AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0252790

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0252790 MtrunA17_Chr2g0311601 98.305 59 1 0 1 59 1 59 2.64e-40 130
Msa0252790 MtrunA17_Chr4g0043421 83.929 56 9 0 4 59 6 61 1.41e-32 111
Msa0252790 MtrunA17_Chr5g0437571 76.471 51 12 0 9 59 2 52 4.65e-25 91.7
Msa0252790 MtrunA17_Chr3g0114061 76.471 51 12 0 9 59 4 54 4.89e-25 91.7
Msa0252790 MtrunA17_Chr3g0106101 72.917 48 13 0 12 59 6 53 1.34e-23 88.2
Msa0252790 MtrunA17_Chr6g0449641 72.000 50 14 0 10 59 6 55 1.65e-23 87.0
Msa0252790 MtrunA17_Chr2g0326041 62.069 58 22 0 8 65 28 85 4.84e-23 84.3
Msa0252790 MtrunA17_Chr6g0449651 72.000 50 14 0 10 59 64 113 8.14e-23 87.0
Msa0252790 MtrunA17_Chr3g0129071 72.000 50 14 0 9 58 43 92 7.19e-22 85.1
Msa0252790 MtrunA17_Chr5g0438091 70.000 50 15 0 9 58 35 84 9.23e-22 84.0
Msa0252790 MtrunA17_Chr7g0227511 70.000 50 15 0 10 59 8 57 1.07e-21 83.2
Msa0252790 MtrunA17_Chr5g0402611 70.213 47 14 0 12 58 7 53 1.25e-21 85.9
Msa0252790 MtrunA17_Chr5g0432451 63.636 55 20 0 4 58 34 88 1.69e-21 84.0
Msa0252790 MtrunA17_Chr4g0058651 70.833 48 14 0 12 59 10 57 1.14e-20 80.9
Msa0252790 MtrunA17_Chr8g0353981 49.333 75 32 1 10 78 4 78 3.54e-20 80.5
Msa0252790 MtrunA17_Chr3g0117121 70.833 48 14 0 12 59 9 56 4.17e-20 79.7
Msa0252790 MtrunA17_Chr3g0115431 66.667 48 16 0 12 59 8 55 1.36e-19 79.0
Msa0252790 MtrunA17_Chr7g0260971 58.929 56 22 1 4 58 5 60 2.46e-19 78.2
Msa0252790 MtrunA17_Chr5g0444351 67.391 46 15 0 14 59 6 51 3.34e-19 76.3
Msa0252790 MtrunA17_Chr7g0225111 64.583 48 17 0 12 59 4 51 4.72e-19 75.1
Msa0252790 MtrunA17_Chr3g0097221 60.417 48 19 0 12 59 6 53 1.08e-18 77.8
Msa0252790 MtrunA17_Chr4g0030001 68.000 50 15 1 11 59 22 71 1.87e-18 75.5
Msa0252790 MtrunA17_Chr3g0113891 61.111 54 21 0 5 58 6 59 4.45e-18 74.3
Msa0252790 MtrunA17_Chr6g0452671 55.556 54 23 1 10 63 8 60 4.64e-18 74.7
Msa0252790 MtrunA17_Chr5g0437401 59.259 54 22 0 5 58 3 56 1.36e-17 72.8
Msa0252790 MtrunA17_Chr6g0452661 60.870 46 18 0 14 59 10 55 1.83e-17 73.9
Msa0252790 MtrunA17_Chr4g0059901 56.604 53 23 0 7 59 4 56 8.91e-17 72.4
Msa0252790 MtrunA17_Chr8g0351721 55.172 58 25 1 2 58 7 64 2.07e-16 70.5
Msa0252790 MtrunA17_Chr1g0184281 50.877 57 27 1 3 58 5 61 3.68e-16 69.7
Msa0252790 MtrunA17_Chr1g0200201 63.043 46 17 0 14 59 73 118 9.89e-16 68.9
Msa0252790 MtrunA17_Chr6g0460951 59.184 49 19 1 11 58 38 86 1.21e-15 68.6
Msa0252790 MtrunA17_Chr6g0452691 58.696 46 19 0 14 59 10 55 1.58e-15 67.8
Msa0252790 MtrunA17_Chr8g0342351 53.571 56 22 1 10 65 9 60 2.29e-15 68.6
Msa0252790 MtrunA17_Chr5g0435641 56.863 51 21 1 9 58 3 53 2.86e-15 67.0
Msa0252790 MtrunA17_Chr7g0261031 54.902 51 22 1 9 58 4 54 6.90e-15 66.6
Msa0252790 MtrunA17_Chr8g0351701 58.333 48 19 1 13 59 23 70 1.22e-14 66.2
Msa0252790 MtrunA17_Chr7g0245871 59.574 47 18 1 13 58 27 73 1.68e-14 65.9
Msa0252790 MtrunA17_Chr8g0374581 55.769 52 22 1 11 61 6 57 2.54e-14 65.1
Msa0252790 MtrunA17_Chr8g0374601 53.061 49 23 0 11 59 24 72 2.77e-14 65.9
Msa0252790 MtrunA17_Chr4g0040831 43.396 53 30 0 7 59 9 61 2.81e-14 64.7
Msa0252790 MtrunA17_Chr1g0184271 57.447 47 19 1 13 58 12 58 2.94e-14 65.1
Msa0252790 MtrunA17_Chr8g0374591 53.061 49 23 0 11 59 6 54 4.48e-14 62.8
Msa0252790 MtrunA17_Chr5g0439111 53.333 45 21 0 14 58 10 54 6.14e-14 64.3
Msa0252790 MtrunA17_Chr4g0055441 53.704 54 24 1 14 67 3 55 2.29e-13 61.6
Msa0252790 MtrunA17_Chr2g0330201 45.098 51 28 0 9 59 15 65 3.43e-13 62.8
Msa0252790 MtrunA17_Chr6g0460941 51.020 49 23 1 13 60 7 55 1.63e-12 57.8
Msa0252790 MtrunA17_Chr7g0245861 54.000 50 20 2 12 58 11 60 1.66e-11 56.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0252790 AT1G31320.1 79.661 59 12 0 1 59 1 59 7.95e-32 109
Msa0252790 AT2G30130.1 83.333 48 8 0 12 59 7 54 1.30e-25 94.4
Msa0252790 AT1G16530.1 73.770 61 14 2 1 59 1 61 1.34e-25 93.6
Msa0252790 AT2G40470.2 75.510 49 12 0 10 58 17 65 6.78e-23 87.4
Msa0252790 AT2G40470.1 53.947 76 29 1 9 78 41 116 9.44e-23 87.8
Msa0252790 AT2G30340.1 68.519 54 17 0 5 58 44 97 1.99e-22 87.8
Msa0252790 AT2G30340.2 68.519 54 17 0 5 58 45 98 2.00e-22 87.8
Msa0252790 AT3G27650.1 72.000 50 14 0 10 59 36 85 2.41e-22 85.1
Msa0252790 AT1G65620.1 70.000 50 15 0 10 59 6 55 2.13e-21 83.6
Msa0252790 AT1G65620.4 70.000 50 15 0 10 59 6 55 2.13e-21 83.6
Msa0252790 AT1G65620.3 70.000 50 15 0 10 59 6 55 2.13e-21 83.6
Msa0252790 AT1G65620.5 70.000 50 15 0 10 59 6 55 2.13e-21 83.6
Msa0252790 AT1G65620.2 70.000 50 15 0 10 59 6 55 2.13e-21 83.6
Msa0252790 AT5G63090.4 72.917 48 13 0 12 59 10 57 2.43e-21 83.2
Msa0252790 AT5G63090.3 72.917 48 13 0 12 59 10 57 2.43e-21 83.2
Msa0252790 AT5G63090.2 72.917 48 13 0 12 59 10 57 2.43e-21 83.2
Msa0252790 AT5G63090.1 72.917 48 13 0 12 59 10 57 2.43e-21 83.2
Msa0252790 AT5G66870.1 72.340 47 13 0 12 58 6 52 3.30e-21 85.1
Msa0252790 AT3G26660.1 68.627 51 14 1 11 59 1 51 1.69e-20 79.3
Msa0252790 AT3G26620.1 71.739 46 13 0 14 59 6 51 1.91e-20 79.0
Msa0252790 AT2G23660.2 68.085 47 15 0 12 58 4 50 3.77e-19 79.7
Msa0252790 AT2G23660.3 68.085 47 15 0 12 58 4 50 3.77e-19 79.7
Msa0252790 AT2G23660.1 68.085 47 15 0 12 58 4 50 3.77e-19 79.7
Msa0252790 AT2G42430.1 58.182 55 22 1 5 58 7 61 9.04e-19 77.8
Msa0252790 AT1G07900.1 65.306 49 17 0 11 59 31 79 9.25e-19 76.6
Msa0252790 AT2G28500.1 65.306 49 17 0 11 59 53 101 1.48e-18 77.0
Msa0252790 AT3G47870.1 54.717 53 24 0 7 59 30 82 1.50e-16 72.8
Msa0252790 AT3G11090.1 43.750 80 39 1 5 78 3 82 1.66e-16 70.1
Msa0252790 AT3G03760.1 57.143 49 20 1 12 59 50 98 3.80e-16 71.2
Msa0252790 AT4G00210.1 56.364 55 23 1 5 58 3 57 1.72e-15 68.6
Msa0252790 AT2G42440.1 56.863 51 21 1 9 58 3 53 2.00e-15 68.9
Msa0252790 AT3G50510.1 57.447 47 20 0 12 58 11 57 2.01e-15 68.2
Msa0252790 AT3G50510.2 57.447 47 20 0 12 58 11 57 2.01e-15 68.2
Msa0252790 AT5G06080.1 58.333 48 19 1 12 58 6 53 7.04e-15 66.2
Msa0252790 AT1G72980.1 40.000 85 44 2 9 87 9 92 8.29e-15 66.6
Msa0252790 AT3G58190.1 59.574 47 18 1 13 58 11 57 1.23e-14 66.2
Msa0252790 AT2G45410.1 63.636 44 15 1 16 58 19 62 1.43e-13 63.2
Msa0252790 AT2G31310.1 52.941 51 23 1 9 58 3 53 1.64e-13 62.8
Msa0252790 AT3G13850.1 54.348 46 21 0 14 59 37 82 3.69e-13 62.8
Msa0252790 AT1G06280.1 48.936 47 24 0 14 60 25 71 6.27e-13 61.6
Msa0252790 AT2G19820.1 37.662 77 48 0 3 79 2 78 2.08e-12 58.5
Msa0252790 AT4G00220.1 56.818 44 18 1 16 58 20 63 5.31e-12 59.3
Msa0252790 AT2G45420.1 56.818 44 18 1 16 58 40 83 1.39e-11 58.5

Find 16 sgRNAs with CRISPR-Local

Find 18 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCTGATGAACCTCACAAATT+TGG 0.273735 2_2:-44379049 Msa0252790:CDS
GGTTCATCAGCTGGAAAATA+TGG 0.335863 2_2:+44379061 None:intergenic
ATGTAAACGATTGGAATATC+AGG 0.364761 2_2:+44378923 None:intergenic
CAATGTGAACAAAATGTTAC+AGG 0.368869 2_2:-44378999 Msa0252790:CDS
GAAGGATGGTGGTAGAAAAC+AGG 0.392084 2_2:-44379152 Msa0252790:CDS
GATGATAACATGATAGAGAT+AGG 0.433930 2_2:+44378947 None:intergenic
CTGCATGCAAGCTTCTTAGA+AGG 0.457783 2_2:-44379111 Msa0252790:CDS
ATAATTATCATGTAAACGAT+TGG 0.500549 2_2:+44378914 None:intergenic
AATTTGTGAGGTTCATCAGC+TGG 0.500821 2_2:+44379052 None:intergenic
TGATAGAGATAGGAAAGATT+AGG 0.504367 2_2:+44378957 None:intergenic
TCGTTTACATGATAATTATG+TGG 0.531701 2_2:-44378910 Msa0252790:CDS
TGGAGGAACATGAAGGATGG+TGG 0.550713 2_2:-44379163 None:intergenic
AATTGGAGGAACATGAAGGA+TGG 0.564311 2_2:-44379166 None:intergenic
AGAAGCTTGCATGCAGCACA+TGG 0.590179 2_2:+44379118 None:intergenic
TGGACACTGCCAAATTTGTG+AGG 0.657276 2_2:+44379040 None:intergenic
AAGGATGGTGGTAGAAAACA+GGG 0.667923 2_2:-44379151 Msa0252790:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAATTATCATGTAAACGAT+TGG + chr2_2:44379150-44379169 None:intergenic 20.0%
! TCGTTTACATGATAATTATG+TGG - chr2_2:44379151-44379170 Msa0252790:CDS 25.0%
CAATGTGAACAAAATGTTAC+AGG - chr2_2:44379062-44379081 Msa0252790:CDS 30.0%
TGATAGAGATAGGAAAGATT+AGG + chr2_2:44379107-44379126 None:intergenic 30.0%
GATGATAACATGATAGAGAT+AGG + chr2_2:44379117-44379136 None:intergenic 30.0%
ATGTAAACGATTGGAATATC+AGG + chr2_2:44379141-44379160 None:intergenic 30.0%
! AAGGATGGTGGTAGAAAACA+GGG - chr2_2:44378910-44378929 Msa0252790:CDS 40.0%
GGTTCATCAGCTGGAAAATA+TGG + chr2_2:44379003-44379022 None:intergenic 40.0%
AATTTGTGAGGTTCATCAGC+TGG + chr2_2:44379012-44379031 None:intergenic 40.0%
GCTGATGAACCTCACAAATT+TGG - chr2_2:44379012-44379031 Msa0252790:CDS 40.0%
! GCAGTGTCCACAAGATTTTT+GGG - chr2_2:44379034-44379053 Msa0252790:CDS 40.0%
! CAGTGTCCACAAGATTTTTG+GGG - chr2_2:44379035-44379054 Msa0252790:CDS 40.0%
! GAAGGATGGTGGTAGAAAAC+AGG - chr2_2:44378909-44378928 Msa0252790:CDS 45.0%
CTGCATGCAAGCTTCTTAGA+AGG - chr2_2:44378950-44378969 Msa0252790:CDS 45.0%
TGGACACTGCCAAATTTGTG+AGG + chr2_2:44379024-44379043 None:intergenic 45.0%
! GGCAGTGTCCACAAGATTTT+TGG - chr2_2:44379033-44379052 Msa0252790:CDS 45.0%
TGCTAGCCCCAAAAATCTTG+TGG + chr2_2:44379044-44379063 None:intergenic 45.0%
AGAAGCTTGCATGCAGCACA+TGG + chr2_2:44378946-44378965 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr2_2 gene 44378907 44379176 44378907 ID=Msa0252790;Name=Msa0252790
chr2_2 mRNA 44378907 44379176 44378907 ID=Msa0252790-mRNA-1;Parent=Msa0252790;Name=Msa0252790-mRNA-1;_AED=0.57;_eAED=0.57;_QI=0|-1|0|1|-1|1|1|0|89
chr2_2 exon 44378907 44379176 44378907 ID=Msa0252790-mRNA-1:exon:13633;Parent=Msa0252790-mRNA-1
chr2_2 CDS 44378907 44379176 44378907 ID=Msa0252790-mRNA-1:cds;Parent=Msa0252790-mRNA-1
Gene Sequence

>Msa0252790

ATGAAGGATGGTGGTAGAAAACAGGGTACAATGTCACCATGTGCTGCATGCAAGCTTCTTAGAAGGAGATGTGCTAAAGATTGTGTGTTTGCTCCATATTTTCCAGCTGATGAACCTCACAAATTTGGCAGTGTCCACAAGATTTTTGGGGCTAGCAATGTGAACAAAATGTTACAGGTTCAAATTAAATTCATGCACCTAATCTTTCCTATCTCTATCATGTTATCATCACCTGATATTCCAATCGTTTACATGATAATTATGTGGTAG
Protein sequence

>Msa0252790

MKDGGRKQGTMSPCAACKLLRRRCAKDCVFAPYFPADEPHKFGSVHKIFGASNVNKMLQVQIKFMHLIFPISIMLSSPDIPIVYMIIMW*