AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1232060

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1232060 MtrunA17_Chr8g0341161 87.387 111 14 0 1 111 107 217 1.34e-65 197
Msa1232060 MtrunA17_Chr8g0341211 78.378 111 24 0 1 111 31 141 5.46e-60 180
Msa1232060 MtrunA17_Chr8g0347671 72.072 111 31 0 1 111 115 225 1.64e-52 164
Msa1232060 MtrunA17_Chr8g0347661 73.874 111 29 0 1 111 766 876 7.48e-52 174
Msa1232060 MtrunA17_Chr8g0341121 68.468 111 35 0 1 111 52 162 3.19e-51 159
Msa1232060 MtrunA17_Chr8g0340931 71.171 111 32 0 1 111 760 870 9.88e-51 171
Msa1232060 MtrunA17_Chr8g0341251 70.000 110 33 0 1 110 222 331 2.08e-48 157
Msa1232060 MtrunA17_Chr8g0341101 68.224 107 34 0 1 107 811 917 2.00e-47 162
Msa1232060 MtrunA17_Chr8g0340911 68.468 111 35 0 1 111 760 870 4.31e-47 160
Msa1232060 MtrunA17_Chr8g0341151 67.290 107 35 0 1 107 754 860 1.47e-46 159
Msa1232060 MtrunA17_Chr8g0340871 66.964 112 36 1 1 111 769 880 1.22e-44 154
Msa1232060 MtrunA17_Chr8g0340881 65.766 111 38 0 1 111 765 875 1.95e-44 153
Msa1232060 MtrunA17_Chr8g0358831 82.143 84 15 0 1 84 728 811 2.47e-44 152
Msa1232060 MtrunA17_Chr8g0341051 62.162 111 42 0 1 111 128 238 1.08e-43 142
Msa1232060 MtrunA17_Chr8g0341081 61.261 111 43 0 1 111 221 331 4.63e-43 143
Msa1232060 MtrunA17_Chr8g0341011 64.865 111 39 0 1 111 764 874 5.04e-43 149
Msa1232060 MtrunA17_Chr8g0341111 60.360 111 44 0 1 111 674 784 4.95e-41 143
Msa1232060 MtrunA17_Chr8g0340891 63.393 112 38 2 1 111 758 867 4.14e-38 135
Msa1232060 MtrunA17_Chr8g0340921 67.568 74 24 0 38 111 2 75 2.37e-30 103
Msa1232060 MtrunA17_Chr5g0423891 46.341 82 44 0 1 82 358 439 1.12e-20 85.5
Msa1232060 MtrunA17_Chr8g0341361 37.113 97 60 1 1 97 384 479 8.81e-19 80.1
Msa1232060 MtrunA17_Chr8g0341341 36.842 114 66 4 1 109 118 230 2.06e-17 74.3
Msa1232060 MtrunA17_Chr6g0487571 33.884 121 69 2 1 111 777 896 1.36e-16 73.9
Msa1232060 MtrunA17_Chr2g0330591 38.095 84 51 1 1 84 768 850 1.27e-15 71.2
Msa1232060 MtrunA17_Chr3g0145591 41.975 81 45 1 1 79 344 424 2.40e-14 67.4
Msa1232060 MtrunA17_Chr1g0181731 29.204 113 74 3 1 111 793 901 2.89e-11 58.9
Msa1232060 MtrunA17_Chr4g0036981 42.308 78 44 1 1 77 498 575 3.03e-11 58.9
Msa1232060 MtrunA17_Chr7g0263591 34.884 86 52 2 1 83 799 883 6.47e-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
Msa1232060 AT3G46410.1 36.111 108 67 1 6 111 183 290 8.13e-20 82.0
Msa1232060 AT3G21340.1 46.250 80 43 0 2 81 787 866 1.01e-19 83.2
Msa1232060 AT3G45920.1 39.130 92 54 1 2 91 76 167 1.36e-19 79.7
Msa1232060 AT3G46370.2 37.719 114 64 3 2 111 682 792 1.57e-19 82.8
Msa1232060 AT3G46370.1 37.719 114 64 3 2 111 682 792 1.57e-19 82.8
Msa1232060 AT4G29180.3 37.113 97 60 1 1 96 771 867 3.35e-19 82.0
Msa1232060 AT4G29180.1 37.113 97 60 1 1 96 772 868 3.35e-19 82.0
Msa1232060 AT4G29180.2 37.113 97 60 1 1 96 774 870 3.35e-19 82.0
Msa1232060 AT2G29000.1 37.864 103 59 2 2 104 760 857 3.40e-19 82.0
Msa1232060 AT3G46400.1 38.261 115 64 4 1 111 771 882 4.97e-19 81.3
Msa1232060 AT4G29450.1 42.353 85 48 1 1 84 772 856 1.20e-18 80.1
Msa1232060 AT1G51830.1 37.719 114 65 2 2 111 581 692 1.33e-18 80.1
Msa1232060 AT1G51830.2 37.719 114 65 2 2 111 588 699 1.33e-18 80.1
Msa1232060 AT3G46420.1 41.975 81 46 1 1 81 726 805 1.67e-18 79.7
Msa1232060 AT3G46330.2 39.130 92 54 1 2 91 738 829 1.75e-18 79.7
Msa1232060 AT3G46330.1 39.130 92 54 1 2 91 762 853 1.86e-18 79.7
Msa1232060 AT5G59670.2 35.965 114 65 3 1 111 759 867 2.64e-18 79.3
Msa1232060 AT5G59670.1 35.965 114 65 3 1 111 759 867 2.64e-18 79.3
Msa1232060 AT1G51800.1 39.535 86 51 1 6 91 784 868 2.86e-18 79.3
Msa1232060 AT5G59680.1 41.818 110 58 2 6 111 779 886 4.97e-18 78.6
Msa1232060 AT2G04300.1 41.250 80 47 0 2 81 736 815 5.26e-18 78.6
Msa1232060 AT2G04300.2 41.250 80 47 0 2 81 777 856 5.27e-18 78.6
Msa1232060 AT3G46355.1 40.506 79 47 0 2 80 179 257 1.03e-17 76.6
Msa1232060 AT2G28970.1 34.783 115 68 3 1 111 674 785 1.14e-17 77.4
Msa1232060 AT2G28990.2 41.772 79 46 0 2 80 772 850 1.53e-17 77.0
Msa1232060 AT2G28990.1 41.772 79 46 0 2 80 772 850 1.53e-17 77.0
Msa1232060 AT2G28970.2 34.783 115 68 3 1 111 639 750 1.67e-17 77.0
Msa1232060 AT1G51890.2 33.929 112 72 1 2 111 786 897 1.88e-17 77.0
Msa1232060 AT1G51890.1 33.929 112 72 1 2 111 764 875 1.99e-17 76.6
Msa1232060 AT1G51890.4 33.929 112 72 1 2 111 700 811 2.32e-17 76.6
Msa1232060 AT1G51890.5 33.929 112 72 1 2 111 492 603 2.77e-17 76.3
Msa1232060 AT1G51880.1 35.052 97 58 1 2 98 760 851 3.18e-17 76.3
Msa1232060 AT1G51880.3 35.052 97 58 1 2 98 786 877 3.21e-17 76.3
Msa1232060 AT1G51880.2 35.052 97 58 1 2 98 778 869 3.31e-17 76.3
Msa1232060 AT1G49100.1 40.244 82 49 0 2 83 776 857 3.64e-17 75.9
Msa1232060 AT1G51850.1 39.604 101 58 2 1 101 753 850 4.59e-17 75.9
Msa1232060 AT1G51850.2 39.604 101 58 2 1 101 773 870 4.83e-17 75.9
Msa1232060 AT1G07560.1 42.500 80 39 1 17 96 777 849 6.71e-17 75.5
Msa1232060 AT2G28960.2 40.230 87 51 1 1 87 768 853 6.92e-17 75.1
Msa1232060 AT1G51810.1 43.421 76 43 0 6 81 649 724 1.09e-16 74.7
Msa1232060 AT2G28960.1 40.230 87 51 1 1 87 636 721 1.15e-16 74.7
Msa1232060 AT4G20450.1 41.772 79 46 0 2 80 786 864 1.18e-16 74.7
Msa1232060 AT4G20450.2 41.772 79 46 0 2 80 771 849 1.34e-16 74.3
Msa1232060 AT1G07550.1 42.500 80 45 1 1 80 753 831 1.46e-16 74.3
Msa1232060 AT3G46340.1 37.975 79 49 0 2 80 781 859 2.52e-16 73.6
Msa1232060 AT5G59660.3 47.761 67 35 0 14 80 692 758 2.74e-16 73.6
Msa1232060 AT5G59660.2 47.761 67 35 0 14 80 667 733 2.76e-16 73.6
Msa1232060 AT5G59660.1 47.761 67 35 0 14 80 689 755 2.77e-16 73.6
Msa1232060 AT5G59650.2 36.937 111 68 2 2 111 782 891 2.83e-16 73.6
Msa1232060 AT5G59650.1 36.937 111 68 2 2 111 774 883 3.18e-16 73.6
Msa1232060 AT1G51860.1 31.776 107 68 1 2 108 778 879 3.18e-16 73.6
Msa1232060 AT1G51860.2 31.776 107 68 1 2 108 634 735 4.86e-16 72.8
Msa1232060 AT1G51820.1 43.210 81 45 1 1 81 773 852 6.34e-16 72.4
Msa1232060 AT1G51910.1 38.372 86 53 0 2 87 765 850 7.40e-16 72.4
Msa1232060 AT5G16900.1 39.241 79 48 0 2 80 768 846 9.99e-16 72.0
Msa1232060 AT5G16900.3 39.241 79 48 0 2 80 768 846 9.99e-16 72.0
Msa1232060 AT1G51790.3 35.644 101 61 2 1 98 770 869 1.03e-15 72.0
Msa1232060 AT1G51790.1 35.644 101 61 2 1 98 770 869 1.03e-15 72.0
Msa1232060 AT1G51790.2 35.644 101 61 2 1 98 822 921 1.36e-15 71.6
Msa1232060 AT5G16900.4 39.241 79 48 0 2 80 582 660 1.49e-15 71.2
Msa1232060 AT1G51820.2 43.210 81 45 1 1 81 511 590 1.49e-15 71.2
Msa1232060 AT1G51805.1 42.500 80 45 1 1 80 772 850 1.88e-15 71.2
Msa1232060 AT1G51805.2 42.500 80 45 1 1 80 748 826 2.09e-15 70.9
Msa1232060 AT1G51870.1 34.884 86 56 0 2 87 725 810 3.39e-15 70.5
Msa1232060 AT1G51870.2 34.884 86 56 0 2 87 777 862 3.94e-15 70.1
Msa1232060 AT2G14510.1 35.802 81 51 1 2 82 758 837 6.33e-15 69.7
Msa1232060 AT2G14510.2 35.802 81 51 1 2 82 766 845 7.40e-15 69.3
Msa1232060 AT4G29990.1 32.743 113 70 2 1 111 767 875 8.90e-15 69.3
Msa1232060 AT2G19210.1 40.964 83 47 1 1 81 769 851 1.31e-14 68.9
Msa1232060 AT1G05700.2 35.870 92 53 2 1 91 794 880 3.15e-14 67.8
Msa1232060 AT1G05700.1 35.870 92 53 2 1 91 763 849 3.78e-14 67.4
Msa1232060 AT2G19190.1 31.532 111 74 1 1 111 767 875 7.05e-14 66.6
Msa1232060 AT2G14440.1 34.146 82 53 1 1 82 758 838 2.49e-13 65.1
Msa1232060 AT1G51620.1 41.379 87 49 2 6 92 171 255 3.62e-13 63.9
Msa1232060 AT1G51620.2 41.379 87 49 2 6 92 245 329 4.83e-13 63.9
Msa1232060 AT1G72540.1 34.259 108 64 4 1 106 284 386 8.95e-13 63.5
Msa1232060 AT3G28690.1 34.091 88 54 3 1 85 229 315 7.09e-12 60.8
Msa1232060 AT3G28690.2 34.091 88 54 3 1 85 329 415 9.50e-12 60.5
Msa1232060 AT3G28690.3 34.091 88 54 3 1 85 278 364 1.10e-11 60.5
Msa1232060 AT2G19230.2 40.741 81 47 1 1 80 762 842 1.76e-11 59.7
Msa1232060 AT2G19230.1 40.741 81 47 1 1 80 763 843 2.09e-11 59.7

Find 24 sgRNAs with CRISPR-Local

Find 24 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATATCTCCACCTTCAATTA+TGG 0.175023 8_2:-8337917 None:intergenic
CCCTCAGTTCTGCCAGTATT+TGG 0.212681 8_2:-8338056 None:intergenic
AAGATATTTCAGAGAAATAA+TGG 0.250707 8_2:+8338093 Msa1232060:CDS
CACTAGACCTAGAGATGAAT+TGG 0.322019 8_2:+8338119 Msa1232060:CDS
CTAAATTTACCCTCCAACTT+TGG 0.322162 8_2:-8337955 None:intergenic
TCTGGCCTTTCTGCTGCATT+TGG 0.336131 8_2:-8338027 None:intergenic
GCCAGTATTTGGCTCATGTC+TGG 0.344936 8_2:-8338045 None:intergenic
ATATCTCCACCTTCAATTAT+GGG 0.407581 8_2:-8337916 None:intergenic
GCCAGACATGAGCCAAATAC+TGG 0.414443 8_2:+8338044 Msa1232060:CDS
TCAGAAACCATTCCTTTAGC+TGG 0.423733 8_2:+8338159 Msa1232060:CDS
AAAACATCCACATACTTCAA+TGG 0.431037 8_2:+8337887 Msa1232060:CDS
ATTCTATTTGTGTTGATCAC+TGG 0.443566 8_2:+8337835 None:intergenic
AAACATCCACATACTTCAAT+GGG 0.480868 8_2:+8337888 Msa1232060:CDS
TGGGTTATTCCCATAATTGA+AGG 0.492356 8_2:+8337907 Msa1232060:CDS
CAAGCAATAGTAAGAGCAGC+TGG 0.501598 8_2:+8337862 Msa1232060:CDS
AATGGTGGTTATCCAGCTAA+AGG 0.503157 8_2:-8338171 None:intergenic
ACAGAAACCAATTCATCTCT+AGG 0.516553 8_2:-8338126 None:intergenic
CCAAATACTGGCAGAACTGA+GGG 0.579747 8_2:+8338056 Msa1232060:CDS
GCCAAATACTGGCAGAACTG+AGG 0.583488 8_2:+8338055 Msa1232060:CDS
TTTCACCAAATGCAGCAGAA+AGG 0.593232 8_2:+8338022 Msa1232060:CDS
GTTATTCCCATAATTGAAGG+TGG 0.596168 8_2:+8337910 Msa1232060:CDS
TGGTTATCCAGCTAAAGGAA+TGG 0.607493 8_2:-8338166 None:intergenic
GAATAACCCATTGAAGTATG+TGG 0.615328 8_2:-8337894 None:intergenic
ATTTGGTGAAATGCATGACA+TGG 0.700462 8_2:-8338010 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAGATATTTCAGAGAAATAA+TGG + chr8_2:8338093-8338112 Msa1232060:CDS 20.0%
AAAACATCCACATACTTCAA+TGG + chr8_2:8337887-8337906 Msa1232060:CDS 30.0%
AAACATCCACATACTTCAAT+GGG + chr8_2:8337888-8337907 Msa1232060:CDS 30.0%
ATATCTCCACCTTCAATTAT+GGG - chr8_2:8337919-8337938 None:intergenic 30.0%
AATATCTCCACCTTCAATTA+TGG - chr8_2:8337920-8337939 None:intergenic 30.0%
! GAAACTTTTTGATCCAAAGT+TGG + chr8_2:8337942-8337961 Msa1232060:CDS 30.0%
GAATAACCCATTGAAGTATG+TGG - chr8_2:8337897-8337916 None:intergenic 35.0%
TGGGTTATTCCCATAATTGA+AGG + chr8_2:8337907-8337926 Msa1232060:CDS 35.0%
GTTATTCCCATAATTGAAGG+TGG + chr8_2:8337910-8337929 Msa1232060:CDS 35.0%
! ACTTTTTGATCCAAAGTTGG+AGG + chr8_2:8337945-8337964 Msa1232060:CDS 35.0%
! CTTTTTGATCCAAAGTTGGA+GGG + chr8_2:8337946-8337965 Msa1232060:CDS 35.0%
CTAAATTTACCCTCCAACTT+TGG - chr8_2:8337958-8337977 None:intergenic 35.0%
! ATTTGGTGAAATGCATGACA+TGG - chr8_2:8338013-8338032 None:intergenic 35.0%
ACAGAAACCAATTCATCTCT+AGG - chr8_2:8338129-8338148 None:intergenic 35.0%
TTTCACCAAATGCAGCAGAA+AGG + chr8_2:8338022-8338041 Msa1232060:CDS 40.0%
CACTAGACCTAGAGATGAAT+TGG + chr8_2:8338119-8338138 Msa1232060:CDS 40.0%
TCAGAAACCATTCCTTTAGC+TGG + chr8_2:8338159-8338178 Msa1232060:CDS 40.0%
CAAGCAATAGTAAGAGCAGC+TGG + chr8_2:8337862-8337881 Msa1232060:CDS 45.0%
CCAAATACTGGCAGAACTGA+GGG + chr8_2:8338056-8338075 Msa1232060:CDS 45.0%
! TCTGGCCTTTCTGCTGCATT+TGG - chr8_2:8338030-8338049 None:intergenic 50.0%
GCCAGACATGAGCCAAATAC+TGG + chr8_2:8338044-8338063 Msa1232060:CDS 50.0%
! GCCAGTATTTGGCTCATGTC+TGG - chr8_2:8338048-8338067 None:intergenic 50.0%
GCCAAATACTGGCAGAACTG+AGG + chr8_2:8338055-8338074 Msa1232060:CDS 50.0%
CCCTCAGTTCTGCCAGTATT+TGG - chr8_2:8338059-8338078 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr8_2 gene 8337847 8338185 8337847 ID=Msa1232060;Name=Msa1232060
chr8_2 mRNA 8337847 8338185 8337847 ID=Msa1232060-mRNA-1;Parent=Msa1232060;Name=Msa1232060-mRNA-1;_AED=0.49;_eAED=0.49;_QI=0|-1|0|1|-1|1|1|0|112
chr8_2 exon 8337847 8338185 8337847 ID=Msa1232060-mRNA-1:exon:3230;Parent=Msa1232060-mRNA-1
chr8_2 CDS 8337847 8338185 8337847 ID=Msa1232060-mRNA-1:cds;Parent=Msa1232060-mRNA-1
Gene Sequence

>Msa1232060

TTGATCACTGGTCGTCAAGCAATAGTAAGAGCAGCTGGAGAAAACATCCACATACTTCAATGGGTTATTCCCATAATTGAAGGTGGAGATATTCAGAAACTTTTTGATCCAAAGTTGGAGGGTAAATTTAGCATCAATTCAGCACGAAAAGCTGTAGAGATTGCCATGTCATGCATTTCACCAAATGCAGCAGAAAGGCCAGACATGAGCCAAATACTGGCAGAACTGAGGGAGTGTCTATCTTTGAAGATATTTCAGAGAAATAATGGAAACACTAGACCTAGAGATGAATTGGTTTCTGTAGCTACTGTATCAGAAACCATTCCTTTAGCTGGATAA
Protein sequence

>Msa1232060

LITGRQAIVRAAGENIHILQWVIPIIEGGDIQKLFDPKLEGKFSINSARKAVEIAMSCISPNAAERPDMSQILAELRECLSLKIFQRNNGNTRPRDELVSVATVSETIPLAG*