BLASTN 2.3.0+
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: homo-hairpin.fasta
1,881 sequences; 154,002 total letters
Query= GAAGGCACTGCGGGCACGCTTCCTGCCTGGTCGGCCTGAAGGGAAGG
Length=47
Score E
Sequences producing significant alignments: (Bits) Value
[14879]hsa-mir-3928 MI0016438 Homo sapiens miR-3928 stem-loop 21.4 1.5
[6074]hsa-mir-1538 MI0007259 Homo sapiens miR-1538 stem-loop 21.4 1.5
[4420]hsa-mir-874 MI0005532 Homo sapiens miR-874 stem-loop 21.4 1.5
[2949]hsa-mir-518e MI0003169 Homo sapiens miR-518e stem-loop 21.4 1.5
>[14879]hsa-mir-3928 MI0016438 Homo sapiens miR-3928 stem-loop
Length=58
Score = 21.4 bits (11), Expect = 1.5
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Minus
Query 17 CGCTTCCTGCC 27
|||||||||||
Sbjct 37 CGCTTCCTGCC 27
>[6074]hsa-mir-1538 MI0007259 Homo sapiens miR-1538 stem-loop
Length=61
Score = 21.4 bits (11), Expect = 1.5
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 17 CGCTTCCTGCC 27
|||||||||||
Sbjct 24 CGCTTCCTGCC 34
>[4420]hsa-mir-874 MI0005532 Homo sapiens miR-874 stem-loop
Length=78
Score = 21.4 bits (11), Expect = 1.5
Identities = 14/15 (93%), Gaps = 1/15 (7%)
Strand=Plus/Plus
Query 17 CGCTTCCTGCC-TGG 30
||||||||||| |||
Sbjct 41 CGCTTCCTGCCCTGG 55
>[2949]hsa-mir-518e MI0003169 Homo sapiens miR-518e stem-loop
Length=88
Score = 21.4 bits (11), Expect = 1.5
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Minus
Query 36 CTGAAGGGAAG 46
|||||||||||
Sbjct 70 CTGAAGGGAAG 60
Lambda K H
1.33 0.621 1.12
Gapped
Lambda K H
1.28 0.460 0.850
Effective search space used: 4213044
Database: homo-hairpin.fasta
Posted date: Sep 23, 2016 6:16 PM
Number of letters in database: 154,002
Number of sequences in database: 1,881
Matrix: blastn matrix 1 -2
Gap Penalties: Existence: 0, Extension: 2.5