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= TATTTTAATTTTT
Length=13
Score E
Sequences producing significant alignments: (Bits) Value
[14442]hsa-mir-3606 MI0015996 Homo sapiens miR-3606 stem-loop 25.1 0.011
[15851]hsa-mir-4775 MI0017418 Homo sapiens miR-4775 stem-loop 21.4 0.14
[14505]hsa-mir-3660 MI0016061 Homo sapiens miR-3660 stem-loop 21.4 0.14
[5208]hsa-mir-1302-5 MI0006366 Homo sapiens miR-1302-5 stem-loop 21.4 0.14
>[14442]hsa-mir-3606 MI0015996 Homo sapiens miR-3606 stem-loop
Length=63
Score = 25.1 bits (13), Expect = 0.011
Identities = 13/13 (100%), Gaps = 0/13 (0%)
Strand=Plus/Plus
Query 1 TATTTTAATTTTT 13
|||||||||||||
Sbjct 27 TATTTTAATTTTT 39
>[15851]hsa-mir-4775 MI0017418 Homo sapiens miR-4775 stem-loop
Length=75
Score = 21.4 bits (11), Expect = 0.14
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 3 TTTTAATTTTT 13
|||||||||||
Sbjct 8 TTTTAATTTTT 18
Score = 21.4 bits (11), Expect = 0.14
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Minus
Query 3 TTTTAATTTTT 13
|||||||||||
Sbjct 68 TTTTAATTTTT 58
>[14505]hsa-mir-3660 MI0016061 Homo sapiens miR-3660 stem-loop
Length=100
Score = 21.4 bits (11), Expect = 0.14
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Minus
Query 2 ATTTTAATTTT 12
|||||||||||
Sbjct 27 ATTTTAATTTT 17
>[5208]hsa-mir-1302-5 MI0006366 Homo sapiens miR-1302-5 stem-loop
Length=150
Score = 21.4 bits (11), Expect = 0.14
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 2 ATTTTAATTTT 12
|||||||||||
Sbjct 122 ATTTTAATTTT 132
Lambda K H
1.33 0.621 1.12
Gapped
Lambda K H
1.28 0.460 0.850
Effective search space used: 405576
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