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= CTGGTCGGCCTGAAGGGAAGGGCCAATCCCTGAGTATCTCGGG
Length=43
Score E
Sequences producing significant alignments: (Bits) Value
[16402]hsa-mir-5088 MI0017977 Homo sapiens miR-5088 stem-loop 23.3 0.36
[3415]hsa-mir-628 MI0003642 Homo sapiens miR-628 stem-loop 23.3 0.36
[17694]hsa-mir-5689 MI0019294 Homo sapiens miR-5689 stem-loop 21.4 1.3
[5117]hsa-mir-1178 MI0006271 Homo sapiens miR-1178 stem-loop 21.4 1.3
[2949]hsa-mir-518e MI0003169 Homo sapiens miR-518e stem-loop 21.4 1.3
>[16402]hsa-mir-5088 MI0017977 Homo sapiens miR-5088 stem-loop
Length=79
Score = 23.3 bits (12), Expect = 0.36
Identities = 12/12 (100%), Gaps = 0/12 (0%)
Strand=Plus/Minus
Query 23 CCAATCCCTGAG 34
||||||||||||
Sbjct 22 CCAATCCCTGAG 11
>[3415]hsa-mir-628 MI0003642 Homo sapiens miR-628 stem-loop
Length=95
Score = 23.3 bits (12), Expect = 0.36
Identities = 12/12 (100%), Gaps = 0/12 (0%)
Strand=Plus/Plus
Query 12 GAAGGGAAGGGC 23
||||||||||||
Sbjct 80 GAAGGGAAGGGC 91
>[17694]hsa-mir-5689 MI0019294 Homo sapiens miR-5689 stem-loop
Length=78
Score = 21.4 bits (11), Expect = 1.3
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Minus
Query 29 CCTGAGTATCT 39
|||||||||||
Sbjct 38 CCTGAGTATCT 28
>[5117]hsa-mir-1178 MI0006271 Homo sapiens miR-1178 stem-loop
Length=91
Score = 21.4 bits (11), Expect = 1.3
Identities = 14/15 (93%), Gaps = 1/15 (7%)
Strand=Plus/Plus
Query 12 GAAGGGAAGGG-CCA 25
||||||||||| |||
Sbjct 17 GAAGGGAAGGGTCCA 31
>[2949]hsa-mir-518e MI0003169 Homo sapiens miR-518e stem-loop
Length=88
Score = 21.4 bits (11), Expect = 1.3
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Minus
Query 10 CTGAAGGGAAG 20
|||||||||||
Sbjct 70 CTGAAGGGAAG 60
Lambda K H
1.33 0.621 1.12
Gapped
Lambda K H
1.28 0.460 0.850
Effective search space used: 3702372
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