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= GAGGGGGCGGGGCG
Length=14
Score E
Sequences producing significant alignments: (Bits) Value
[24070]hsa-mir-8078 MI0025914 Homo sapiens miR-8078 stem-loop 27.0 0.003
[23677]hsa-mir-7851 MI0025521 Homo sapiens miR-7851 stem-loop 23.3 0.039
[12735]hsa-mir-3196 MI0014241 Homo sapiens miR-3196 stem-loop 23.3 0.039
[21734]hsa-mir-6089-2 MI0023563 Homo sapiens miR-6089-2 stem-loop 21.4 0.14
[21150]hsa-mir-7108 MI0022959 Homo sapiens miR-7108 stem-loop 21.4 0.14
[20822]hsa-mir-6786 MI0022631 Homo sapiens miR-6786 stem-loop 21.4 0.14
[18625]hsa-mir-6090 MI0020367 Homo sapiens miR-6090 stem-loop 21.4 0.14
[18624]hsa-mir-6089-1 MI0020366 Homo sapiens miR-6089-1 stem-loop 21.4 0.14
[5171]hsa-mir-1237 MI0006327 Homo sapiens miR-1237 stem-loop 21.4 0.14
[3427]hsa-mir-639 MI0003654 Homo sapiens miR-639 stem-loop 21.4 0.14
>[24070]hsa-mir-8078 MI0025914 Homo sapiens miR-8078 stem-loop
Length=84
Score = 27.0 bits (14), Expect = 0.003
Identities = 14/14 (100%), Gaps = 0/14 (0%)
Strand=Plus/Minus
Query 1 GAGGGGGCGGGGCG 14
||||||||||||||
Sbjct 16 GAGGGGGCGGGGCG 3
>[23677]hsa-mir-7851 MI0025521 Homo sapiens miR-7851 stem-loop
Length=160
Score = 23.3 bits (12), Expect = 0.039
Identities = 12/12 (100%), Gaps = 0/12 (0%)
Strand=Plus/Minus
Query 1 GAGGGGGCGGGG 12
||||||||||||
Sbjct 28 GAGGGGGCGGGG 17
>[12735]hsa-mir-3196 MI0014241 Homo sapiens miR-3196 stem-loop
Length=64
Score = 23.3 bits (12), Expect = 0.039
Identities = 12/12 (100%), Gaps = 0/12 (0%)
Strand=Plus/Plus
Query 3 GGGGGCGGGGCG 14
||||||||||||
Sbjct 5 GGGGGCGGGGCG 16
>[21734]hsa-mir-6089-2 MI0023563 Homo sapiens miR-6089-2 stem-loop
Length=64
Score = 21.4 bits (11), Expect = 0.14
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 4 GGGGCGGGGCG 14
|||||||||||
Sbjct 51 GGGGCGGGGCG 61
>[21150]hsa-mir-7108 MI0022959 Homo sapiens miR-7108 stem-loop
Length=87
Score = 21.4 bits (11), Expect = 0.14
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Minus
Query 4 GGGGCGGGGCG 14
|||||||||||
Sbjct 55 GGGGCGGGGCG 45
>[20822]hsa-mir-6786 MI0022631 Homo sapiens miR-6786 stem-loop
Length=113
Score = 21.4 bits (11), Expect = 0.14
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 4 GGGGCGGGGCG 14
|||||||||||
Sbjct 8 GGGGCGGGGCG 18
>[18625]hsa-mir-6090 MI0020367 Homo sapiens miR-6090 stem-loop
Length=60
Score = 21.4 bits (11), Expect = 0.14
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 4 GGGGCGGGGCG 14
|||||||||||
Sbjct 50 GGGGCGGGGCG 60
>[18624]hsa-mir-6089-1 MI0020366 Homo sapiens miR-6089-1 stem-loop
Length=64
Score = 21.4 bits (11), Expect = 0.14
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 4 GGGGCGGGGCG 14
|||||||||||
Sbjct 51 GGGGCGGGGCG 61
>[5171]hsa-mir-1237 MI0006327 Homo sapiens miR-1237 stem-loop
Length=102
Score = 21.4 bits (11), Expect = 0.14
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 3 GGGGGCGGGGC 13
|||||||||||
Sbjct 51 GGGGGCGGGGC 61
>[3427]hsa-mir-639 MI0003654 Homo sapiens miR-639 stem-loop
Length=98
Score = 21.4 bits (11), Expect = 0.14
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 4 GGGGCGGGGCG 14
|||||||||||
Sbjct 28 GGGGCGGGGCG 38
Lambda K H
1.33 0.621 1.12
Gapped
Lambda K H
1.28 0.460 0.850
Effective search space used: 399933
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