# fasta34 FASTA searches a protein or DNA sequence data bank version 3.4t25 Nov 12, 2004 Please cite: W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448 asparagine-tRNA1.2,, 76 nt vs base.fasta library 546 residues in 6 sequences Altschul/Gish params: n0: 76 Lambda: 0.192 K: 0.177 H: 0.360 FASTA (3.47 Mar 2004) function [optimized, +5/-4 matrix (5:-4)] ktup: 6 join: 45, opt: 30, open/ext: -12/-4, width: 16 The best scores are: opt bits E(6) trnS Bacillus subtilis. ( 75) [f] 170 50.4 2.7e-11 trnB Bacillus subtilis. ( 75) [f] 170 50.4 2.7e-11 trnD Bacillus subtilis. ( 75) [f] 152 45.4 8.6e-10 long fasta-finding Bacillus subtilis ( 181) [f] 151 45.0 1.2e-09 trnI Bacillus subtilis. ( 75) [f] 142 42.7 5.9e-09 short fasta-finding Bacillus subtilis ( 65) [f] 131 39.7 4.7e-08 long fasta-finding Bacillus subtilis ( 181) [r] 0 3.2 3 trnD Bacillus subtilis. ( 75) [r] 0 3.3 7.3 trnI Bacillus subtilis. ( 75) [r] 0 3.3 7.3 trnS Bacillus subtilis. ( 75) [r] 0 3.3 7.3 trnB Bacillus subtilis. ( 75) [r] 0 3.3 7.3 short fasta-finding Bacillus subtilis ( 65) [r] 0 3.4 8.4 >>trnS Bacillus subtilis. (75 nt) initn: 133 init1: 133 opt: 170 Z-score: 250.6 bits: 50.4 E(): 2.7e-11 banded Smith-Waterman score: 170; 71.053% identity (71.053% similar) in 76 nt overlap (1-76:1-75) 10 20 30 40 50 60 aspara TCCTCTGTAGTTCAGTCGGTAGAACGGCGGACTGTTAATCCGTATGTCACTGGTTCGAGT ::: : :::: ::::: :::::: : : ::::::: : : ::: : ::::::: : trnS TCCACAGTAGCTCAGT-GGTAGAGCTATCGGCTGTTAACCGATCGGTCGCAGGTTCGAAT 10 20 30 40 50 70 aspara CCAGTCAGAGGAGCCA :: : : : ::::::: trnS CCTGCCTGTGGAGCCA 60 70 >>trnB Bacillus subtilis. (75 nt) initn: 133 init1: 133 opt: 170 Z-score: 250.6 bits: 50.4 E(): 2.7e-11 banded Smith-Waterman score: 170; 71.053% identity (71.053% similar) in 76 nt overlap (1-76:1-75) 10 20 30 40 50 60 aspara TCCTCTGTAGTTCAGTCGGTAGAACGGCGGACTGTTAATCCGTATGTCACTGGTTCGAGT ::: : :::: ::::: :::::: : : ::::::: : : ::: : ::::::: : trnB TCCACAGTAGCTCAGT-GGTAGAGCTATCGGCTGTTAACCGATCGGTCGCAGGTTCGAAT 10 20 30 40 50 70 aspara CCAGTCAGAGGAGCCA :: : : : ::::::: trnB CCTGCCTGTGGAGCCA 60 70 >>trnD Bacillus subtilis. (75 nt) initn: 115 init1: 115 opt: 152 Z-score: 223.7 bits: 45.4 E(): 8.6e-10 banded Smith-Waterman score: 152; 68.421% identity (68.421% similar) in 76 nt overlap (1-76:1-75) 10 20 30 40 50 60 aspara TCCTCTGTAGTTCAGTCGGTAGAACGGCGGACTGTTAATCCGTATGTCACTGGTTCGAGT ::: : :::: ::::: :::::: : : ::::::: : : ::: ::::::: : trnD TCCGCAGTAGCTCAGT-GGTAGAGCTATCGGCTGTTAACCGATCGGTCGTAGGTTCGAAT 10 20 30 40 50 70 aspara CCAGTCAGAGGAGCCA :: : : ::::::: trnD CCTACCTGCGGAGCCA 60 70 >>long fasta-finding Bacillus subtilis (181 nt) initn: 65 init1: 65 opt: 151 Z-score: 214.4 bits: 45.0 E(): 1.2e-09 banded Smith-Waterman score: 151; 72.308% identity (72.308% similar) in 65 nt overlap (5-68:27-91) 10 20 30 aspara TCCTCTGTAGTTCAG-TCGGTAGAACGGCGGACTGTTA :::::: :::: : : :::: :: : ::: :: long TGTTCCTTGAATAAGTTAAGATGGGCCTGTAGCTCAGCTGGTTAGAGCGCACGCCTGATA 10 20 30 40 50 60 40 50 60 70 aspara ATCCGTATGTCACTGGTTCGAGTCCAGTCAGAGGAGCCA : : : ::: ::::::::::::: :::: long AGCGTGAGGTCGGTGGTTCGAGTCCACTCAGGCCCACCATCTTATATAACGGGGCCTTAG 70 80 90 100 110 120 long CTCAGCTGGGAGAGCGCCTGCTTTGCACGCAGGAGGTCAGCGGTTCGATCCCGCTAGGCT 130 140 150 160 170 180 >>trnI Bacillus subtilis. (75 nt) initn: 79 init1: 79 opt: 142 Z-score: 208.7 bits: 42.7 E(): 5.9e-09 banded Smith-Waterman score: 142; 67.568% identity (67.568% similar) in 74 nt overlap (1-74:1-73) 10 20 30 40 50 60 aspara TCCTCTGTAGTTCAGTCGGTAGAACGGCGGACTGTTAATCCGTATGTCACTGGTTCGAGT ::: : :::: ::::: :::::: : : ::::::: : : ::: ::::::: : trnI TCCGCAGTAGCTCAGT-GGTAGAGCTATCGGCTGTTAACCGATCGGTCGTAGGTTCGAAT 10 20 30 40 50 70 aspara CCAGTCAGAGGAGCCA :: : : ::::: trnI CCTACCTGCGGAGCAT 60 70 >>short fasta-finding Bacillus subtilis (65 nt) initn: 65 init1: 65 opt: 131 Z-score: 193.7 bits: 39.7 E(): 4.7e-08 banded Smith-Waterman score: 131; 70.492% identity (70.492% similar) in 61 nt overlap (9-68:1-61) 10 20 30 40 50 aspara TCCTCTGTAGTTCAG-TCGGTAGAACGGCGGACTGTTAATCCGTATGTCACTGGTTCGAG :: :::: : : :::: :: : ::: ::: : : ::: ::::::::: short AGCTCAGCTGGTTAGAGCGCACGCCTGATAAGCGTGAGGTCGGTGGTTCGAG 10 20 30 40 50 60 70 aspara TCCAGTCAGAGGAGCCA :::: :::: short TCCACTCAGGCCC 60 76 residues in 1 query sequences 546 residues in 6 library sequences Scomplib [34t25] start: Sun Oct 1 10:42:53 2006 done: Sun Oct 1 10:43:36 2006 Total Scan time: 0.000 Total Display time: 0.000 Function used was FASTA [version 3.4t25 Nov 12, 2004]