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= AAGCGCGGAGGTGGGCGAGGGGGACCGAGGCCAGGACTCTCCTTGGGGTTTGGGGGCTTGACCTGGGT
GCGCTTTCTGGACAGAC
Length=85
Score E
Sequences producing significant alignments: (Bits) Value
[20892]hsa-mir-6855 MI0022701 Homo sapiens miR-6855 stem-loop 27.0 0.067
[20765]hsa-mir-6729 MI0022574 Homo sapiens miR-6729 stem-loop 23.3 0.86
[15709]hsa-mir-4649 MI0017276 Homo sapiens miR-4649 stem-loop 21.4 3.1
[15327]hsa-mir-4523 MI0016890 Homo sapiens miR-4523 stem-loop 21.4 3.1
[14506]hsa-mir-3661 MI0016062 Homo sapiens miR-3661 stem-loop 21.4 3.1
[14314]hsa-mir-4258 MI0015857 Homo sapiens miR-4258 stem-loop 21.4 3.1
[9317]hsa-mir-2110 MI0010629 Homo sapiens miR-2110 stem-loop 21.4 3.1
[5163]hsa-mir-1229 MI0006319 Homo sapiens miR-1229 stem-loop 21.4 3.1
[278]hsa-mir-219a-1 MI0000296 Homo sapiens miR-219a-1 stem-loop 21.4 3.1
[258]hsa-mir-181c MI0000271 Homo sapiens miR-181c stem-loop 21.4 3.1
>[20892]hsa-mir-6855 MI0022701 Homo sapiens miR-6855 stem-loop
Length=67
Score = 27.0 bits (14), Expect = 0.067
Identities = 14/14 (100%), Gaps = 0/14 (0%)
Strand=Plus/Plus
Query 42 CTTGGGGTTTGGGG 55
||||||||||||||
Sbjct 5 CTTGGGGTTTGGGG 18
>[20765]hsa-mir-6729 MI0022574 Homo sapiens miR-6729 stem-loop
Length=65
Score = 23.3 bits (12), Expect = 0.86
Identities = 12/12 (100%), Gaps = 0/12 (0%)
Strand=Plus/Plus
Query 10 GGTGGGCGAGGG 21
||||||||||||
Sbjct 4 GGTGGGCGAGGG 15
Score = 23.3 bits (12), Expect = 0.86
Identities = 12/12 (100%), Gaps = 0/12 (0%)
Strand=Plus/Minus
Query 13 GGGCGAGGGGGA 24
||||||||||||
Sbjct 59 GGGCGAGGGGGA 48
>[15709]hsa-mir-4649 MI0017276 Homo sapiens miR-4649 stem-loop
Length=64
Score = 21.4 bits (11), Expect = 3.1
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 12 TGGGCGAGGGG 22
|||||||||||
Sbjct 3 TGGGCGAGGGG 13
>[15327]hsa-mir-4523 MI0016890 Homo sapiens miR-4523 stem-loop
Length=69
Score = 21.4 bits (11), Expect = 3.1
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 19 GGGGGACCGAG 29
|||||||||||
Sbjct 3 GGGGGACCGAG 13
>[14506]hsa-mir-3661 MI0016062 Homo sapiens miR-3661 stem-loop
Length=96
Score = 21.4 bits (11), Expect = 3.1
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 57 CTTGACCTGGG 67
|||||||||||
Sbjct 19 CTTGACCTGGG 29
>[14314]hsa-mir-4258 MI0015857 Homo sapiens miR-4258 stem-loop
Length=91
Score = 21.4 bits (11), Expect = 3.1
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 47 GGTTTGGGGGC 57
|||||||||||
Sbjct 70 GGTTTGGGGGC 80
>[9317]hsa-mir-2110 MI0010629 Homo sapiens miR-2110 stem-loop
Length=75
Score = 21.4 bits (11), Expect = 3.1
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 45 GGGGTTTGGGG 55
|||||||||||
Sbjct 3 GGGGTTTGGGG 13
>[5163]hsa-mir-1229 MI0006319 Homo sapiens miR-1229 stem-loop
Length=69
Score = 21.4 bits (11), Expect = 3.1
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 46 GGGTTTGGGGG 56
|||||||||||
Sbjct 8 GGGTTTGGGGG 18
>[278]hsa-mir-219a-1 MI0000296 Homo sapiens miR-219a-1 stem-loop
Length=110
Score = 21.4 bits (11), Expect = 3.1
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Minus
Query 47 GGTTTGGGGGC 57
|||||||||||
Sbjct 101 GGTTTGGGGGC 91
>[258]hsa-mir-181c MI0000271 Homo sapiens miR-181c stem-loop
Length=110
Score = 21.4 bits (11), Expect = 3.1
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 46 GGGTTTGGGGG 56
|||||||||||
Sbjct 16 GGGTTTGGGGG 26
Lambda K H
1.33 0.621 1.12
Gapped
Lambda K H
1.28 0.460 0.850
Effective search space used: 8805090
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