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= CGCGGAGGTGGGCGAGGGGGACCGAGGCCAGGACTCTCCTTGGGGT
Length=46
Score E
Sequences producing significant alignments: (Bits) Value
[20765]hsa-mir-6729 MI0022574 Homo sapiens miR-6729 stem-loop 23.3 0.40
[15709]hsa-mir-4649 MI0017276 Homo sapiens miR-4649 stem-loop 21.4 1.4
[15327]hsa-mir-4523 MI0016890 Homo sapiens miR-4523 stem-loop 21.4 1.4
>[20765]hsa-mir-6729 MI0022574 Homo sapiens miR-6729 stem-loop
Length=65
Score = 23.3 bits (12), Expect = 0.40
Identities = 12/12 (100%), Gaps = 0/12 (0%)
Strand=Plus/Plus
Query 7 GGTGGGCGAGGG 18
||||||||||||
Sbjct 4 GGTGGGCGAGGG 15
Score = 23.3 bits (12), Expect = 0.40
Identities = 12/12 (100%), Gaps = 0/12 (0%)
Strand=Plus/Minus
Query 10 GGGCGAGGGGGA 21
||||||||||||
Sbjct 59 GGGCGAGGGGGA 48
>[15709]hsa-mir-4649 MI0017276 Homo sapiens miR-4649 stem-loop
Length=64
Score = 21.4 bits (11), Expect = 1.4
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 9 TGGGCGAGGGG 19
|||||||||||
Sbjct 3 TGGGCGAGGGG 13
>[15327]hsa-mir-4523 MI0016890 Homo sapiens miR-4523 stem-loop
Length=69
Score = 21.4 bits (11), Expect = 1.4
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 16 GGGGGACCGAG 26
|||||||||||
Sbjct 3 GGGGGACCGAG 13
Lambda K H
1.33 0.621 1.12
Gapped
Lambda K H
1.28 0.460 0.850
Effective search space used: 4085376
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