0 0 69.05 40.62 28.43 Both chrB 12 1029549 1029478 Glu TTC catccaaata ttttcttttt 0 0 62.99 35.57 27.42 Both chrB 18 636782 636711 Glu TTC ataacaagta tgtttttttt 0 0 62.99 35.57 27.42 Both chrB 9 915687 915758 Glu TTC atggttacta tatttttgaa 0 0 62.99 35.57 27.42 Both chrC 19 475788 475717 Glu TTC atcaatatca tattattttt 0 0 62.99 35.57 27.42 Both chrC 2 489024 489095 Glu TTC tcaattatta tatcttttta 0 0 62.99 35.57 27.42 Both chrE 14 2119065 2119136 Glu TTC tatccaagtg tgtttcattt 0 0 62.99 35.57 27.42 Both chrF 23 2360887 2360816 Glu TTC aaagttacta tgttcttttt 0 0 62.99 35.57 27.42 Both chrF 3 707161 707232 Glu TTC ataacaatta tatttttttc 0 0 62.99 35.57 27.42 Both   chrF 11 1538923 1538993 Gly CCC actatagaac ttttcttctt 0 0 64.77 43.90 20.87 Both chrA 15 944501 944431 Gly GCC taactactaa ttcttttttg 0 0 66.84 42.97 23.87 Both chrA 3 338524 338594 Gly GCC caacaaagta ttcttttttc 0 0 66.84 42.97 23.87 Both chrD 18 1325213 1325283 Gly GCC taactactaa ttctttttat 0 0 66.84 42.97 23.87 Both chrD 19 1329593 1329663 Gly GCC taactactaa ttcttttttg 0 0 66.84 42.97 23.87 Both chrE 17 1494645 1494575 Gly GCC caaccaacaa ttcttttttc 0 0 66.84 42.97 23.87 Both chrF 16 2142776 2142846 Gly GCC aaactactaa ttctttttat 0 0 66.84 42.97 23.87 Both chrF 33 1407887 1407817 Gly GCC caaatactag ttctttttca 0 0 66.84 42.97 23.87 Both chrA 1 26345 26444 Gly TCC acaggcattg attttttctt 26383 26409 68.85 43.25 25.60 Both chrD 4 310699 310809 Gly TCC aacaaaatag tattttttaa 310737 310774 67.15 41.19 25.96 Both   chrMT 15 7063 6993 His GTG ataattatag ctttgcccca 0 0 43.12 11.31 31.81 Both chrE 12 1809819 1809890 His GTG acaaaaataa ttattttttc 0 0 68.23 41.35 26.88 Both chrF 20 2470952 2470881 His GTG tgtatcctgc tctattattt 0 0 68.23 41.35 26.88 Both chrF 25 2118239 2118168 His GTG aaagtactat gttacaattg 0 0 68.23 41.35 26.88 Both chrF 30 1910167 1910096 His GTG aatgaattcg ttcttttttg 0 0 68.23 41.35 26.88 Both   chrA 2 337927 338000 Ile AAT catccaagtt tttttttgcc 0 0 72.37 45.46 26.91 Both chrB 13 943595 943522 Ile AAT tcaagaaatt ttcttttttt 0 0 72.37 45.46 26.91 Both chrB 6 611056 611129 Ile AAT acaagaagtt ttcttttttt 0 0 72.37 45.46 26.91 Both chrC 15 1481745 1481672 Ile AAT accacaaatt ttcttttttt 0 0 72.37 45.46 26.91 Both chrE 3 759480 759553 Ile AAT cataagatct ttctttttac 0 0 72.37 45.46 26.91 Both chrF 2 565690 565763 Ile AAT caacaaattt ttatttttat 0 0 72.37 45.46 26.91 Both chrF 4 1092866 1092939 Ile AAT ataagaaatt ttcttttttg 0 0 72.37 45.46 26.91 Both chrMT 20 5714 5642 Ile GAT ggggagcata tatatattta 0 0 44.85 12.13 32.72 Both chrA 21 385985 385847 Ile TAT catcattgaa tctatttttt 385947 385883 70.75 47.62 23.13 Both   chrF 5 1116489 1116604 Leu CAA atcaatatat ttatcttttt 1116527 1116560 55.30 30.08 25.22 Both chrF 9 1392272 1392387 Leu CAA atcgcactat ttaatttttt 1392310 1392343 54.52 29.30 25.22 Both chrF 32 1625279 1625164 Leu CAA caattaatat tttctttttt 1625241 1625208 54.66 29.44 25.22 Both chrF 14 1995860 1995975 Leu CAA tcacgaaatt tttctttttt 1995898 1995931 54.52 29.30 25.22 Both chrF 27 2117832 2117717 Leu CAA tcacgaaatt ttatttttaa 2117794 2117761 54.52 29.30 25.22 Both chrD 29 543943 543828 Leu CAA tcattcaaat ttattttttt 543905 543872 54.66 29.44 25.22 Both chrD 35 85556 85441 Leu CAA caaccaaact ttatttttta 85518 85485 54.66 29.44 25.22 Both chrD 16 1309318 1309399 Leu GAG aatgaatttt ttatattttt 0 0 67.48 43.02 24.46 Both chrMT 9 8237 8156 Leu TAA aggcatataa atatatatat 0 0 35.99 13.09 22.90 Both chrD 32 261911 261828 Leu TAA cataaagatt ttacttttta 0 0 70.04 39.16 30.88 Both chrD 3 263097 263180 Leu TAA gaaatatatt ttactttttg 0 0 70.31 38.16 32.15 Both chrD 31 263589 263506 Leu TAA tcagaaaact ttactttttg 0 0 70.31 38.16 32.15 Both chrD 5 335455 335585 Leu TAG caaaaattac ttatcttcta 335492 335541 57.89 33.09 24.80 Both chrD 6 366089 366219 Leu TAG aacaaattac ttattttttt 366126 366175 57.25 32.45 24.80 Both   chrA 13 970437 970509 Lys CTT caagaaaccg ttctttttca 0 0 77.59 52.05 25.54 Both chrA 17 841293 841221 Lys CTT caagaaatag ttctttttcc 0 0 77.59 52.05 25.54 Both chrA 5 621223 621295 Lys CTT aagaaattag ttcttttttc 0 0 77.59 52.05 25.54 Both chrA 6 625123 625195 Lys CTT aagaaattag ttcttttttt 0 0 77.59 52.05 25.54 Both chrE 4 856274 856346 Lys CTT gaaacaaaga ttgtttttta 0 0 77.59 52.05 25.54 Both chrB 1 373654 373726 Lys CTT caagaattag ttcttttttt 0 0 79.43 55.73 23.70 Both chrB 27 115211 115139 Lys CTT gcatcttaat ttattttttc 0 0 79.43 55.73 23.70 Both chrB 3 559891 559963 Lys CTT catcaattct ttctttttac 0 0 79.43 55.73 23.70 Both chrF 19 2570832 2570760 Lys CTT aatttacata ttccattttt 0 0 79.43 55.73 23.70 Both chrMT 11 7949 7878 Lys TTT ccctggagga tatattatat 0 0 35.87 15.59 20.28 Both chrE 1 120819 120908 Lys TTT tgagaactcg ttcttatttt 120856 120872 68.45 44.72 23.73 Both chrD 21 1311170 1311081 Lys TTT caagaactcg ttcttacatt 1311133 1311117 68.45 44.72 23.73 Both chrF 10 1515694 1515783 Lys TTT tgagaactcg ttcttatttt 1515731 1515747 68.45 44.72 23.73 Both chrC 1 301073 301162 Lys TTT aagagactcg tccctttatt 301110 301126 67.82 44.09 23.73 Both   Sequence Name tRNA # tRNA Bounds tRNA Isotype Anticodon Upstream Region Downstream Region Intron Bounds Scores First-Pass Scanner Begin End Begin End Total (Cove) HMM 2' Str chrMT 16 6840 6768 Met CAT atatataata ttaaaaatat 0 0 49.00 30.50 18.50 Both chrD 10 794667 794739 Met CAT caaaggaatt ttattttttt 0 0 73.94 56.20 17.74 Both chrE 21 146127 146055 Met CAT caagaaattt tttcaattta 0 0 73.94 56.20 17.74 Both chrF 17 2159002 2159074 Met CAT tcgtatactt ttatttttgt 0 0 73.94 56.20 17.74 Both chrD 14 1228695 1228766 Met CAT aagaatagtc gtaattcttt 0 0 74.04 46.25 27.79 Both chrA 14 977210 977281 Met CAT ttaatttgtt ttattacttt 0 0 74.96 47.76 27.20 Both chrF 22 2376832 2376761 Met CAT catctttgac ttttttgatt 0 0 74.96 47.76 27.20 Both   chrMT 8 8314 8243 Phe GAA aaatattata tataagctac 0 0 48.72 20.34 28.38 Eufind chrB 2 386048 386120 Phe GAA aacgaaagtt tttcgattta 0 0 76.93 47.08 29.85 Both chrC 11 1524116 1524188 Phe GAA aacagaaatc tttctttttt 0 0 76.93 47.08 29.85 Both chrE 2 597877 597949 Phe GAA tcaacaagtc tattttttct 0 0 76.93 47.08 29.85 Both chrE 5 950420 950492 Phe GAA aattaatttg aattggtttt 0 0 76.93 47.08 29.85 Both chrE 8 1248065 1248137 Phe GAA tcaagaagtc tttcttttta 0 0 76.93 47.08 29.85 Both   chrF 7 1176653 1176724 Pro AGG tgacctaaat ctgtgtgtta 0 0 71.39 55.24 16.15 Both chrD 22 1236995 1236874 Pro TGG aaattatata aattttgatt 1236959 1236910 60.36 38.56 21.80 Both chrD 1 154028 154149 Pro TGG aattttatat gaaattattt 154064 154113 60.36 38.56 21.80 Both chrF 15 2002117 2002238 Pro TGG aaaattgcga agattttttt 2002153 2002202 59.72 37.92 21.80 Both chrE 15 2021805 2021684 Pro TGG acaattatta gaattttttt 2021769 2021720 60.08 38.28 21.80 Both chrC 18 518069 517949 Pro TGG aaatatatta aattaatttt 518033 517985 58.81 37.02 21.79 Both chrD 28 697169 697048 Pro TGG tgaaacatta aattttcttt 697133 697084 59.72 37.92 21.80 Both chrF 36 875041 874920 Pro TGG tcataaatta aaattttttt 875005 874956 59.72 37.92 21.80 Both   chrMT 6 14616 14545 Pseudo CAT gtcaatttat attatataat 0 0 45.49 9.13 36.36 tRNAscan chrMT 17 6035 5951 Pseudo GTA tatttatata aatatatagt 0 0 27.94 -9.17 37.11 Eufind chrMT 14 7254 7183 Pseudo GTC attatataat taataggaaa 0 0 21.61 -4.40 26.01 tRNAscan chrMT 13 7647 7576 Pseudo TCC taaaaataat atatatataa 0 0 43.58 3.34 40.24 tRNAscan chrMT 7 14355 14284 Pseudo TGG tatataataa ataaattaaa 0 0 31.00 -4.33 35.33 Eufind chrMT 3 22439 22368 Pseudo TTC taatataaca tatattttat 0 0 37.68 9.40 28.28 Eufind chrMT 10 8140 8068 Pseudo TTG tatatatata tatatatccc 0 0 27.64 -10.85 38.49 tRNAscan   chrMT 4 15659 15589 SeC TCA cgcgggtaaa tttattattt 0 0 46.58 0.00 0.00 Both   chrA 23 214177 214096 Ser AGA tcaagaaaga ttattttttg 0 0 82.65 54.35 28.30 Both chrA 9 785743 785824 Ser AGA aagttatcta ttatcttttt 0 0 82.65 54.35 28.30 Both chrC 3 566067 566148 Ser AGA atcataagct ttatttttta 0 0 82.65 54.35 28.30 Both chrD 25 831132 831051 Ser AGA acagaaatta ttattttttt 0 0 82.65 54.35 28.30 Both chrD 26 830627 830546 Ser AGA acagaaattg tcattttttt 0 0 82.65 54.35 28.30 Both chrE 13 1980854 1980935 Ser AGA catataacat ttatttttaa 0 0 82.65 54.35 28.30 Both chrC 17 771217 771124 Ser CGA gttgttttac ttattttttt 771180 771169 75.55 52.74 22.81 Both chrC 12 1605044 1604950 Ser GCT ctgaactcat ccattttttt 1605007 1604995 70.94 38.44 32.50 Both chrD 30 397066 396972 Ser GCT acaacatctg ccaatttttt 397029 397017 66.20 36.96 29.24 Both chrMT 21 5628 5543 Ser TGA atatttaaat tatataatat 0 0 51.01 21.41 29.60 Both chrB 15 818983 818902 Ser TGA aagaaattta ttattttttt 0 0 84.16 62.98 21.18 Both chrC 4 709414 709495 Ser TGA gcaaaatttt ttattttttg 0 0 84.16 62.98 21.18 Both   chrB 7 747257 747329 Thr AGT acaacaataa tttttttgaa 0 0 71.56 46.22 25.34 Both chrC 8 1035240 1035312 Thr AGT acaagaaaca tttttttgga 0 0 71.56 46.22 25.34 Both chrD 23 1228189 1228117 Thr AGT gaaattaaca tattttcttt 0 0 71.56 46.22 25.34 Both chrD 33 118674 118602 Thr AGT cgaaataaca attttttaag 0 0 71.56 46.22 25.34 Both chrE 11 1570786 1570858 Thr AGT gaaattaaca ttttcttttt 0 0 71.56 46.22 25.34 Both chrF 31 1691389 1691317 Thr AGT gagaataaca ttattttctt 0 0 71.56 46.22 25.34 Both chrB 10 1246831 1246902 Thr CGT attgtttcca aagaaaacct 0 0 77.41 58.21 19.20 Both chrMT 2 22512 22440 Thr TGT gttaatagta gaccttatcg 0 0 67.25 38.98 28.27 Both chrA 11 810512 810583 Thr TGT ctgtaaagat tttatctttt 0 0 79.33 61.25 18.08 Both chrD 15 1247371 1247442 Thr TGT tagatttcgt ttcatctttt 0 0 79.33 61.25 18.08 Both   chrC 16 1031592 1031485 Trp CCA cttcagagat tttttaattt 1031556 1031521 66.27 45.43 20.84 Both chrD 12 1215339 1215447 Trp CCA tttcaagaat ttttttaaca 1215375 1215411 66.54 45.70 20.84 Both chrF 18 2459676 2459784 Trp CCA attcaagaat tttttttagt 2459712 2459748 66.54 45.70 20.84 Both chrE 19 438614 438507 Trp CCA ccttaagaat tttttgcatt 438578 438543 66.91 46.07 20.84 Both   chrD 17 1318811 1318909 Tyr GTA caagtaactc cttttttttt 1318850 1318873 70.95 40.62 30.33 Both chrC 9 1337615 1337713 Tyr GTA caagtaactt cttatctttt 1337654 1337677 70.95 40.62 30.33 Both chrB 4 584364 584462 Tyr GTA caattagtac cttctttttg 584403 584426 70.95 40.62 30.33 Both chrA 20 731842 731744 Tyr GTA cgcaagcttc cttatctttt 731803 731780 70.95 40.62 30.33 Both chrA 16 932543 932445 Tyr GTA caagtaactc cttatttttt 932504 932481 70.95 40.62 30.33 Both   chrB 11 1201071 1200998 Val AAC acaacaagtt tttgtttttc 0 0 68.42 45.91 22.51 Both chrC 10 1355909 1355982 Val AAC acaacaagtt tttgttttta 0 0 68.42 45.91 22.51 Both chrC 13 1592689 1592616 Val AAC tcaacaagtt tttgtttttt 0 0 68.42 45.91 22.51 Both chrF 13 1873730 1873803 Val AAC ccaataaggt tttgtttttt 0 0 68.42 45.91 22.51 Both chrF 21 2460899 2460826 Val AAC ctcacaagat tttttttcat 0 0 68.42 45.91 22.51 Both chrF 26 2118129 2118056 Val AAC acttttcaac aatgagaacg 0 0 68.42 45.91 22.51 Both chrF 6 1176163 1176236 Val AAC acagcaaagt ttttcttttt 0 0 68.42 45.91 22.51 Both chrC 6 823593 823665 Val CAC attaagatct tttttttgct 0 0 74.52 45.70 28.82 Both chrB 26 336424 336352 Val CAC gttaagagct tttcccctta 0 0 80.22 52.48 27.74 Both chrMT 1 35975 35904 Val TAC ataataataa tatatattaa 0 0 50.68 24.53 26.15 Both chrA 12 926295 926368 Val TAC agttgtcgca tgttcaactt 0 0 71.06 45.05 26.01 Both

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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.