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= CCGGACTACATTTTCCAGAAGGCACTGCGGGCACGCTTCCTGCCTGGTCGGCCTGAAGGGA
Length=61
Score E
Sequences producing significant alignments: (Bits) Value
[14879]hsa-mir-3928 MI0016438 Homo sapiens miR-3928 stem-loop 21.4 2.0
[6074]hsa-mir-1538 MI0007259 Homo sapiens miR-1538 stem-loop 21.4 2.0
[5227]hsa-mir-1250 MI0006385 Homo sapiens miR-1250 stem-loop 21.4 2.0
[4420]hsa-mir-874 MI0005532 Homo sapiens miR-874 stem-loop 21.4 2.0
>[14879]hsa-mir-3928 MI0016438 Homo sapiens miR-3928 stem-loop
Length=58
Score = 21.4 bits (11), Expect = 2.0
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Minus
Query 34 CGCTTCCTGCC 44
|||||||||||
Sbjct 37 CGCTTCCTGCC 27
>[6074]hsa-mir-1538 MI0007259 Homo sapiens miR-1538 stem-loop
Length=61
Score = 21.4 bits (11), Expect = 2.0
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 34 CGCTTCCTGCC 44
|||||||||||
Sbjct 24 CGCTTCCTGCC 34
>[5227]hsa-mir-1250 MI0006385 Homo sapiens miR-1250 stem-loop
Length=113
Score = 21.4 bits (11), Expect = 2.0
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 8 ACATTTTCCAG 18
|||||||||||
Sbjct 63 ACATTTTCCAG 73
>[4420]hsa-mir-874 MI0005532 Homo sapiens miR-874 stem-loop
Length=78
Score = 21.4 bits (11), Expect = 2.0
Identities = 14/15 (93%), Gaps = 1/15 (7%)
Strand=Plus/Plus
Query 34 CGCTTCCTGCC-TGG 47
||||||||||| |||
Sbjct 41 CGCTTCCTGCCCTGG 55
Lambda K H
1.33 0.621 1.12
Gapped
Lambda K H
1.28 0.460 0.850
Effective search space used: 5786202
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