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= TGGCAGTGTTTAAAAGTATCTGTTTTTCTCATATTGTTTTATTTTAATTT
Length=50
Score E
Sequences producing significant alignments: (Bits) Value
[15813]hsa-mir-4742 MI0017380 Homo sapiens miR-4742 stem-loop 23.3 0.43
[452]hsa-mir-186 MI0000483 Homo sapiens miR-186 stem-loop 23.3 0.43
[16293]hsa-mir-4999 MI0017865 Homo sapiens miR-4999 stem-loop 21.4 1.6
[15785]hsa-mir-4717 MI0017352 Homo sapiens miR-4717 stem-loop 21.4 1.6
[15731]hsa-mir-4668 MI0017298 Homo sapiens miR-4668 stem-loop 21.4 1.6
[14442]hsa-mir-3606 MI0015996 Homo sapiens miR-3606 stem-loop 21.4 1.6
[3407]hsa-mir-620 MI0003634 Homo sapiens miR-620 stem-loop 21.4 1.6
[3351]hsa-mir-570 MI0003577 Homo sapiens miR-570 stem-loop 21.4 1.6
[3334]hsa-mir-553 MI0003558 Homo sapiens miR-553 stem-loop 21.4 1.6
>[15813]hsa-mir-4742 MI0017380 Homo sapiens miR-4742 stem-loop
Length=85
Score = 23.3 bits (12), Expect = 0.43
Identities = 15/16 (94%), Gaps = 1/16 (6%)
Strand=Plus/Minus
Query 9 TTT-AAAAGTATCTGT 23
||| ||||||||||||
Sbjct 34 TTTAAAAAGTATCTGT 19
>[452]hsa-mir-186 MI0000483 Homo sapiens miR-186 stem-loop
Length=86
Score = 23.3 bits (12), Expect = 0.43
Identities = 12/12 (100%), Gaps = 0/12 (0%)
Strand=Plus/Plus
Query 36 GTTTTATTTTAA 47
||||||||||||
Sbjct 42 GTTTTATTTTAA 53
>[16293]hsa-mir-4999 MI0017865 Homo sapiens miR-4999 stem-loop
Length=91
Score = 21.4 bits (11), Expect = 1.6
Identities = 14/15 (93%), Gaps = 1/15 (7%)
Strand=Plus/Minus
Query 32 TAT-TGTTTTATTTT 45
||| |||||||||||
Sbjct 19 TATGTGTTTTATTTT 5
>[15785]hsa-mir-4717 MI0017352 Homo sapiens miR-4717 stem-loop
Length=72
Score = 21.4 bits (11), Expect = 1.6
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 2 GGCAGTGTTTA 12
|||||||||||
Sbjct 1 GGCAGTGTTTA 11
Score = 21.4 bits (11), Expect = 1.6
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Minus
Query 2 GGCAGTGTTTA 12
|||||||||||
Sbjct 72 GGCAGTGTTTA 62
>[15731]hsa-mir-4668 MI0017298 Homo sapiens miR-4668 stem-loop
Length=70
Score = 21.4 bits (11), Expect = 1.6
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 31 ATATTGTTTTA 41
|||||||||||
Sbjct 35 ATATTGTTTTA 45
>[14442]hsa-mir-3606 MI0015996 Homo sapiens miR-3606 stem-loop
Length=63
Score = 21.4 bits (11), Expect = 1.6
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 40 TATTTTAATTT 50
|||||||||||
Sbjct 27 TATTTTAATTT 37
>[3407]hsa-mir-620 MI0003634 Homo sapiens miR-620 stem-loop
Length=95
Score = 21.4 bits (11), Expect = 1.6
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Minus
Query 34 TTGTTTTATTT 44
|||||||||||
Sbjct 87 TTGTTTTATTT 77
>[3351]hsa-mir-570 MI0003577 Homo sapiens miR-570 stem-loop
Length=97
Score = 21.4 bits (11), Expect = 1.6
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 39 TTATTTTAATT 49
|||||||||||
Sbjct 48 TTATTTTAATT 58
>[3334]hsa-mir-553 MI0003558 Homo sapiens miR-553 stem-loop
Length=68
Score = 21.4 bits (11), Expect = 1.6
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 37 TTTTATTTTAA 47
|||||||||||
Sbjct 7 TTTTATTTTAA 17
Lambda K H
1.33 0.621 1.12
Gapped
Lambda K H
1.28 0.460 0.850
Effective search space used: 4402545
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