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= GCGGAGGTGGGCGAGGGGGACCGAGGCCAGGACTCTCCTTGGGGTTTGGGGGCTTGACCTG
Length=61
Score E
Sequences producing significant alignments: (Bits) Value
[20892]hsa-mir-6855 MI0022701 Homo sapiens miR-6855 stem-loop 27.0 0.044
[20765]hsa-mir-6729 MI0022574 Homo sapiens miR-6729 stem-loop 23.3 0.57
[15709]hsa-mir-4649 MI0017276 Homo sapiens miR-4649 stem-loop 21.4 2.0
[15327]hsa-mir-4523 MI0016890 Homo sapiens miR-4523 stem-loop 21.4 2.0
[14314]hsa-mir-4258 MI0015857 Homo sapiens miR-4258 stem-loop 21.4 2.0
[9317]hsa-mir-2110 MI0010629 Homo sapiens miR-2110 stem-loop 21.4 2.0
[5163]hsa-mir-1229 MI0006319 Homo sapiens miR-1229 stem-loop 21.4 2.0
[278]hsa-mir-219a-1 MI0000296 Homo sapiens miR-219a-1 stem-loop 21.4 2.0
[258]hsa-mir-181c MI0000271 Homo sapiens miR-181c stem-loop 21.4 2.0
>[20892]hsa-mir-6855 MI0022701 Homo sapiens miR-6855 stem-loop
Length=67
Score = 27.0 bits (14), Expect = 0.044
Identities = 14/14 (100%), Gaps = 0/14 (0%)
Strand=Plus/Plus
Query 38 CTTGGGGTTTGGGG 51
||||||||||||||
Sbjct 5 CTTGGGGTTTGGGG 18
>[20765]hsa-mir-6729 MI0022574 Homo sapiens miR-6729 stem-loop
Length=65
Score = 23.3 bits (12), Expect = 0.57
Identities = 12/12 (100%), Gaps = 0/12 (0%)
Strand=Plus/Plus
Query 6 GGTGGGCGAGGG 17
||||||||||||
Sbjct 4 GGTGGGCGAGGG 15
Score = 23.3 bits (12), Expect = 0.57
Identities = 12/12 (100%), Gaps = 0/12 (0%)
Strand=Plus/Minus
Query 9 GGGCGAGGGGGA 20
||||||||||||
Sbjct 59 GGGCGAGGGGGA 48
>[15709]hsa-mir-4649 MI0017276 Homo sapiens miR-4649 stem-loop
Length=64
Score = 21.4 bits (11), Expect = 2.0
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 8 TGGGCGAGGGG 18
|||||||||||
Sbjct 3 TGGGCGAGGGG 13
>[15327]hsa-mir-4523 MI0016890 Homo sapiens miR-4523 stem-loop
Length=69
Score = 21.4 bits (11), Expect = 2.0
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 15 GGGGGACCGAG 25
|||||||||||
Sbjct 3 GGGGGACCGAG 13
>[14314]hsa-mir-4258 MI0015857 Homo sapiens miR-4258 stem-loop
Length=91
Score = 21.4 bits (11), Expect = 2.0
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 43 GGTTTGGGGGC 53
|||||||||||
Sbjct 70 GGTTTGGGGGC 80
>[9317]hsa-mir-2110 MI0010629 Homo sapiens miR-2110 stem-loop
Length=75
Score = 21.4 bits (11), Expect = 2.0
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 41 GGGGTTTGGGG 51
|||||||||||
Sbjct 3 GGGGTTTGGGG 13
>[5163]hsa-mir-1229 MI0006319 Homo sapiens miR-1229 stem-loop
Length=69
Score = 21.4 bits (11), Expect = 2.0
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 42 GGGTTTGGGGG 52
|||||||||||
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 = 2.0
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Minus
Query 43 GGTTTGGGGGC 53
|||||||||||
Sbjct 101 GGTTTGGGGGC 91
>[258]hsa-mir-181c MI0000271 Homo sapiens miR-181c stem-loop
Length=110
Score = 21.4 bits (11), Expect = 2.0
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 42 GGGTTTGGGGG 52
|||||||||||
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: 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