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= ATCTGTTTTTCTCATATTGTTTTATTTTAATTTTT
Length=35
Score E
Sequences producing significant alignments: (Bits) Value
[14442]hsa-mir-3606 MI0015996 Homo sapiens miR-3606 stem-loop 25.1 0.073
[452]hsa-mir-186 MI0000483 Homo sapiens miR-186 stem-loop 23.3 0.26
[16293]hsa-mir-4999 MI0017865 Homo sapiens miR-4999 stem-loop 21.4 0.95
[15851]hsa-mir-4775 MI0017418 Homo sapiens miR-4775 stem-loop 21.4 0.95
[15731]hsa-mir-4668 MI0017298 Homo sapiens miR-4668 stem-loop 21.4 0.95
[14505]hsa-mir-3660 MI0016061 Homo sapiens miR-3660 stem-loop 21.4 0.95
[5208]hsa-mir-1302-5 MI0006366 Homo sapiens miR-1302-5 stem-loop 21.4 0.95
[3407]hsa-mir-620 MI0003634 Homo sapiens miR-620 stem-loop 21.4 0.95
[3351]hsa-mir-570 MI0003577 Homo sapiens miR-570 stem-loop 21.4 0.95
[3334]hsa-mir-553 MI0003558 Homo sapiens miR-553 stem-loop 21.4 0.95
>[14442]hsa-mir-3606 MI0015996 Homo sapiens miR-3606 stem-loop
Length=63
Score = 25.1 bits (13), Expect = 0.073
Identities = 13/13 (100%), Gaps = 0/13 (0%)
Strand=Plus/Plus
Query 23 TATTTTAATTTTT 35
|||||||||||||
Sbjct 27 TATTTTAATTTTT 39
>[452]hsa-mir-186 MI0000483 Homo sapiens miR-186 stem-loop
Length=86
Score = 23.3 bits (12), Expect = 0.26
Identities = 12/12 (100%), Gaps = 0/12 (0%)
Strand=Plus/Plus
Query 19 GTTTTATTTTAA 30
||||||||||||
Sbjct 42 GTTTTATTTTAA 53
>[16293]hsa-mir-4999 MI0017865 Homo sapiens miR-4999 stem-loop
Length=91
Score = 21.4 bits (11), Expect = 0.95
Identities = 14/15 (93%), Gaps = 1/15 (7%)
Strand=Plus/Minus
Query 15 TAT-TGTTTTATTTT 28
||| |||||||||||
Sbjct 19 TATGTGTTTTATTTT 5
>[15851]hsa-mir-4775 MI0017418 Homo sapiens miR-4775 stem-loop
Length=75
Score = 21.4 bits (11), Expect = 0.95
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 25 TTTTAATTTTT 35
|||||||||||
Sbjct 8 TTTTAATTTTT 18
Score = 21.4 bits (11), Expect = 0.95
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Minus
Query 25 TTTTAATTTTT 35
|||||||||||
Sbjct 68 TTTTAATTTTT 58
>[15731]hsa-mir-4668 MI0017298 Homo sapiens miR-4668 stem-loop
Length=70
Score = 21.4 bits (11), Expect = 0.95
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 14 ATATTGTTTTA 24
|||||||||||
Sbjct 35 ATATTGTTTTA 45
>[14505]hsa-mir-3660 MI0016061 Homo sapiens miR-3660 stem-loop
Length=100
Score = 21.4 bits (11), Expect = 0.95
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Minus
Query 24 ATTTTAATTTT 34
|||||||||||
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 = 0.95
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 24 ATTTTAATTTT 34
|||||||||||
Sbjct 122 ATTTTAATTTT 132
>[3407]hsa-mir-620 MI0003634 Homo sapiens miR-620 stem-loop
Length=95
Score = 21.4 bits (11), Expect = 0.95
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Minus
Query 17 TTGTTTTATTT 27
|||||||||||
Sbjct 87 TTGTTTTATTT 77
>[3351]hsa-mir-570 MI0003577 Homo sapiens miR-570 stem-loop
Length=97
Score = 21.4 bits (11), Expect = 0.95
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 22 TTATTTTAATT 32
|||||||||||
Sbjct 48 TTATTTTAATT 58
>[3334]hsa-mir-553 MI0003558 Homo sapiens miR-553 stem-loop
Length=68
Score = 21.4 bits (11), Expect = 0.95
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 20 TTTTATTTTAA 30
|||||||||||
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: 2681028
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