Building a new DB, current time: 10/08/2018 15:33:31 New DB name: /export/sites/biostar-engine/export/media/jobs/job-ef88abad/xdb/ebola New DB title: KM233118.fa Sequence type: Nucleotide Keep MBits: T Maximum file size: 1000000000B Adding sequences from FASTA; added 1 sequences in 0.00592995 seconds. ********************************************************* Blastn on the 40bp query ********************************************************* BLASTN 2.7.1+ Reference: Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000), "A greedy algorithm for aligning DNA sequences", J Comput Biol 2000; 7(1-2):203-14. Database: KM233118.fa 1 sequences; 18,613 total letters Query= KM233118.1 Zaire ebolavirus isolate Ebola virus/H.sapiens-wt/SLE/2014/Makona-NM042.3, complete genome Length=40 Score E Sequences producing significant alignments: (Bits) Value KM233118.1 Zaire ebolavirus isolate Ebola virus/H.sapiens-wt/SLE... 75.0 1e-17 >KM233118.1 Zaire ebolavirus isolate Ebola virus/H.sapiens-wt/SLE/2014/Makona-NM042.3, complete genome Length=18613 Score = 75.0 bits (40), Expect = 1e-17 Identities = 40/40 (100%), Gaps = 0/40 (0%) Strand=Plus/Plus Query 1 AATCATACCTGGTTTGTTTCAGAGCCATATCACCAAGATA 40 |||||||||||||||||||||||||||||||||||||||| Sbjct 1 AATCATACCTGGTTTGTTTCAGAGCCATATCACCAAGATA 40 Lambda K H 1.33 0.621 1.12 Gapped Lambda K H 1.28 0.460 0.850 Effective search space used: 520828 Database: KM233118.fa Posted date: Oct 8, 2018 3:33 PM Number of letters in database: 18,613 Number of sequences in database: 1 Matrix: blastn matrix 1 -2 Gap Penalties: Existence: 0, Extension: 2.5 ********************************************************* Blastn on the 15bp query: ********************************************************* BLASTN 2.7.1+ Reference: Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000), "A greedy algorithm for aligning DNA sequences", J Comput Biol 2000; 7(1-2):203-14. Database: KM233118.fa 1 sequences; 18,613 total letters Query= KM233118.1 Zaire ebolavirus isolate Ebola virus/H.sapiens-wt/SLE/2014/Makona-NM042.3, complete genome Length=15 ***** No hits found ***** Lambda K H 1.33 0.621 1.12 Gapped Lambda K H 1.28 0.460 0.850 Effective search space used: 93015 Database: KM233118.fa Posted date: Oct 8, 2018 3:33 PM Number of letters in database: 18,613 Number of sequences in database: 1 Matrix: blastn matrix 1 -2 Gap Penalties: Existence: 0, Extension: 2.5 ********************************************************* Blastn with the 'blastn' task on the 15bp query: ********************************************************* BLASTN 2.7.1+ Reference: Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Database: KM233118.fa 1 sequences; 18,613 total letters Query= KM233118.1 Zaire ebolavirus isolate Ebola virus/H.sapiens-wt/SLE/2014/Makona-NM042.3, complete genome Length=15 Score E Sequences producing significant alignments: (Bits) Value KM233118.1 Zaire ebolavirus isolate Ebola virus/H.sapiens-wt/SLE... 28.3 2e-04 >KM233118.1 Zaire ebolavirus isolate Ebola virus/H.sapiens-wt/SLE/2014/Makona-NM042.3, complete genome Length=18613 Score = 28.3 bits (30), Expect = 2e-04 Identities = 15/15 (100%), Gaps = 0/15 (0%) Strand=Plus/Plus Query 1 AATCATACCTGGTTT 15 ||||||||||||||| Sbjct 1 AATCATACCTGGTTT 15 Lambda K H 0.634 0.408 0.912 Gapped Lambda K H 0.625 0.410 0.780 Effective search space used: 74408 Database: KM233118.fa Posted date: Oct 8, 2018 3:33 PM Number of letters in database: 18,613 Number of sequences in database: 1 Matrix: blastn matrix 2 -3 Gap Penalties: Existence: 5, Extension: 2 ********************************************************* Blastn with the 'blastn-short' task on the 15bp query Note how many hits it generates! ********************************************************* BLASTN 2.7.1+ Reference: Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Database: KM233118.fa 1 sequences; 18,613 total letters Query= KM233118.1 Zaire ebolavirus isolate Ebola virus/H.sapiens-wt/SLE/2014/Makona-NM042.3, complete genome Length=15 Score E Sequences producing significant alignments: (Bits) Value KM233118.1 Zaire ebolavirus isolate Ebola virus/H.sapiens-wt/SLE... 30.2 1e-04 >KM233118.1 Zaire ebolavirus isolate Ebola virus/H.sapiens-wt/SLE/2014/Makona-NM042.3, complete genome Length=18613 Score = 30.2 bits (15), Expect = 1e-04 Identities = 15/15 (100%), Gaps = 0/15 (0%) Strand=Plus/Plus Query 1 AATCATACCTGGTTT 15 ||||||||||||||| Sbjct 1 AATCATACCTGGTTT 15 Score = 18.3 bits (9), Expect = 0.39 Identities = 9/9 (100%), Gaps = 0/9 (0%) Strand=Plus/Minus Query 2 ATCATACCT 10 ||||||||| Sbjct 9426 ATCATACCT 9418 Score = 16.4 bits (8), Expect = 1.6 Identities = 8/8 (100%), Gaps = 0/8 (0%) Strand=Plus/Minus Query 8 CCTGGTTT 15 |||||||| Sbjct 4823 CCTGGTTT 4816 Score = 16.4 bits (8), Expect = 1.6 Identities = 8/8 (100%), Gaps = 0/8 (0%) Strand=Plus/Minus Query 8 CCTGGTTT 15 |||||||| Sbjct 11169 CCTGGTTT 11162 Score = 16.4 bits (8), Expect = 1.6 Identities = 8/8 (100%), Gaps = 0/8 (0%) Strand=Plus/Minus Query 3 TCATACCT 10 |||||||| Sbjct 13387 TCATACCT 13380 Score = 16.4 bits (8), Expect = 1.6 Identities = 8/8 (100%), Gaps = 0/8 (0%) Strand=Plus/Minus Query 1 AATCATAC 8 |||||||| Sbjct 14867 AATCATAC 14860 Score = 16.4 bits (8), Expect = 1.6 Identities = 8/8 (100%), Gaps = 0/8 (0%) Strand=Plus/Plus Query 8 CCTGGTTT 15 |||||||| Sbjct 3704 CCTGGTTT 3711 Score = 16.4 bits (8), Expect = 1.6 Identities = 8/8 (100%), Gaps = 0/8 (0%) Strand=Plus/Plus Query 1 AATCATAC 8 |||||||| Sbjct 10776 AATCATAC 10783 Score = 14.4 bits (7), Expect = 6.2 Identities = 7/7 (100%), Gaps = 0/7 (0%) Strand=Plus/Minus Query 2 ATCATAC 8 ||||||| Sbjct 3697 ATCATAC 3691 Score = 14.4 bits (7), Expect = 6.2 Identities = 7/7 (100%), Gaps = 0/7 (0%) Strand=Plus/Minus Query 2 ATCATAC 8 ||||||| Sbjct 6406 ATCATAC 6400 Score = 14.4 bits (7), Expect = 6.2 Identities = 7/7 (100%), Gaps = 0/7 (0%) Strand=Plus/Minus Query 5 ATACCTG 11 ||||||| Sbjct 7883 ATACCTG 7877 Score = 14.4 bits (7), Expect = 6.2 Identities = 7/7 (100%), Gaps = 0/7 (0%) Strand=Plus/Minus Query 1 AATCATA 7 ||||||| Sbjct 9588 AATCATA 9582 Score = 14.4 bits (7), Expect = 6.2 Identities = 7/7 (100%), Gaps = 0/7 (0%) Strand=Plus/Minus Query 7 ACCTGGT 13 ||||||| Sbjct 10045 ACCTGGT 10039 Score = 14.4 bits (7), Expect = 6.2 Identities = 7/7 (100%), Gaps = 0/7 (0%) Strand=Plus/Minus Query 3 TCATACC 9 ||||||| Sbjct 11920 TCATACC 11914 Score = 14.4 bits (7), Expect = 6.2 Identities = 7/7 (100%), Gaps = 0/7 (0%) Strand=Plus/Minus Query 7 ACCTGGT 13 ||||||| Sbjct 12773 ACCTGGT 12767 Score = 14.4 bits (7), Expect = 6.2 Identities = 7/7 (100%), Gaps = 0/7 (0%) Strand=Plus/Minus Query 5 ATACCTG 11 ||||||| Sbjct 17675 ATACCTG 17669 Score = 14.4 bits (7), Expect = 6.2 Identities = 7/7 (100%), Gaps = 0/7 (0%) Strand=Plus/Plus Query 2 ATCATAC 8 ||||||| Sbjct 514 ATCATAC 520 Score = 14.4 bits (7), Expect = 6.2 Identities = 7/7 (100%), Gaps = 0/7 (0%) Strand=Plus/Plus Query 1 AATCATA 7 ||||||| Sbjct 3245 AATCATA 3251 Score = 14.4 bits (7), Expect = 6.2 Identities = 7/7 (100%), Gaps = 0/7 (0%) Strand=Plus/Plus Query 5 ATACCTG 11 ||||||| Sbjct 5514 ATACCTG 5520 Score = 14.4 bits (7), Expect = 6.2 Identities = 7/7 (100%), Gaps = 0/7 (0%) Strand=Plus/Plus Query 1 AATCATA 7 ||||||| Sbjct 8112 AATCATA 8118 Score = 14.4 bits (7), Expect = 6.2 Identities = 7/7 (100%), Gaps = 0/7 (0%) Strand=Plus/Plus Query 1 AATCATA 7 ||||||| Sbjct 9451 AATCATA 9457 Score = 14.4 bits (7), Expect = 6.2 Identities = 7/7 (100%), Gaps = 0/7 (0%) Strand=Plus/Plus Query 4 CATACCT 10 ||||||| Sbjct 9490 CATACCT 9496 Score = 14.4 bits (7), Expect = 6.2 Identities = 7/7 (100%), Gaps = 0/7 (0%) Strand=Plus/Plus Query 2 ATCATAC 8 ||||||| Sbjct 11558 ATCATAC 11564 Score = 14.4 bits (7), Expect = 6.2 Identities = 7/7 (100%), Gaps = 0/7 (0%) Strand=Plus/Plus Query 9 CTGGTTT 15 ||||||| Sbjct 13651 CTGGTTT 13657 Score = 14.4 bits (7), Expect = 6.2 Identities = 7/7 (100%), Gaps = 0/7 (0%) Strand=Plus/Plus Query 7 ACCTGGT 13 ||||||| Sbjct 14933 ACCTGGT 14939 Lambda K H 1.37 0.711 1.31 Gapped Lambda K H 1.37 0.711 1.31 Effective search space used: 130235 Database: KM233118.fa Posted date: Oct 8, 2018 3:33 PM Number of letters in database: 18,613 Number of sequences in database: 1 Matrix: blastn matrix 1 -3 Gap Penalties: Existence: 5, Extension: 2 Building a new DB, current time: 10/08/2018 15:33:32 New DB name: /export/sites/biostar-engine/export/media/jobs/job-ef88abad/xdb/yeast New DB title: NC_001133.fa Sequence type: Nucleotide Keep MBits: T Maximum file size: 1000000000B Adding sequences from FASTA; added 1 sequences in 0.00698996 seconds. ********************************************************* Blastn with the on the 80bp query. No hits!!!! Why?????? ********************************************************* BLASTN 2.7.1+ Reference: Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000), "A greedy algorithm for aligning DNA sequences", J Comput Biol 2000; 7(1-2):203-14. Database: NC_001133.fa 1 sequences; 230,218 total letters Query= NC_001133.9 Saccharomyces cerevisiae S288C chromosome I, complete sequence Length=80 ***** No hits found ***** Lambda K H 1.33 0.621 1.12 Gapped Lambda K H 1.28 0.460 0.850 Effective search space used: 14732928 Database: NC_001133.fa Posted date: Oct 8, 2018 3:33 PM Number of letters in database: 230,218 Number of sequences in database: 1 Matrix: blastn matrix 1 -2 Gap Penalties: Existence: 0, Extension: 2.5 ********************************************************* Blastn with the '--dust-no' task on the 80bp query: ********************************************************* BLASTN 2.7.1+ Reference: Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000), "A greedy algorithm for aligning DNA sequences", J Comput Biol 2000; 7(1-2):203-14. Database: NC_001133.fa 1 sequences; 230,218 total letters Query= NC_001133.9 Saccharomyces cerevisiae S288C chromosome I, complete sequence Length=80 Score E Sequences producing significant alignments: (Bits) Value NC_001133.9 Saccharomyces cerevisiae S288C chromosome I, complet... 148 2e-38 >NC_001133.9 Saccharomyces cerevisiae S288C chromosome I, complete sequence Length=230218 Score = 148 bits (80), Expect = 2e-38 Identities = 80/80 (100%), Gaps = 0/80 (0%) Strand=Plus/Plus Query 1 CCACACCACACCCACACACCCACACACCACACCACACACCACACCACACCCACACACACA 60 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 1 CCACACCACACCCACACACCCACACACCACACCACACACCACACCACACCCACACACACA 60 Query 61 CATCCTAACACTACCCTAAC 80 |||||||||||||||||||| Sbjct 61 CATCCTAACACTACCCTAAC 80 Lambda K H 1.33 0.621 1.12 Gapped Lambda K H 1.28 0.460 0.850 Effective search space used: 14732928 Database: NC_001133.fa Posted date: Oct 8, 2018 3:33 PM Number of letters in database: 230,218 Number of sequences in database: 1 Matrix: blastn matrix 1 -2 Gap Penalties: Existence: 0, Extension: 2.5