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= GAAGGCACTGCGGGCACGCTTCCTGCCTGGTCGGCCTGAAGGGAAGGGCCAATCCCTGAGTATCTCGG
GAAGGAGGTGTCCGGAGCCGCGGACCTAG
Length=97
Score E
Sequences producing significant alignments: (Bits) Value
[16402]hsa-mir-5088 MI0017977 Homo sapiens miR-5088 stem-loop 23.3 1.0
[3415]hsa-mir-628 MI0003642 Homo sapiens miR-628 stem-loop 23.3 1.0
[17694]hsa-mir-5689 MI0019294 Homo sapiens miR-5689 stem-loop 21.4 3.6
[14879]hsa-mir-3928 MI0016438 Homo sapiens miR-3928 stem-loop 21.4 3.6
[12738]hsa-mir-3197 MI0014245 Homo sapiens miR-3197 stem-loop 21.4 3.6
[6074]hsa-mir-1538 MI0007259 Homo sapiens miR-1538 stem-loop 21.4 3.6
[5481]hsa-mir-513c MI0006649 Homo sapiens miR-513c stem-loop 21.4 3.6
[5480]hsa-mir-513b MI0006648 Homo sapiens miR-513b stem-loop 21.4 3.6
[5117]hsa-mir-1178 MI0006271 Homo sapiens miR-1178 stem-loop 21.4 3.6
[4420]hsa-mir-874 MI0005532 Homo sapiens miR-874 stem-loop 21.4 3.6
[2949]hsa-mir-518e MI0003169 Homo sapiens miR-518e stem-loop 21.4 3.6
>[16402]hsa-mir-5088 MI0017977 Homo sapiens miR-5088 stem-loop
Length=79
Score = 23.3 bits (12), Expect = 1.0
Identities = 12/12 (100%), Gaps = 0/12 (0%)
Strand=Plus/Minus
Query 49 CCAATCCCTGAG 60
||||||||||||
Sbjct 22 CCAATCCCTGAG 11
>[3415]hsa-mir-628 MI0003642 Homo sapiens miR-628 stem-loop
Length=95
Score = 23.3 bits (12), Expect = 1.0
Identities = 12/12 (100%), Gaps = 0/12 (0%)
Strand=Plus/Plus
Query 38 GAAGGGAAGGGC 49
||||||||||||
Sbjct 80 GAAGGGAAGGGC 91
>[17694]hsa-mir-5689 MI0019294 Homo sapiens miR-5689 stem-loop
Length=78
Score = 21.4 bits (11), Expect = 3.6
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Minus
Query 55 CCTGAGTATCT 65
|||||||||||
Sbjct 38 CCTGAGTATCT 28
>[14879]hsa-mir-3928 MI0016438 Homo sapiens miR-3928 stem-loop
Length=58
Score = 21.4 bits (11), Expect = 3.6
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Minus
Query 17 CGCTTCCTGCC 27
|||||||||||
Sbjct 37 CGCTTCCTGCC 27
>[12738]hsa-mir-3197 MI0014245 Homo sapiens miR-3197 stem-loop
Length=73
Score = 21.4 bits (11), Expect = 3.6
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Minus
Query 65 TCGGGAAGGAG 75
|||||||||||
Sbjct 55 TCGGGAAGGAG 45
>[6074]hsa-mir-1538 MI0007259 Homo sapiens miR-1538 stem-loop
Length=61
Score = 21.4 bits (11), Expect = 3.6
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 17 CGCTTCCTGCC 27
|||||||||||
Sbjct 24 CGCTTCCTGCC 34
>[5481]hsa-mir-513c MI0006649 Homo sapiens miR-513c stem-loop
Length=84
Score = 21.4 bits (11), Expect = 3.6
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 70 AAGGAGGTGTC 80
|||||||||||
Sbjct 19 AAGGAGGTGTC 29
>[5480]hsa-mir-513b MI0006648 Homo sapiens miR-513b stem-loop
Length=84
Score = 21.4 bits (11), Expect = 3.6
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 70 AAGGAGGTGTC 80
|||||||||||
Sbjct 19 AAGGAGGTGTC 29
>[5117]hsa-mir-1178 MI0006271 Homo sapiens miR-1178 stem-loop
Length=91
Score = 21.4 bits (11), Expect = 3.6
Identities = 14/15 (93%), Gaps = 1/15 (7%)
Strand=Plus/Plus
Query 38 GAAGGGAAGGG-CCA 51
||||||||||| |||
Sbjct 17 GAAGGGAAGGGTCCA 31
>[4420]hsa-mir-874 MI0005532 Homo sapiens miR-874 stem-loop
Length=78
Score = 21.4 bits (11), Expect = 3.6
Identities = 14/15 (93%), Gaps = 1/15 (7%)
Strand=Plus/Plus
Query 17 CGCTTCCTGCC-TGG 30
||||||||||| |||
Sbjct 41 CGCTTCCTGCCCTGG 55
>[2949]hsa-mir-518e MI0003169 Homo sapiens miR-518e stem-loop
Length=88
Score = 21.4 bits (11), Expect = 3.6
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Minus
Query 36 CTGAAGGGAAG 46
|||||||||||
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: 10314534
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