AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0179930

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0179930 MtrunA17_Chr1g0205861 71.053 114 27 2 8 121 12 119 9.53e-50 154
Msa0179930 MtrunA17_Chr1g0206781 43.182 88 45 1 8 95 7 89 6.11e-21 81.6
Msa0179930 MtrunA17_Chr1g0206771 52.113 71 34 0 9 79 13 83 7.74e-19 77.8
Msa0179930 MtrunA17_Chr1g0206771 51.429 70 34 0 11 80 94 163 4.62e-17 73.2
Msa0179930 MtrunA17_Chr1g0205811 44.737 76 42 0 5 80 7 82 1.31e-18 75.9
Msa0179930 MtrunA17_Chr8g0364231 47.368 76 40 0 5 80 35 110 1.36e-18 80.5
Msa0179930 MtrunA17_Chr5g0415031 49.315 73 37 0 8 80 39 111 3.37e-18 79.3
Msa0179930 MtrunA17_Chr1g0205821 43.750 80 45 0 1 80 88 167 1.23e-17 74.7
Msa0179930 MtrunA17_Chr1g0205821 48.649 74 38 0 7 80 8 81 4.46e-15 67.8
Msa0179930 MtrunA17_Chr6g0452001 43.333 90 44 2 8 97 59 141 1.50e-17 77.8
Msa0179930 MtrunA17_Chr1g0205801 50.725 69 34 0 12 80 12 80 3.06e-17 72.0
Msa0179930 MtrunA17_Chr7g0256011 46.377 69 37 0 12 80 16 84 4.98e-17 71.6
Msa0179930 MtrunA17_Chr3g0077891 43.182 88 45 2 2 84 89 176 2.11e-16 71.2
Msa0179930 MtrunA17_Chr3g0077861 48.485 66 33 1 11 75 89 154 1.99e-14 65.9
Msa0179930 MtrunA17_Chr6g0452021 39.744 78 47 0 8 85 39 116 2.29e-14 68.6
Msa0179930 MtrunA17_Chr3g0077941 41.860 86 45 2 4 84 90 175 5.10e-14 65.1
Msa0179930 MtrunA17_Chr8g0364021 41.975 81 45 1 1 79 31 111 6.19e-14 65.9
Msa0179930 MtrunA17_Chr3g0077911 48.485 66 33 1 11 75 89 154 1.68e-13 63.5
Msa0179930 MtrunA17_Chr7g0218911 43.548 62 35 0 19 80 5 66 3.41e-13 61.6
Msa0179930 MtrunA17_Chr4g0075971 43.939 66 37 0 15 80 175 240 5.39e-13 64.3
Msa0179930 MtrunA17_Chr4g0075971 43.836 73 41 0 8 80 85 157 4.40e-12 62.0
Msa0179930 MtrunA17_Chr4g0075971 40.476 84 43 2 11 90 11 91 3.42e-11 59.3
Msa0179930 MtrunA17_Chr1g0205831 44.118 68 38 0 12 79 2 69 1.13e-12 61.6
Msa0179930 MtrunA17_Chr1g0205831 45.455 66 36 0 15 80 76 141 2.75e-12 60.5
Msa0179930 MtrunA17_Chr4g0075861 45.205 73 40 0 8 80 85 157 2.85e-12 62.4
Msa0179930 MtrunA17_Chr4g0075861 43.939 66 37 0 15 80 175 240 3.08e-12 62.0
Msa0179930 MtrunA17_Chr3g0077881 40.000 80 47 1 2 80 89 168 1.34e-11 58.9
Msa0179930 MtrunA17_Chr3g0077881 36.145 83 52 1 12 93 8 90 7.43e-11 56.6
Msa0179930 MtrunA17_Chr1g0209201 44.262 61 33 1 19 79 23 82 1.38e-11 58.2
Msa0179930 MtrunA17_Chr2g0328701 41.667 84 42 2 11 90 28 108 2.74e-11 57.0
Msa0179930 MtrunA17_Chr7g0218891 42.029 69 38 1 13 79 186 254 3.76e-11 58.5
Msa0179930 MtrunA17_Chr7g0218891 43.750 64 34 1 13 74 14 77 8.52e-11 57.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0179930 AT1G24190.3 51.250 80 35 1 5 80 3 82 1.52e-20 86.7
Msa0179930 AT1G24190.2 51.250 80 35 1 5 80 3 82 1.68e-20 86.7
Msa0179930 AT1G24190.1 51.250 80 35 1 5 80 3 82 1.74e-20 86.3
Msa0179930 AT1G70060.2 52.055 73 35 0 8 80 10 82 4.80e-19 82.4
Msa0179930 AT1G70060.1 52.055 73 35 0 8 80 10 82 4.80e-19 82.4
Msa0179930 AT3G01320.2 46.575 73 39 0 8 80 53 125 2.18e-18 80.5
Msa0179930 AT3G01320.1 46.575 73 39 0 8 80 53 125 2.22e-18 80.5
Msa0179930 AT5G15020.2 44.000 75 42 0 8 82 48 122 2.55e-17 77.4
Msa0179930 AT5G15020.1 44.000 75 42 0 8 82 48 122 2.76e-17 77.4
Msa0179930 AT1G24200.1 36.937 111 61 3 1 109 1 104 7.80e-17 73.2
Msa0179930 AT1G70030.3 41.558 77 43 1 8 82 18 94 4.73e-15 67.0
Msa0179930 AT1G70030.1 34.951 103 62 2 8 105 7 109 6.08e-15 67.4
Msa0179930 AT1G59890.1 44.928 69 38 0 12 80 45 113 1.02e-14 70.1
Msa0179930 AT1G70030.2 41.558 77 43 1 8 82 18 94 1.03e-14 66.6
Msa0179930 AT1G59890.3 44.928 69 38 0 12 80 45 113 1.06e-14 69.7
Msa0179930 AT1G59890.2 44.928 69 38 0 12 80 45 113 1.06e-14 69.7
Msa0179930 AT1G59890.4 44.928 69 38 0 12 80 45 113 1.09e-14 69.7
Msa0179930 AT4G12020.5 46.667 75 39 1 6 80 235 308 1.24e-14 69.7
Msa0179930 AT4G12020.11 46.667 75 39 1 6 80 302 375 1.24e-14 69.7
Msa0179930 AT4G12020.10 46.667 75 39 1 6 80 302 375 1.24e-14 69.7
Msa0179930 AT4G12020.2 46.667 75 39 1 6 80 302 375 1.25e-14 69.7
Msa0179930 AT4G12020.6 46.667 75 39 1 6 80 302 375 1.29e-14 69.7
Msa0179930 AT4G12020.8 46.667 75 39 1 6 80 302 375 1.29e-14 69.7
Msa0179930 AT4G12020.3 46.667 75 39 1 6 80 302 375 1.30e-14 69.7
Msa0179930 AT4G12020.1 46.667 75 39 1 6 80 302 375 1.31e-14 69.7
Msa0179930 AT4G12020.9 46.667 75 39 1 6 80 302 375 1.31e-14 69.7
Msa0179930 AT4G12020.4 46.667 75 39 1 6 80 302 375 1.33e-14 69.7
Msa0179930 AT4G12020.7 46.667 75 39 1 6 80 302 375 1.34e-14 69.7
Msa0179930 AT5G15025.1 36.842 76 48 0 7 82 42 117 5.43e-14 64.3
Msa0179930 AT1G27250.1 37.037 81 51 0 9 89 18 98 8.09e-14 63.9
Msa0179930 AT1G24230.1 43.478 69 38 1 7 74 9 77 1.00e-11 60.5
Msa0179930 AT1G27280.1 35.714 70 45 0 9 78 78 147 2.27e-11 59.3
Msa0179930 AT1G10450.2 37.681 69 43 0 12 80 33 101 2.36e-11 60.5
Msa0179930 AT1G10450.1 37.681 69 43 0 12 80 33 101 2.36e-11 60.5
Msa0179930 AT1G10450.3 37.681 69 43 0 12 80 84 152 2.44e-11 60.1
Msa0179930 AT1G23810.1 42.188 64 37 0 9 72 106 169 3.81e-11 58.9
Msa0179930 AT1G27220.1 33.784 74 49 0 8 81 10 83 4.29e-11 57.8

Find 27 sgRNAs with CRISPR-Local

Find 26 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGATAAAATATTAGAGATTT+TGG 0.199052 1_4:-67623625 Msa0179930:CDS
TGAAAGTCCTAAGCGATTAC+AGG 0.315902 1_4:-67623875 Msa0179930:CDS
AGGATGGAGGAGCTGTTTAA+AGG 0.330709 1_4:-67623819 Msa0179930:CDS
AAGAACCCACCTGATCGAAT+AGG 0.409769 1_4:-67623699 Msa0179930:CDS
CTCTGGGCAATGCAGGATAA+AGG 0.410594 1_4:-67623987 None:intergenic
AAACGCTATTGCTTCTTCCT+TGG 0.423218 1_4:+67623953 None:intergenic
CAGTGATGACACTGGAGAAA+AGG 0.440953 1_4:-67623742 Msa0179930:CDS
TCACTGATTTGAGATGGCTT+TGG 0.444928 1_4:+67623759 None:intergenic
GGATGGAGGAGCTGTTTAAA+GGG 0.456905 1_4:-67623818 Msa0179930:CDS
AGAACCCACCTGATCGAATA+GGG 0.457483 1_4:-67623698 Msa0179930:CDS
ATTTGCGACCCTATTCGATC+AGG 0.474283 1_4:+67623690 None:intergenic
TTGAGATGGCTTTGGCGTAA+AGG 0.479351 1_4:+67623767 None:intergenic
AGTTAAACTTCTGTCTCAAA+AGG 0.482056 1_4:-67623649 Msa0179930:CDS
TGCGACCCTATTCGATCAGG+TGG 0.509774 1_4:+67623693 None:intergenic
GCTAAAAGAGTTGATATAGC+AGG 0.529069 1_4:-67623852 Msa0179930:CDS
GTGTCATCACTGATTTGAGA+TGG 0.558119 1_4:+67623753 None:intergenic
GAAAGTCCTAAGCGATTACA+GGG 0.564984 1_4:-67623874 Msa0179930:CDS
AGTTAAGTTTCAAGACAAGA+GGG 0.571152 1_4:-67623916 Msa0179930:CDS
AAGTTAAGTTTCAAGACAAG+AGG 0.577150 1_4:-67623917 Msa0179930:CDS
AGCAGGTGTGACAACAAGGA+TGG 0.585519 1_4:-67623835 Msa0179930:CDS
GCGACCCTATTCGATCAGGT+GGG 0.613931 1_4:+67623694 None:intergenic
ATATAGCAGGTGTGACAACA+AGG 0.623415 1_4:-67623839 Msa0179930:CDS
TCTCAAATCAGTGATGACAC+TGG 0.643527 1_4:-67623750 Msa0179930:CDS
GCAATGCAGGATAAAGGTGG+TGG 0.647014 1_4:-67623981 Msa0179930:CDS
AGGTGTGACAACAAGGATGG+AGG 0.648111 1_4:-67623832 Msa0179930:CDS
TAAAGGTGGTGGTGTAACCA+AGG 0.651615 1_4:-67623970 Msa0179930:CDS
TGGGCAATGCAGGATAAAGG+TGG 0.685630 1_4:-67623984 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGATAAAATATTAGAGATTT+TGG - chr1_4:67623958-67623977 Msa0179930:CDS 15.0%
!!! TAAAATATTAGAGATTTTGG+AGG - chr1_4:67623961-67623980 Msa0179930:CDS 20.0%
AAGTTAAGTTTCAAGACAAG+AGG - chr1_4:67623666-67623685 Msa0179930:CDS 30.0%
AGTTAAGTTTCAAGACAAGA+GGG - chr1_4:67623667-67623686 Msa0179930:CDS 30.0%
AGTTAAACTTCTGTCTCAAA+AGG - chr1_4:67623934-67623953 Msa0179930:CDS 30.0%
!! GCTAAAAGAGTTGATATAGC+AGG - chr1_4:67623731-67623750 Msa0179930:CDS 35.0%
AAACGCTATTGCTTCTTCCT+TGG + chr1_4:67623633-67623652 None:intergenic 40.0%
TGAAAGTCCTAAGCGATTAC+AGG - chr1_4:67623708-67623727 Msa0179930:CDS 40.0%
GAAAGTCCTAAGCGATTACA+GGG - chr1_4:67623709-67623728 Msa0179930:CDS 40.0%
! TTTTAGCCCTGTAATCGCTT+AGG + chr1_4:67623718-67623737 None:intergenic 40.0%
ATATAGCAGGTGTGACAACA+AGG - chr1_4:67623744-67623763 Msa0179930:CDS 40.0%
!! TCACTGATTTGAGATGGCTT+TGG + chr1_4:67623827-67623846 None:intergenic 40.0%
!! GTGTCATCACTGATTTGAGA+TGG + chr1_4:67623833-67623852 None:intergenic 40.0%
TCTCAAATCAGTGATGACAC+TGG - chr1_4:67623833-67623852 Msa0179930:CDS 40.0%
! TAAAGGTGGTGGTGTAACCA+AGG - chr1_4:67623613-67623632 Msa0179930:CDS 45.0%
AGGATGGAGGAGCTGTTTAA+AGG - chr1_4:67623764-67623783 Msa0179930:CDS 45.0%
GGATGGAGGAGCTGTTTAAA+GGG - chr1_4:67623765-67623784 Msa0179930:CDS 45.0%
!! TTGAGATGGCTTTGGCGTAA+AGG + chr1_4:67623819-67623838 None:intergenic 45.0%
CAGTGATGACACTGGAGAAA+AGG - chr1_4:67623841-67623860 Msa0179930:CDS 45.0%
AAGAACCCACCTGATCGAAT+AGG - chr1_4:67623884-67623903 Msa0179930:CDS 45.0%
AGAACCCACCTGATCGAATA+GGG - chr1_4:67623885-67623904 Msa0179930:CDS 45.0%
ATTTGCGACCCTATTCGATC+AGG + chr1_4:67623896-67623915 None:intergenic 45.0%
AGCAGGTGTGACAACAAGGA+TGG - chr1_4:67623748-67623767 Msa0179930:CDS 50.0%
AGGTGTGACAACAAGGATGG+AGG - chr1_4:67623751-67623770 Msa0179930:CDS 50.0%
GCGACCCTATTCGATCAGGT+GGG + chr1_4:67623892-67623911 None:intergenic 55.0%
TGCGACCCTATTCGATCAGG+TGG + chr1_4:67623893-67623912 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr1_4 gene 67623605 67624000 67623605 ID=Msa0179930;Name=Msa0179930
chr1_4 mRNA 67623605 67624000 67623605 ID=Msa0179930-mRNA-1;Parent=Msa0179930;Name=Msa0179930-mRNA-1;_AED=0.29;_eAED=0.29;_QI=0|-1|0|1|-1|1|1|0|131
chr1_4 exon 67623605 67624000 67623605 ID=Msa0179930-mRNA-1:exon:22305;Parent=Msa0179930-mRNA-1
chr1_4 CDS 67623605 67624000 67623605 ID=Msa0179930-mRNA-1:cds;Parent=Msa0179930-mRNA-1
Gene Sequence

>Msa0179930

ATGCAGGATAAAGGTGGTGGTGTAACCAAGGAAGAAGCAATAGCGTTTGTATGTGATGTAAAAGTTAAGTTTCAAGACAAGAGGGAAATGTATGATGAATTTTTGAAAGTCCTAAGCGATTACAGGGCTAAAAGAGTTGATATAGCAGGTGTGACAACAAGGATGGAGGAGCTGTTTAAAGGGCATTCAGATTTGATTTTGAAATTCAAATCCTTTACGCCAAAGCCATCTCAAATCAGTGATGACACTGGAGAAAAGGAAGAAGACACTGATGAACAGAAGAACCCACCTGATCGAATAGGGTCGCAAATTCAACTTATATCTCAAGAAGTTAAACTTCTGTCTCAAAAGGCTGATAAAATATTAGAGATTTTGGAGGAGAAGAAGCAAGCATAA
Protein sequence

>Msa0179930

MQDKGGGVTKEEAIAFVCDVKVKFQDKREMYDEFLKVLSDYRAKRVDIAGVTTRMEELFKGHSDLILKFKSFTPKPSQISDDTGEKEEDTDEQKNPPDRIGSQIQLISQEVKLLSQKADKILEILEEKKQA*