tRNAscan-SE v.1.23 (April 2002) - scan sequences for transfer RNAs Please cite: Lowe, T.M. & Eddy, S.R. (1997) "tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence" Nucl. Acids Res. 25: 955-964. This program uses a modified, optimized version of tRNAscan v1.3 (Fichant & Burks, J. Mol. Biol. 1991, 220: 659-671), a new implementation of a multistep weight matrix algorithm for identification of eukaryotic tRNA promoter regions (Pavesi et al., Nucl. Acids Res. 1994, 22: 1247-1256), as well as the RNA covariance analysis package Cove v.2.4.2 (Eddy & Durbin, Nucl. Acids Res. 1994, 22: 2079-2088). ------------------------------------------------------------ Sequence file(s) to search: /seq/genomes/Student_Projects/2009/L.mexicana/genome.fa Search Mode: Eukaryotic Results written to: Standard output Output format: Tabular Searching with: tRNAscan + EufindtRNA -> Cove Covariance model: TRNA2-euk.cm tRNAscan parameters: Strict EufindtRNA parameters: Relaxed (Int Cutoff= -32.1) ------------------------------------------------------------ Sequence tRNA Bounds tRNA Anti Intron Bounds Cove Name tRNA # Begin End Type Codon Begin End Score -------- ------ ---- ------ ---- ----- ----- ---- ------ mex336o11.p1k 1 10970 11041 Gln CTG 0 0 70.34 mex225n05.q1k 1 31466 31394 Lys CTT 0 0 84.21 mex285a04.p1k 1 966 1037 Asp GTC 0 0 78.09 mex285a04.p1k 2 1149 1078 Glu CTC 0 0 69.92 mex153i14.q1k 1 5933 6004 Thr CGT 0 0 73.34 mex117h11.q1k 1 26341 26412 Arg ACG 0 0 70.89 mex163g10.p1k 1 58220 58291 Gln CTG 0 0 70.34 mex233m05.p1k 1 7821 7893 Arg TCT 0 0 77.82 mex233m05.p1k 2 7953 8025 Arg CCT 0 0 78.04 mex110e14.q1k 1 117308 117379 Arg ACG 0 0 70.89 1036_mexFOS1_21p19.q1kpIBR 1 66312 66392 Ser AGA 0 0 72.93 1036_mexFOS1_21p19.q1kpIBR 2 66507 66435 Phe GAA 0 0 86.47 1036_mexFOS1_15p03.q1kpIBR 1 43499 43427 Lys CTT 0 0 84.21 mex334o09.q1k 1 13763 13834 Gln CTG 0 0 70.34 mex334o09.q1k 2 14237 14310 Ile AAT 0 0 80.15 mex334o09.q1k 3 15358 15431 Ile AAT 0 0 80.15 mex334o09.q1k 4 14155 14074 Leu TAA 0 0 56.87 mex223f18.p1k 1 14540 14611 Glu CTC 0 0 69.92 mex223f18.p1k 2 14731 14661 Gly GCC 0 0 75.20 mex115a10.p1k 1 25187 25258 Pro AGG 0 0 71.70 mex115a10.p1k 2 25406 25479 Val AAC 0 0 68.41 mex115a10.p1k 3 25545 25617 Lys CTT 0 0 84.21 mex180i09.q1k 1 1958 2030 Met CAT 0 0 73.12 mex180i09.q1k 2 199848 199919 Ala CGC 0 0 70.10 mex180i09.q1k 3 199980 200050 Gly CCC 0 0 74.97 mex180i09.q1k 4 205163 205244 Leu AAG 0 0 66.27 mex180i09.q1k 5 205089 205018 Ala CGC 0 0 70.10 mex180i09.q1k 6 199774 199693 Leu AAG 0 0 66.27 mex180i09.q1k 7 1882 1811 Arg ACG 0 0 70.89 mex380g23.q1k 1 45111 45040 Thr CGT 0 0 73.34 mex380g23.q1k 2 44973 44890 Tyr GTA 44936 44926 69.74 mex380g23.q1k 3 44830 44758 Asn GTT 0 0 79.10 mex414p22.p1k 1 16812 16883 Thr AGT 0 0 71.69 mex414p22.p1k 2 16975 17058 Tyr GTA 17012 17022 69.74 mex414p22.p1k 3 16032 15961 Thr AGT 0 0 71.69 mex414p22.p1k 4 15869 15786 Tyr GTA 15832 15822 69.74 mex336m23.q1k 1 3024 3095 Asp GTC 0 0 78.09 mex336m23.q1k 2 2947 2867 Ser GCT 0 0 75.67 mex336m23.q1k 3 2806 2734 Ala AGC 0 0 60.04 1036_mexFOS1_20m22.q1kpIBR 1 17588 17659 Gly TCC 0 0 69.57 1036_mexFOS1_20m22.q1kpIBR 2 18233 18304 Thr TGT 0 0 74.23 1036_mexFOS1_20m22.q1kpIBR 3 18364 18446 Leu CAG 0 0 72.97 1036_mexFOS1_20m22.q1kpIBR 4 18666 18737 Arg ACG 0 0 70.89 1036_mexFOS1_20m22.q1kpIBR 5 18981 19052 Gln TTG 0 0 81.95 1036_mexFOS1_20m22.q1kpIBR 6 19120 19192 Val TAC 0 0 72.15 1036_mexFOS1_20m22.q1kpIBR 7 19318 19245 Ile TAT 0 0 81.51 1036_mexFOS1_20m22.q1kpIBR 8 18160 18089 Arg TCG 0 0 73.56 1036_mexFOS1_20m22.q1kpIBR 9 17772 17700 Lys TTT 0 0 76.96 1036_mexFOS1_20m22.q1kpIBR 10 17512 17441 Trp CCA 0 0 70.81 mex424o21.q1k 1 16340 16410 Gly GCC 0 0 75.20 mex424o21.q1k 2 16986 17057 Pro AGG 0 0 75.62 mex424o21.q1k 3 16912 16842 Gly GCC 0 0 75.20 mex424o21.q1k 4 16778 16707 Thr AGT 0 0 71.69 mex235e08.p1k 1 14609 14681 Ala AGC 0 0 60.04 mex552k21.q1k 1 41504 41575 Pro CGG 0 0 74.35 mex106a04.p1k 1 70954 70883 Met CAT 0 0 75.16 mex106a04.p1k 2 70821 70739 Leu CAG 0 0 72.97 mex484k20.q1k 1 21719 21791 Val CAC 0 0 70.56 mex484k20.q1k 2 22028 22099 Glu TTC 0 0 65.42 mex484k20.q1k 3 32091 32163 Phe GAA 0 0 86.47 mex484k20.q1k 4 32742 32670 Val CAC 0 0 70.56 mex484k20.q1k 5 32425 32355 His GTG 0 0 59.58 mex484k20.q1k 6 21644 21573 Arg CCG 0 0 65.42 mex484k20.q1k 7 21508 21438 His GTG 0 0 59.58 1036_mexFOS1_31j04.p1kpIBF 1 84717 84788 Cys GCA 0 0 75.22 1036_mexFOS1_31j04.p1kpIBF 2 85841 85912 Pro TGG 0 0 71.29 1036_mexFOS1_31j04.p1kpIBF 3 85768 85697 Met CAT 0 0 75.16 1036_mexFOS1_31j04.p1kpIBF 4 85633 85552 Leu AAG 0 0 66.27 mex560e20.q1k 1 2957 3037 Ser CGA 0 0 72.54 mex560e20.q1k 2 3093 3174 Leu CAA 0 0 73.13 mex287b04.p1k 1 89820 89892 Lys CTT 0 0 84.21 mex287b04.p1k 2 90129 90057 Asn GTT 0 0 79.10 mex287b04.p1k 3 90000 89930 Gly GCC 0 0 75.20 mex413k18.q1k 1 5726 5805 Leu TAG 0 0 73.76 mex413k18.q1k 2 6278 6351 Val AAC 0 0 68.41 mex413k18.q1k 3 6045 5972 Ile AAT 0 0 80.15 mex413k18.q1k 4 5911 5839 Met CAT 0 0 73.12 mex413k18.q1k 5 5651 5571 Ser TGA 0 0 72.53 mex301n16.q1k 1 62307 62227 Ser GCT 0 0 77.56 mex516e01.p1k 1 5266 5195 Asp GTC 0 0 78.09