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= CCAGCTAAAGCGGCTGAACACATTTACTCTCTGGCAGTGTTTAAAAGTATCTGTTTTTCTCATATTGT
TTTATTTTAATTT
Length=81
Score E
Sequences producing significant alignments: (Bits) Value
[15813]hsa-mir-4742 MI0017380 Homo sapiens miR-4742 stem-loop 23.3 0.82
[452]hsa-mir-186 MI0000483 Homo sapiens miR-186 stem-loop 23.3 0.82
[16293]hsa-mir-4999 MI0017865 Homo sapiens miR-4999 stem-loop 21.4 2.9
[15785]hsa-mir-4717 MI0017352 Homo sapiens miR-4717 stem-loop 21.4 2.9
[15731]hsa-mir-4668 MI0017298 Homo sapiens miR-4668 stem-loop 21.4 2.9
[14442]hsa-mir-3606 MI0015996 Homo sapiens miR-3606 stem-loop 21.4 2.9
[3407]hsa-mir-620 MI0003634 Homo sapiens miR-620 stem-loop 21.4 2.9
[3351]hsa-mir-570 MI0003577 Homo sapiens miR-570 stem-loop 21.4 2.9
[3334]hsa-mir-553 MI0003558 Homo sapiens miR-553 stem-loop 21.4 2.9
[76]hsa-mir-22 MI0000078 Homo sapiens miR-22 stem-loop 21.4 2.9
>[15813]hsa-mir-4742 MI0017380 Homo sapiens miR-4742 stem-loop
Length=85
Score = 23.3 bits (12), Expect = 0.82
Identities = 15/16 (94%), Gaps = 1/16 (6%)
Strand=Plus/Minus
Query 40 TTT-AAAAGTATCTGT 54
||| ||||||||||||
Sbjct 34 TTTAAAAAGTATCTGT 19
>[452]hsa-mir-186 MI0000483 Homo sapiens miR-186 stem-loop
Length=86
Score = 23.3 bits (12), Expect = 0.82
Identities = 12/12 (100%), Gaps = 0/12 (0%)
Strand=Plus/Plus
Query 67 GTTTTATTTTAA 78
||||||||||||
Sbjct 42 GTTTTATTTTAA 53
>[16293]hsa-mir-4999 MI0017865 Homo sapiens miR-4999 stem-loop
Length=91
Score = 21.4 bits (11), Expect = 2.9
Identities = 14/15 (93%), Gaps = 1/15 (7%)
Strand=Plus/Minus
Query 63 TAT-TGTTTTATTTT 76
||| |||||||||||
Sbjct 19 TATGTGTTTTATTTT 5
>[15785]hsa-mir-4717 MI0017352 Homo sapiens miR-4717 stem-loop
Length=72
Score = 21.4 bits (11), Expect = 2.9
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 33 GGCAGTGTTTA 43
|||||||||||
Sbjct 1 GGCAGTGTTTA 11
Score = 21.4 bits (11), Expect = 2.9
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Minus
Query 33 GGCAGTGTTTA 43
|||||||||||
Sbjct 72 GGCAGTGTTTA 62
>[15731]hsa-mir-4668 MI0017298 Homo sapiens miR-4668 stem-loop
Length=70
Score = 21.4 bits (11), Expect = 2.9
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 62 ATATTGTTTTA 72
|||||||||||
Sbjct 35 ATATTGTTTTA 45
>[14442]hsa-mir-3606 MI0015996 Homo sapiens miR-3606 stem-loop
Length=63
Score = 21.4 bits (11), Expect = 2.9
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 71 TATTTTAATTT 81
|||||||||||
Sbjct 27 TATTTTAATTT 37
>[3407]hsa-mir-620 MI0003634 Homo sapiens miR-620 stem-loop
Length=95
Score = 21.4 bits (11), Expect = 2.9
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Minus
Query 65 TTGTTTTATTT 75
|||||||||||
Sbjct 87 TTGTTTTATTT 77
>[3351]hsa-mir-570 MI0003577 Homo sapiens miR-570 stem-loop
Length=97
Score = 21.4 bits (11), Expect = 2.9
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 70 TTATTTTAATT 80
|||||||||||
Sbjct 48 TTATTTTAATT 58
>[3334]hsa-mir-553 MI0003558 Homo sapiens miR-553 stem-loop
Length=68
Score = 21.4 bits (11), Expect = 2.9
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 68 TTTTATTTTAA 78
|||||||||||
Sbjct 7 TTTTATTTTAA 17
>[76]hsa-mir-22 MI0000078 Homo sapiens miR-22 stem-loop
Length=85
Score = 21.4 bits (11), Expect = 2.9
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 1 CCAGCTAAAGC 11
|||||||||||
Sbjct 46 CCAGCTAAAGC 56
Lambda K H
1.33 0.621 1.12
Gapped
Lambda K H
1.28 0.460 0.850
Effective search space used: 8301942
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