# fasta34 tRNA.fasta bs_genome.fasta 6 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 U00096, 76 nt vs bs_genome.fasta library opt E() < 20 0 0: 22 0 0: one = represents 1 library sequences 24 0 0: 26 0 0: 28 0 0: 30 0 0: 32 0 0: 34 0 1:* 36 4 1:*=== 38 1 2:=* 40 4 3:==*= 42 4 3:==*= 44 4 4:===* 46 3 4:===* 48 2 4:== * 50 3 3:==* 52 2 3:==* 54 3 3:==* 56 5 2:=*=== 58 1 2:=* 60 2 1:*= 62 1 1:* 64 0 1:* 66 0 1:* 68 1 1:* 70 0 0: 72 0 0: 74 0 0: 76 0 0: 78 0 0: 80 0 0: 82 0 0: 84 0 0: 86 0 0: 88 0 0: 90 0 0: 92 1 0:= 94 0 0: 96 0 0: 98 0 0: 100 0 0: 102 0 0: 104 0 0: 106 0 0: 108 0 0: 110 0 0: 112 0 0: 114 0 0: 116 0 0: 118 0 0: >120 1 0:= 474432 residues in 21 sequences MLE_cen statistics: Lambda= 0.1269; K=0.001276 (cen=2) Kolmogorov-Smirnov statistic: 0.0686 (N=15) at 44 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(21) Z99104 Z99104 Bacillus subtilis complete genom (213080) [f] 137 34.7 0.0013 Z99108 Z99108 Bacillus subtilis complete genom (197409) [f] 102 28.3 0.11 Z99123 Z99123 Bacillus subtilis complete genom (201139) [f] 79 24.1 2 Z99116 Z99116 Bacillus subtilis complete genom (204537) [r] 73 23.0 4.2 Z99104 Z99104 Bacillus subtilis complete genom (213080) [r] 70 22.4 5.9 Z99120 Z99120 Bacillus subtilis complete genom (201059) [r] 69 22.2 6.7 Z99115 Z99115 Bacillus subtilis complete genom (201375) [f] 69 22.2 6.7 Z99122 Z99122 Bacillus subtilis complete genom (200690) [r] 67 21.9 8.4 Z99111 Z99111 Bacillus subtilis complete genom (191980) [f] 67 21.9 8.4 Z99106 Z99106 Bacillus subtilis complete genom (195912) [r] 67 21.9 8.4 Z99114 Z99114 Bacillus subtilis complete genom (192961) [r] 67 21.9 8.4 Z99110 Z99110 Bacillus subtilis complete genom (201241) [r] 66 21.7 9.4 Z99105 Z99105 Bacillus subtilis complete genom (202768) [r] 65 21.5 10 Z99113 Z99113 Bacillus subtilis complete genom (207829) [f] 65 21.5 10 Z99110 Z99110 Bacillus subtilis complete genom (201241) [f] 64 21.3 12 Z99107 Z99107 Bacillus subtilis complete genom (202089) [r] 63 21.1 13 Z99117 Z99117 Bacillus subtilis complete genom (199173) [f] 62 21.0 14 Z99119 Z99119 Bacillus subtilis complete genom (199922) [r] 62 21.0 14 Z99114 Z99114 Bacillus subtilis complete genom (192961) [f] 62 21.0 14 Z99116 Z99116 Bacillus subtilis complete genom (204537) [f] 61 20.8 16 >>Z99104 Z99104 Bacillus subtilis complete genome (secti (213080 nt) initn: 125 init1: 125 opt: 137 Z-score: 126.4 bits: 34.7 E(): 0.0013 banded Smith-Waterman score: 137; 64.474% identity (64.474% similar) in 76 nt overlap (1-76:11550-11625) 10 20 30 U00096 GGGTCGTTAGCTCAGTTGGTAGAGCAGTTG ::: : ::::::::: ::: ::::: :: Z99104 AGTCCACTCAGGCCCACCATCTTATATAACGGGGCCTTAGCTCAGCTGGGAGAGCGCCTG 11520 11530 11540 11550 11560 11570 40 50 60 70 U00096 ACTTTTAATCAATTGGTCGCAGGTTCGAATCCTGCACGACCCACCA :: : :: :::: ::::::: :: : : :::::: Z99104 CTTTGCACGCAGGAGGTCAGCGGTTCGATCCCGCTAGGCTCCACCAACGTGTTCTTTGAA 11580 11590 11600 11610 11620 11630 Z99104 AACTAGATAACAGTAGACATCACATTCAATTAGTAACACAAGATATCACATAGTGATTCT 11640 11650 11660 11670 11680 11690 >>Z99108 Z99108 Bacillus subtilis complete genome (secti (197409 nt) initn: 40 init1: 40 opt: 102 Z-score: 91.8 bits: 28.3 E(): 0.11 banded Smith-Waterman score: 102; 70.833% identity (70.833% similar) in 48 nt overlap (2-49:3170-3216) 10 20 30 U00096 GGGTCGTTAGCTCAGTTGGTAGAGCAGTTGA :::::::: : :::: : :::: :: :: Z99108 GGCGTATGATGGACAGCTGCCGGCAGGGATGGTCGTTA-TTGAGTTCGGAGAGGAGCGGA 3140 3150 3160 3170 3180 3190 40 50 60 70 U00096 CTTTTAATCAATTGGTCGCAGGTTCGAATCCTGCACGACCCACCA : : :: : :::: ::: Z99108 CATATATTGGATTGATCGTCAATCCTTTGTACCGGCTTAAAGGGTATGGAAAACAGATAC 3200 3210 3220 3230 3240 3250 >>Z99123 Z99123 Bacillus subtilis complete genome (secti (201139 nt) initn: 50 init1: 50 opt: 79 Z-score: 69.0 bits: 24.1 E(): 2 banded Smith-Waterman score: 79; 62.500% identity (62.500% similar) in 56 nt overlap (10-65:18077-18129) 10 20 30 U00096 GGGTCGTTAGCTCAGTTGGTAGAGCAGTTGACTTTTAAT : ::: : ::: : ::: : :: :: Z99123 CGTCCTCTATTCCCAGCACAGAGAGACGGGGTTCAATCGGTTCCCCGGTT---TCTTCAT 18050 18060 18070 18080 18090 18100 40 50 60 70 U00096 CAATTGGTCGCAGGTTCGAATCCTGCACGACCCACCA :::: :::::::: : : :::: Z99123 CAATCATGTGCAGGTTCCATTTCTGCTGCCCGTCCCAGCGCGAGCCCATTGTCCCTTGGG 18110 18120 18130 18140 18150 18160 >>Z99116 Z99116 Bacillus subtilis complete genome (secti (204537 nt) rev-comp initn: 80 init1: 55 opt: 73 Z-score: 63.1 bits: 23.0 E(): 4.2 banded Smith-Waterman score: 73; 80.769% identity (80.769% similar) in 26 nt overlap (55-32:6506-6531) 70 60 50 40 30 U0009- TGGTGGGTCGTGCAGGATTCGAACCTGC--GACCAATTGATTAAAAGTCAA :: :::: : ::: ::::::::::: Z99116 TTCTTGATTGAGCGCATTGATATGAAAGTTAAGCTGCCGGCCCATTTGATTAAAAGCGGT 6480 6490 6500 6510 6520 6530 20 10 U0009- CTGCTCTACCAACTGAGCTAACGACCC Z99116 CGCCAGTTCACCGATTTCATCCTGAGTTAAAATCGGGATTTTTGTATCGAACTTGCCCTT 6540 6550 6560 6570 6580 6590 >>Z99104 Z99104 Bacillus subtilis complete genome (secti (213080 nt) rev-comp initn: 80 init1: 55 opt: 70 Z-score: 60.1 bits: 22.4 E(): 5.9 banded Smith-Waterman score: 70; 78.261% identity (78.261% similar) in 23 nt overlap (37-15:7953-7975) 60 50 40 30 20 10 U0009- GTGCAGGATTCGAACCTGCGACCAATTGATTAAAAGTCAACTGCTCTACCAACTGAGCTA :: :: ::::::::::: ::: Z99104 GCCAATGCGAATGTTATCTTAAACAATCTGTACAAACAAACTGCTCTACAAACATCTTTT 7930 7940 7950 7960 7970 7980 U0009- ACGACCC Z99104 GGCATCAACCTGCTTGCGCTTGTTGATGGCCAGCCGAAAGTTTTAACTCTTAAGCAATGC 7990 8000 8010 8020 8030 8040 >>Z99120 Z99120 Bacillus subtilis complete genome (secti (201059 nt) rev-comp initn: 110 init1: 60 opt: 69 Z-score: 59.2 bits: 22.2 E(): 6.7 banded Smith-Waterman score: 69; 77.778% identity (77.778% similar) in 27 nt overlap (49-24:21724-21750) 70 60 50 40 30 U0009- TGGTGGGTCGTGCAGGATTCGAACCTGCGACCAATTG-ATTAAAAGTCAACTGCTCT :: :::: :: : :::::::::::: Z99120 TCGGTTTGACAGCTTTGTCTTTATTGAAGACGGCCAAGTGTACACAAAGTCAACTGCAGC 21700 21710 21720 21730 21740 21750 20 10 U0009- ACCAACTGAGCTAACGACCC Z99120 CATTAAGGTTTTCAGGCATCTGCGAGGCCCATGGCGGCTCTTCGTCCTTTTTTTCGCAGT 21760 21770 21780 21790 21800 21810 >>Z99115 Z99115 Bacillus subtilis complete genome (secti (201375 nt) initn: 65 init1: 65 opt: 69 Z-score: 59.2 bits: 22.2 E(): 6.7 banded Smith-Waterman score: 69; 77.778% identity (77.778% similar) in 27 nt overlap (17-42:4560-4586) 10 20 30 40 U00096 GGGTCGTTAGCTCAGTTGGT-AGAGCAGTTGACTTTTAATCAATTG :::: :::::: ::: : ::::::: Z99115 TCATAATGTAATACTCAAAGCTTCTGAACATGGTAAGAGCATTTGGCGGATAATCAACAA 4530 4540 4550 4560 4570 4580 50 60 70 U00096 GTCGCAGGTTCGAATCCTGCACGACCCACCA Z99115 ACCAGAACAAAAACACAGCTGAAAAGGCCACTGCAATATAAATTAAAAAATTGATCAAAC 4590 4600 4610 4620 4630 4640 >>Z99122 Z99122 Bacillus subtilis complete genome (secti (200690 nt) rev-comp initn: 60 init1: 60 opt: 67 Z-score: 57.2 bits: 21.9 E(): 8.4 banded Smith-Waterman score: 67; 88.235% identity (88.235% similar) in 17 nt overlap (49-33:21810-21826) 70 60 50 40 30 U0009- TGGTGGGTCGTGCAGGATTCGAACCTGCGACCAATTGATTAAAAGTCAACTGCTCTA :: : :::::::::::: Z99122 GCTGATTGAACGAAACAAATACCTCACACACGCCTAATTGATTAAAAAGGGTTCCATACA 21780 21790 21800 21810 21820 21830 20 10 U0009- CCAACTGAGCTAACGACCC Z99122 TTGATGAATAGACAGCATCCATTTTCTATAATGAATCAGAAAATGTTCCTTTAAATACTC 21840 21850 21860 21870 21880 21890 >>Z99111 Z99111 Bacillus subtilis complete genome (secti (191980 nt) initn: 60 init1: 60 opt: 67 Z-score: 57.2 bits: 21.9 E(): 8.4 banded Smith-Waterman score: 67; 88.235% identity (88.235% similar) in 17 nt overlap (16-32:8051-8067) 10 20 30 40 U00096 GGGTCGTTAGCTCAGTTGGTAGAGCAGTTGACTTTTAATCAATTG ::: :::::::::::: Z99111 CTATGAATGAACAGCTTTTTAAGGACTTGTTTGACAGAGCAGTTGACGGAATCGTCCTGT 8030 8040 8050 8060 8070 8080 50 60 70 U00096 GTCGCAGGTTCGAATCCTGCACGACCCACCA Z99111 TTGATAAAGATGGCGGTTTTATTGATGCAAATTTGTCCTTTTGTAAAAGCTTTGAAATCA 8090 8100 8110 8120 8130 8140 >>Z99106 Z99106 Bacillus subtilis complete genome (secti (195912 nt) rev-comp initn: 50 init1: 50 opt: 67 Z-score: 57.2 bits: 21.9 E(): 8.4 banded Smith-Waterman score: 67; 73.077% identity (73.077% similar) in 26 nt overlap (73-48:9911-9936) 70 60 50 U0009- TGGTGGGTCGTGCAGGATTCGAACCTGCGACCA : : ::: :::::::::: :::: Z99106 AGCGCTGCAAGCTTATTCGCATCAGACACTTTGATCGGTGTGGATTCGAACGTGCGCTTT 9890 9900 9910 9920 9930 9940 40 30 20 10 U0009- ATTGATTAAAAGTCAACTGCTCTACCAACTGAGCTAACGACCC Z99106 TCACCGCTGTCCTGCTGTTTTTCCATTTGCTTTTGGCGGTCAACCTGAAGTGTCACGCTT 9950 9960 9970 9980 9990 10000 >>Z99114 Z99114 Bacillus subtilis complete genome (secti (192961 nt) rev-comp initn: 77 init1: 52 opt: 67 Z-score: 57.2 bits: 21.9 E(): 8.4 banded Smith-Waterman score: 67; 73.077% identity (73.077% similar) in 26 nt overlap (53-28:19019-19044) 70 60 50 40 30 U0009- TGGTGGGTCGTGCAGGATTCGAACCTGCGACCAATTGATTAAAAGTCAACTGC :: :: : :: ::::::::: : :: Z99114 TATTCCTTTCCATTAACTGTAATAATAATCCCCGCAAGGAAATGATTAAAATTGAAAGGA 18990 19000 19010 19020 19030 19040 20 10 U0009- TCTACCAACTGAGCTAACGACCC Z99114 AGCATATTGTGATGAAACGACTTTGTTTATGGTTCACCGTCTTTAGCTTGTTTTTGGTTC 19050 19060 19070 19080 19090 19100 >>Z99110 Z99110 Bacillus subtilis complete genome (secti (201241 nt) rev-comp initn: 50 init1: 50 opt: 66 Z-score: 56.2 bits: 21.7 E(): 9.4 banded Smith-Waterman score: 66; 58.333% identity (58.333% similar) in 72 nt overlap (73-4:13538-13603) 70 60 50 U0009- TGGTGGGTCGTGCA--GGATTCGAACCTGCGAC ::: : :::: : :: :::: :: : Z99110 GCGGGATGAGACAGAGGGTTGTCATTGCCATGGCGCTTGCAGCGAATCCGAAACTTCTGA 13510 13520 13530 13540 13550 13560 40 30 20 10 U0009- CAATTGATTAAAAGTCAACTGCTCTACCAACTGAGCTAACGACCC ::: : : :::::::::: ::: :::::: Z99110 TCGCCGATGAGCCGACAACTGCTCT------TGATGTAACGATTCAAGCGCAAATTTTGG 13570 13580 13590 13600 13610 13620 Z99110 AATTAATGAAGGATTTGCAAAAGAAAATTGACACGTCCATCATCTTTATCACACACGATC 13630 13640 13650 13660 13670 13680 >>Z99105 Z99105 Bacillus subtilis complete genome (secti (202768 nt) rev-comp initn: 50 init1: 50 opt: 65 Z-score: 55.2 bits: 21.5 E(): 10 banded Smith-Waterman score: 65; 67.568% identity (67.568% similar) in 37 nt overlap (70-34:13072-13105) 70 60 50 U0009- TGGTGGGTCGTGCAGGATTCGAACCTGCGACCAATT : : : : ::::: : ::: : ::::: Z99105 CTCAGTAAAATCGCGGAAGCCGGGTATAATGCCATTCCGGATTTCATCCT---ATCAATT 13050 13060 13070 13080 13090 40 30 20 10 U0009- GATTAAAAGTCAACTGCTCTACCAACTGAGCTAACGACCC ::::: : Z99105 GATTACAGCAATGGATCTCTGAGAGATGTGGGACAAAGCAAGAGCTATGGGACCGGAGAT 13100 13110 13120 13130 13140 13150 >>Z99113 Z99113 Bacillus subtilis complete genome (secti (207829 nt) initn: 90 init1: 65 opt: 65 Z-score: 55.2 bits: 21.5 E(): 10 banded Smith-Waterman score: 65; 100.000% identity (100.000% similar) in 13 nt overlap (4-16:17303-17315) 10 20 30 U00096 GGGTCGTTAGCTCAGTTGGTAGAGCAGTTGACT ::::::::::::: Z99113 ATTCCGCGTTCCATGCCACAGTCGGTTTTATCGTTAGCTCAGTCAATGCCGCTGGACAAG 17280 17290 17300 17310 17320 17330 40 50 60 70 U00096 TTTAATCAATTGGTCGCAGGTTCGAATCCTGCACGACCCACCA Z99113 CTCAGACGCTGTCTCTTCCATTTGCGTTACAGGAGGTTGATATTTTCAGCCCATGTCCAG 17340 17350 17360 17370 17380 17390 >>Z99110 Z99110 Bacillus subtilis complete genome (secti (201241 nt) initn: 64 init1: 64 opt: 64 Z-score: 54.2 bits: 21.3 E(): 12 banded Smith-Waterman score: 64; 68.966% identity (68.966% similar) in 29 nt overlap (33-61:15338-15366) 10 20 30 40 50 60 U00096 GTCGTTAGCTCAGTTGGTAGAGCAGTTGACTTTTAATCAATTGGTCGCAGGTTCGAATCC :::::: : :: : :: :: :::::: Z99110 TTGCGTCTCTCCGGTGCTTCGCATTCTCGGTTTTAAAAAGGTGCTTGCGGGAGCGAATCT 15310 15320 15330 15340 15350 15360 70 U00096 TGCACGACCCACCA Z99110 GCTGAGAGCGGTCTTTATTATACTGATGGCATACAGCGTCACTCATCACGGACAGGCATT 15370 15380 15390 15400 15410 15420 >>Z99107 Z99107 Bacillus subtilis complete genome (secti (202089 nt) rev-comp initn: 78 init1: 53 opt: 63 Z-score: 53.2 bits: 21.1 E(): 13 banded Smith-Waterman score: 63; 70.370% identity (70.370% similar) in 27 nt overlap (68-42:1096-1122) 70 60 50 40 U0009- TGGTGGGTCGTGCAGGATTCGAACCTGCGACCAATTGA :::::: : :::::: : ::::: Z99107 CAGCAATTCCAAACGAGATTGGCTGATGCCCGTGCATGCCTCGAACTTCACGCCAATCAC 1070 1080 1090 1100 1110 1120 30 20 10 U0009- TTAAAAGTCAACTGCTCTACCAACTGAGCTAACGACCC Z99107 CTTGTTCACGCCTTGCAGCTGATATAAAATCTCGGCTTCCTCTGAACAAAATGACGCCAA 1130 1140 1150 1160 1170 1180 >>Z99117 Z99117 Bacillus subtilis complete genome (secti (199173 nt) initn: 100 init1: 55 opt: 62 Z-score: 52.2 bits: 21.0 E(): 14 banded Smith-Waterman score: 62; 72.000% identity (72.000% similar) in 25 nt overlap (16-40:7075-7099) 10 20 30 40 U00096 GGGTCGTTAGCTCAGTTGGTAGAGCAGTTGACTTTTAATCAATTG :: ::::::::::: : : ::: Z99117 GTATTGCCTTTTCTGACCGCAGCGACCGGCTTTGTAGAGCAGTTATCACCTGATCCCGCA 7050 7060 7070 7080 7090 7100 50 60 70 U00096 GTCGCAGGTTCGAATCCTGCACGACCCACCA Z99117 CAAAAGATCGCGCATTTCAGCCTTTTATTTAATGTGGTGACAGCTCTTTTATTTCTTCCG 7110 7120 7130 7140 7150 7160 >>Z99119 Z99119 Bacillus subtilis complete genome (secti (199922 nt) rev-comp initn: 70 init1: 56 opt: 62 Z-score: 52.2 bits: 21.0 E(): 14 banded Smith-Waterman score: 62; 70.968% identity (70.968% similar) in 31 nt overlap (36-6:3856-3884) 60 50 40 30 20 10 U0009- TGCAGGATTCGAACCTGCGACCAATTGATTAAAAGTCAACTGCTCTACCAACTGAGCTAA :::::: ::::: : ::: : :: ::: Z99119 TTCCTGCAAACTGCAAAGTTTATGCCAAAAAAAAGTTAACTG--CGGCCAGCGCAGTTAA 3830 3840 3850 3860 3870 3880 U0009- CGACCC : Z99119 CCTTTTTTTAATAATTCATATTGTTCATTTGGTTTTGATTTTGGCCTTGGCTTTGGTTTT 3890 3900 3910 3920 3930 3940 >>Z99114 Z99114 Bacillus subtilis complete genome (secti (192961 nt) initn: 62 init1: 62 opt: 62 Z-score: 52.2 bits: 21.0 E(): 14 banded Smith-Waterman score: 62; 87.500% identity (87.500% similar) in 16 nt overlap (28-43:21525-21540) 10 20 30 40 50 U00096 GGGTCGTTAGCTCAGTTGGTAGAGCAGTTGACTTTTAATCAATTGGTCGCAGGTTCG :::::: : ::::::: Z99114 TAAACTTACTATGTAATTCTTTGTCATCGTTTGACTGTCAATCAATATTAGAAGTGAAAT 21500 21510 21520 21530 21540 21550 60 70 U00096 AATCCTGCACGACCCACCA Z99114 CAATCCAGCTAAAACACCTATAAACCAAGCATCGCCAACAGCATAAGAATCATCCAGCAT 21560 21570 21580 21590 21600 21610 >>Z99116 Z99116 Bacillus subtilis complete genome (secti (204537 nt) initn: 52 init1: 52 opt: 61 Z-score: 51.2 bits: 20.8 E(): 16 banded Smith-Waterman score: 61; 71.429% identity (71.429% similar) in 35 nt overlap (34-67:7638-7671) 10 20 30 40 50 60 U00096 TCGTTAGCTCAGTTGGTAGAGCAGTTGACTTTTAATCAATTGGTCGCAGGTTCGAA-TCC : :::::: :: :: : : ::: :: :: Z99116 CGACTTCTCTCGGGCTGAACGGCTTAACAATATAATCATCTGTTC-CCGCTTCAAACCCC 7610 7620 7630 7640 7650 7660 70 U00096 TGCACGACCCACCA ::::: Z99116 TGCACCCGGTTTGCTTCTTCTCCTTTTGCGGTCAGCATAATAATGGGTGTCGCTTTTTTT 7670 7680 7690 7700 7710 7720 76 residues in 1 query sequences 474432 residues in 21 library sequences Scomplib [34t25] start: Mon Oct 9 03:22:50 2006 done: Mon Oct 9 03:23:25 2006 Total Scan time: 0.050 Total Display time: 0.010 Function used was FASTA [version 3.4t25 Nov 12, 2004]