AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1343480

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1343480 MtrunA17_Chr8g0385011 92.523 107 5 2 1 104 1 107 6.69e-60 178
Msa1343480 MtrunA17_Chr3g0130911 74.038 104 23 2 1 104 7 106 8.43e-43 135
Msa1343480 MtrunA17_Chr7g0276101 40.698 86 42 1 3 88 23 99 4.99e-19 75.1
Msa1343480 MtrunA17_Chr3g0127561 41.176 85 41 1 3 87 33 108 7.00e-18 72.8
Msa1343480 MtrunA17_Chr8g0346181 37.647 85 44 1 3 87 27 102 7.47e-17 69.7
Msa1343480 MtrunA17_Chr4g0070071 43.023 86 36 2 3 88 69 141 3.42e-14 64.3
Msa1343480 MtrunA17_Chr2g0301531 39.535 86 41 1 3 88 76 150 1.02e-13 63.2
Msa1343480 MtrunA17_Chr4g0036841 51.389 72 23 2 3 73 35 95 7.99e-13 59.3
Msa1343480 MtrunA17_Chr4g0036861 40.000 80 36 2 1 79 55 123 8.73e-13 59.7
Msa1343480 MtrunA17_Chr4g0036271 42.857 77 32 2 2 77 22 87 1.35e-12 58.5
Msa1343480 MtrunA17_Chr4g0036831 41.026 78 34 2 1 77 24 90 1.55e-12 58.2
Msa1343480 MtrunA17_Chr7g0214201 39.474 76 42 1 28 99 81 156 2.16e-12 59.7
Msa1343480 MtrunA17_Chr1g0179511 46.377 69 24 2 3 71 19 74 2.34e-12 58.5
Msa1343480 MtrunA17_Chr4g0036751 43.590 78 32 2 2 78 19 85 2.86e-12 57.4
Msa1343480 MtrunA17_Chr8g0359011 42.308 78 33 2 1 77 1 67 3.10e-12 57.0
Msa1343480 MtrunA17_Chr4g0036201 41.558 77 33 2 2 77 25 90 3.92e-12 57.4
Msa1343480 MtrunA17_Chr4g0036181 41.250 80 35 2 1 79 81 149 4.16e-12 58.5
Msa1343480 MtrunA17_Chr3g0131991 41.429 70 30 1 1 70 51 109 4.44e-12 58.5
Msa1343480 MtrunA17_Chr4g0036221 41.772 79 33 2 1 78 24 90 5.21e-12 57.0
Msa1343480 MtrunA17_Chr5g0396091 44.444 72 28 2 3 73 29 89 6.51e-12 57.0
Msa1343480 MtrunA17_Chr4g0036461 43.836 73 29 2 2 73 24 85 9.04e-12 56.2
Msa1343480 MtrunA17_Chr3g0121801 41.026 78 34 2 1 77 23 89 1.05e-11 56.2
Msa1343480 MtrunA17_Chr1g0178451 40.000 80 37 2 6 85 52 120 1.61e-11 56.6
Msa1343480 MtrunA17_Chr8g0386131 45.205 73 29 1 6 78 52 113 1.68e-11 57.4
Msa1343480 MtrunA17_Chr4g0036611 44.444 72 28 2 3 73 25 85 1.73e-11 55.8
Msa1343480 MtrunA17_Chr4g0036531 39.744 78 35 2 1 77 23 89 1.75e-11 55.8
Msa1343480 MtrunA17_Chr4g0036521 38.961 77 36 2 3 78 32 98 1.93e-11 55.8
Msa1343480 MtrunA17_Chr4g0036811 43.836 73 29 2 2 73 25 86 2.01e-11 55.5
Msa1343480 MtrunA17_Chr8g0386111 45.205 73 29 1 6 78 48 109 2.61e-11 56.2
Msa1343480 MtrunA17_Chr4g0036191 43.836 73 27 2 5 76 28 87 2.75e-11 55.1
Msa1343480 MtrunA17_Chr4g0036631 40.541 74 32 2 1 73 18 80 3.54e-11 54.7
Msa1343480 MtrunA17_Chr4g0000251 37.209 86 43 1 3 88 70 144 4.50e-11 56.2
Msa1343480 MtrunA17_Chr8g0386121 40.541 74 33 1 6 79 49 111 5.01e-11 55.1
Msa1343480 MtrunA17_Chr4g0036431 41.892 74 31 2 1 73 23 85 5.74e-11 54.3
Msa1343480 MtrunA17_Chr8g0358991 43.836 73 29 2 1 72 23 84 6.05e-11 54.3
Msa1343480 MtrunA17_Chr3g0121721 41.892 74 31 2 1 73 23 85 9.53e-11 53.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1343480 AT2G46690.1 37.363 91 49 1 3 93 24 106 9.81e-19 75.5
Msa1343480 AT4G00880.1 39.759 83 41 1 2 84 27 100 3.93e-16 68.6
Msa1343480 AT5G53590.1 41.772 79 40 2 3 81 46 118 7.10e-16 68.6
Msa1343480 AT3G61900.1 40.000 80 40 1 3 82 30 101 1.17e-14 65.5
Msa1343480 AT5G20810.1 46.479 71 27 1 3 73 79 138 1.77e-12 60.5
Msa1343480 AT3G43120.1 43.421 76 32 1 3 78 79 143 3.17e-12 59.7
Msa1343480 AT5G20810.2 46.479 71 27 1 3 73 79 138 4.46e-12 59.7
Msa1343480 AT4G34780.1 40.000 80 39 2 1 79 26 97 7.43e-12 57.4
Msa1343480 AT4G34800.1 43.836 73 32 2 2 73 20 84 9.25e-12 56.6
Msa1343480 AT4G22620.1 37.333 75 39 1 3 77 79 145 9.84e-12 58.2
Msa1343480 AT4G34790.1 43.056 72 31 2 3 73 39 101 4.45e-11 55.5
Msa1343480 AT4G12410.1 34.667 75 41 1 3 77 76 142 4.93e-11 56.2

Find 23 sgRNAs with CRISPR-Local

Find 23 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GATAAAGCTTATGAGATTTA+TGG 0.119621 tig0006451:+1837 Msa1343480:CDS
GGATGATAAAGATATGAAAT+AGG 0.226231 tig0006451:-1795 None:intergenic
ATGATGGTGGTGATGGTGAT+AGG 0.327003 tig0006451:-1946 None:intergenic
CTAAAAGATGAAGGTGAAGA+AGG 0.393733 tig0006451:+1692 None:intergenic
GATGATAAAGATATGAAATA+GGG 0.436771 tig0006451:-1794 None:intergenic
GTGGTGATGGTGATAGGGTG+TGG 0.458211 tig0006451:-1940 None:intergenic
TCAAGAAGACGCTTGAAAAG+AGG 0.477121 tig0006451:-1816 None:intergenic
TAAAAGATGAAGGTGAAGAA+GGG 0.520859 tig0006451:+1693 None:intergenic
AACGGAACAAGGAAGCTTGA+GGG 0.534951 tig0006451:-1877 None:intergenic
ACAAAGCATGAGGAATCAAA+TGG 0.539588 tig0006451:-1974 None:intergenic
GGTGATGATGATGGTGGTGA+TGG 0.544241 tig0006451:-1953 None:intergenic
GAAGAACACTCTCAAGAAGA+TGG 0.549372 tig0006451:+1744 Msa1343480:CDS
AGATGAAGGTGAAGAAGGGA+TGG 0.553458 tig0006451:+1697 None:intergenic
TGATGGTGGTGATGGTGATA+GGG 0.561787 tig0006451:-1945 None:intergenic
GAATCAAATGGTGATGATGA+TGG 0.574122 tig0006451:-1962 None:intergenic
AGAAAATCATCAACGGAACA+AGG 0.574342 tig0006451:-1888 None:intergenic
CAACGGAACAAGGAAGCTTG+AGG 0.591378 tig0006451:-1878 None:intergenic
ATTTATGGCTACAACACTGA+TGG 0.615584 tig0006451:+1852 Msa1343480:CDS
ACGGAACAAGGAAGCTTGAG+GGG 0.635480 tig0006451:-1876 None:intergenic
GGATGGCTAGCAGTTCAAGT+AGG 0.650962 tig0006451:+1714 Msa1343480:CDS
GAATTGAAATACAAAGCATG+AGG 0.674168 tig0006451:-1984 None:intergenic
GAGGTGAAGAAAATCATCAA+CGG 0.680994 tig0006451:-1895 None:intergenic
TCAAATGGTGATGATGATGG+TGG 0.690349 tig0006451:-1959 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GATGATAAAGATATGAAATA+GGG - tig0006451:1797-1816 None:intergenic 20.0%
! GGATGATAAAGATATGAAAT+AGG - tig0006451:1798-1817 None:intergenic 25.0%
! GATAAAGCTTATGAGATTTA+TGG + tig0006451:1837-1856 Msa1343480:CDS 25.0%
GAATTGAAATACAAAGCATG+AGG - tig0006451:1987-2006 None:intergenic 30.0%
ATTTATGGCTACAACACTGA+TGG + tig0006451:1852-1871 Msa1343480:CDS 35.0%
AGAAAATCATCAACGGAACA+AGG - tig0006451:1891-1910 None:intergenic 35.0%
GAGGTGAAGAAAATCATCAA+CGG - tig0006451:1898-1917 None:intergenic 35.0%
!!! ATTCTTTTTCAACTCGCCAA+CGG - tig0006451:1920-1939 None:intergenic 35.0%
! GAATCAAATGGTGATGATGA+TGG - tig0006451:1965-1984 None:intergenic 35.0%
ACAAAGCATGAGGAATCAAA+TGG - tig0006451:1977-1996 None:intergenic 35.0%
GAAGAACACTCTCAAGAAGA+TGG + tig0006451:1744-1763 Msa1343480:CDS 40.0%
TCAAGAAGACGCTTGAAAAG+AGG - tig0006451:1819-1838 None:intergenic 40.0%
! ATGATTTTCTTCACCTCCGT+TGG + tig0006451:1901-1920 Msa1343480:CDS 40.0%
!! TCAAATGGTGATGATGATGG+TGG - tig0006451:1962-1981 None:intergenic 40.0%
AACGGAACAAGGAAGCTTGA+GGG - tig0006451:1880-1899 None:intergenic 45.0%
!! TGATGGTGGTGATGGTGATA+GGG - tig0006451:1948-1967 None:intergenic 45.0%
!! ATGATGGTGGTGATGGTGAT+AGG - tig0006451:1949-1968 None:intergenic 45.0%
GGATGGCTAGCAGTTCAAGT+AGG + tig0006451:1714-1733 Msa1343480:CDS 50.0%
ACGGAACAAGGAAGCTTGAG+GGG - tig0006451:1879-1898 None:intergenic 50.0%
CAACGGAACAAGGAAGCTTG+AGG - tig0006451:1881-1900 None:intergenic 50.0%
!!! CTTTTTCAACTCGCCAACGG+AGG - tig0006451:1917-1936 None:intergenic 50.0%
!! GGTGATGATGATGGTGGTGA+TGG - tig0006451:1956-1975 None:intergenic 50.0%
!! GTGGTGATGGTGATAGGGTG+TGG - tig0006451:1943-1962 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
tig0006451 gene 1699 2013 1699 ID=Msa1343480;Name=Msa1343480
tig0006451 mRNA 1699 2013 1699 ID=Msa1343480-mRNA-1;Parent=Msa1343480;Name=Msa1343480-mRNA-1;_AED=0.08;_eAED=0.08;_QI=0|-1|0|1|-1|1|1|0|104
tig0006451 exon 1699 2013 1699 ID=Msa1343480-mRNA-1:exon:4178;Parent=Msa1343480-mRNA-1
tig0006451 CDS 1699 2013 1699 ID=Msa1343480-mRNA-1:cds;Parent=Msa1343480-mRNA-1
Gene Sequence

>Msa1343480

ATGAAGGTGAAGAAGGGATGGCTAGCAGTTCAAGTAGGTTCAGAAGAAGAACACTCTCAAGAAGATGGTGTAAGTGATTCTCAAAGATTTGTCATCCCTATTTCATATCTTTATCATCCTCTTTTCAAGCGTCTTCTTGATAAAGCTTATGAGATTTATGGCTACAACACTGATGGTCCCCTCAAGCTTCCTTGTTCCGTTGATGATTTTCTTCACCTCCGTTGGCGAGTTGAAAAAGAATCCACACCCTATCACCATCACCACCATCATCATCACCATTTGATTCCTCATGCTTTGTATTTCAATTCTTGTTGA
Protein sequence

>Msa1343480

MKVKKGWLAVQVGSEEEHSQEDGVSDSQRFVIPISYLYHPLFKRLLDKAYEIYGYNTDGPLKLPCSVDDFLHLRWRVEKESTPYHHHHHHHHHLIPHALYFNSC*