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= GCTGTGCGTGTGTCGGGGCGGGTGGAACCTTAGCGGACCCTGGGAGGAGGCT
Length=52
Score E
Sequences producing significant alignments: (Bits) Value
[20789]hsa-mir-6753 MI0022598 Homo sapiens miR-6753 stem-loop 25.1 0.13
[17514]hsa-mir-3680-2 MI0019113 Homo sapiens miR-3680-2 stem-loop 23.3 0.46
[14522]hsa-mir-3680-1 MI0016081 Homo sapiens miR-3680-1 stem-loop 23.3 0.46
[21153]hsa-mir-7111 MI0022962 Homo sapiens miR-7111 stem-loop 21.4 1.6
[21148]hsa-mir-7106 MI0022957 Homo sapiens miR-7106 stem-loop 21.4 1.6
[20800]hsa-mir-6764 MI0022609 Homo sapiens miR-6764 stem-loop 21.4 1.6
[12663]hsa-mir-3141 MI0014165 Homo sapiens miR-3141 stem-loop 21.4 1.6
[4446]hsa-mir-877 MI0005561 Homo sapiens miR-877 stem-loop 21.4 1.6
[732]hsa-mir-370 MI0000778 Homo sapiens miR-370 stem-loop 21.4 1.6
[268]hsa-mir-210 MI0000286 Homo sapiens miR-210 stem-loop 21.4 1.6
>[20789]hsa-mir-6753 MI0022598 Homo sapiens miR-6753 stem-loop
Length=164
Score = 25.1 bits (13), Expect = 0.13
Identities = 28/34 (82%), Gaps = 6/34 (18%)
Strand=Plus/Minus
Query 14 CGG-GGCGGGTGGAACCTT-AGCGGACCCTGGGA 45
||| |||||| || |||| || |||||||||||
Sbjct 135 CGGTGGCGGG-GG--CCTTCAG-GGACCCTGGGA 106
>[17514]hsa-mir-3680-2 MI0019113 Homo sapiens miR-3680-2 stem-loop
Length=87
Score = 23.3 bits (12), Expect = 0.46
Identities = 14/15 (93%), Gaps = 0/15 (0%)
Strand=Plus/Plus
Query 36 GACCCTGGGAGGAGG 50
||||||||||| |||
Sbjct 58 GACCCTGGGAGTAGG 72
>[14522]hsa-mir-3680-1 MI0016081 Homo sapiens miR-3680-1 stem-loop
Length=87
Score = 23.3 bits (12), Expect = 0.46
Identities = 14/15 (93%), Gaps = 0/15 (0%)
Strand=Plus/Plus
Query 36 GACCCTGGGAGGAGG 50
||||||||||| |||
Sbjct 58 GACCCTGGGAGTAGG 72
>[21153]hsa-mir-7111 MI0022962 Homo sapiens miR-7111 stem-loop
Length=72
Score = 21.4 bits (11), Expect = 1.6
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Minus
Query 40 CTGGGAGGAGG 50
|||||||||||
Sbjct 72 CTGGGAGGAGG 62
>[21148]hsa-mir-7106 MI0022957 Homo sapiens miR-7106 stem-loop
Length=65
Score = 21.4 bits (11), Expect = 1.6
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 40 CTGGGAGGAGG 50
|||||||||||
Sbjct 5 CTGGGAGGAGG 15
>[20800]hsa-mir-6764 MI0022609 Homo sapiens miR-6764 stem-loop
Length=61
Score = 21.4 bits (11), Expect = 1.6
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Minus
Query 36 GACCCTGGGAG 46
|||||||||||
Sbjct 15 GACCCTGGGAG 5
>[12663]hsa-mir-3141 MI0014165 Homo sapiens miR-3141 stem-loop
Length=61
Score = 21.4 bits (11), Expect = 1.6
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 16 GGGCGGGTGGA 26
|||||||||||
Sbjct 12 GGGCGGGTGGA 22
>[4446]hsa-mir-877 MI0005561 Homo sapiens miR-877 stem-loop
Length=86
Score = 21.4 bits (11), Expect = 1.6
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Minus
Query 40 CTGGGAGGAGG 50
|||||||||||
Sbjct 86 CTGGGAGGAGG 76
>[732]hsa-mir-370 MI0000778 Homo sapiens miR-370 stem-loop
Length=75
Score = 21.4 bits (11), Expect = 1.6
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 20 GGGTGGAACCT 30
|||||||||||
Sbjct 56 GGGTGGAACCT 66
>[268]hsa-mir-210 MI0000286 Homo sapiens miR-210 stem-loop
Length=110
Score = 21.4 bits (11), Expect = 1.6
Identities = 11/11 (100%), Gaps = 0/11 (0%)
Strand=Plus/Plus
Query 2 CTGTGCGTGTG 12
|||||||||||
Sbjct 66 CTGTGCGTGTG 76
Lambda K H
1.33 0.621 1.12
Gapped
Lambda K H
1.28 0.460 0.850
Effective search space used: 4654119
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