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= GGGCGGGGCGGCCATTGG
Length=18
Score E
Sequences producing significant alignments: (Bits) Value
[20822]hsa-mir-6786 MI0022631 Homo sapiens miR-6786 stem-loop 25.1 0.022
[12735]hsa-mir-3196 MI0014241 Homo sapiens miR-3196 stem-loop 23.3 0.077
[24070]hsa-mir-8078 MI0025914 Homo sapiens miR-8078 stem-loop 21.4 0.28
[21734]hsa-mir-6089-2 MI0023563 Homo sapiens miR-6089-2 stem-loop 21.4 0.28
[21150]hsa-mir-7108 MI0022959 Homo sapiens miR-7108 stem-loop 21.4 0.28
[18624]hsa-mir-6089-1 MI0020366 Homo sapiens miR-6089-1 stem-loop 21.4 0.28
[15812]hsa-mir-4741 MI0017379 Homo sapiens miR-4741 stem-loop 21.4 0.28
[15286]hsa-mir-4488 MI0016849 Homo sapiens miR-4488 stem-loop 21.4 0.28
[14348]hsa-mir-4285 MI0015891 Homo sapiens miR-4285 stem-loop 21.4 0.28
[3427]hsa-mir-639 MI0003654 Homo sapiens miR-639 stem-loop 21.4 0.28
>[20822]hsa-mir-6786 MI0022631 Homo sapiens miR-6786 stem-loop
Length=113
Score = 25.1 bits (13), Expect = 0.022
Identities = 13/13 (100%), Gaps = 0/13 (0%)
Strand=Plus/Plus
Query 1 GGGCGGGGCGGCC 13
|||||||||||||
Sbjct 9 GGGCGGGGCGGCC 21
>[12735]hsa-mir-3196 MI0014241 Homo sapiens miR-3196 stem-loop
Length=64
Score = 23.3 bits (12), Expect = 0.077
Identities = 12/12 (100%), Gaps = 0/12 (0%)
Strand=Plus/Plus
Query 1 GGGCGGGGCGGC 12
||||||||||||
Sbjct 7 GGGCGGGGCGGC 18
>[24070]hsa-mir-8078 MI0025914 Homo sapiens miR-8078 stem-loop
Length=84
Score = 21.4 bits (11), Expect = 0.28
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Minus
Query 1 GGGCGGGGCGG 11
|||||||||||
Sbjct 12 GGGCGGGGCGG 2
>[21734]hsa-mir-6089-2 MI0023563 Homo sapiens miR-6089-2 stem-loop
Length=64
Score = 21.4 bits (11), Expect = 0.28
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 1 GGGCGGGGCGG 11
|||||||||||
Sbjct 52 GGGCGGGGCGG 62
>[21150]hsa-mir-7108 MI0022959 Homo sapiens miR-7108 stem-loop
Length=87
Score = 21.4 bits (11), Expect = 0.28
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Minus
Query 1 GGGCGGGGCGG 11
|||||||||||
Sbjct 54 GGGCGGGGCGG 44
>[18624]hsa-mir-6089-1 MI0020366 Homo sapiens miR-6089-1 stem-loop
Length=64
Score = 21.4 bits (11), Expect = 0.28
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 1 GGGCGGGGCGG 11
|||||||||||
Sbjct 52 GGGCGGGGCGG 62
>[15812]hsa-mir-4741 MI0017379 Homo sapiens miR-4741 stem-loop
Length=90
Score = 21.4 bits (11), Expect = 0.28
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 1 GGGCGGGGCGG 11
|||||||||||
Sbjct 2 GGGCGGGGCGG 12
>[15286]hsa-mir-4488 MI0016849 Homo sapiens miR-4488 stem-loop
Length=62
Score = 21.4 bits (11), Expect = 0.28
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Minus
Query 1 GGGCGGGGCGG 11
|||||||||||
Sbjct 62 GGGCGGGGCGG 52
>[14348]hsa-mir-4285 MI0015891 Homo sapiens miR-4285 stem-loop
Length=85
Score = 21.4 bits (11), Expect = 0.28
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 2 GGCGGGGCGGC 12
|||||||||||
Sbjct 5 GGCGGGGCGGC 15
>[3427]hsa-mir-639 MI0003654 Homo sapiens miR-639 stem-loop
Length=98
Score = 21.4 bits (11), Expect = 0.28
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 1 GGGCGGGGCGG 11
|||||||||||
Sbjct 29 GGGCGGGGCGG 39
Lambda K H
1.33 0.621 1.12
Gapped
Lambda K H
1.28 0.460 0.850
Effective search space used: 788580
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