AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0709850

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0709850 MtrunA17_Chr3g0141641 98.810 84 1 0 1 84 1 84 1.84e-58 173
Msa0709850 MtrunA17_Chr1g0155181 49.398 83 39 1 2 84 6 85 3.09e-26 92.0
Msa0709850 MtrunA17_Chr3g0144631 53.846 65 30 0 3 67 16 80 5.85e-22 81.3
Msa0709850 MtrunA17_Chr8g0373131 53.333 75 30 2 2 76 4 73 2.05e-21 79.7
Msa0709850 MtrunA17_Chr8g0373111 53.623 69 31 1 2 70 4 71 3.10e-21 79.0
Msa0709850 MtrunA17_Chr8g0373121 53.623 69 31 1 2 70 4 71 3.10e-21 79.0
Msa0709850 MtrunA17_Chr3g0141601 51.471 68 33 0 3 70 7 74 5.36e-21 79.0
Msa0709850 MtrunA17_Chr8g0373101 55.714 70 29 2 3 72 5 72 7.36e-21 78.2
Msa0709850 MtrunA17_Chr5g0404101 43.750 80 41 1 1 76 17 96 9.22e-21 78.6
Msa0709850 MtrunA17_Chr7g0255841 54.098 61 28 0 6 66 15 75 1.06e-18 73.2
Msa0709850 MtrunA17_Chr6g0449111 46.875 64 34 0 2 65 9 72 4.23e-18 71.2
Msa0709850 MtrunA17_Chr5g0404301 53.226 62 28 1 2 63 3 63 4.33e-18 70.9
Msa0709850 MtrunA17_Chr3g0081631 43.056 72 40 1 2 72 9 80 2.57e-15 64.7
Msa0709850 MtrunA17_Chr1g0162081 40.299 67 40 0 3 69 12 78 2.66e-14 65.9
Msa0709850 MtrunA17_Chr5g0436501 42.857 63 36 0 3 65 27 89 1.76e-13 63.2
Msa0709850 MtrunA17_Chr8g0365011 42.857 63 36 0 3 65 8 70 3.35e-13 62.8
Msa0709850 MtrunA17_Chr8g0364741 39.683 63 38 0 3 65 10 72 4.77e-13 59.7
Msa0709850 MtrunA17_Chr5g0429521 44.444 63 35 0 3 65 29 91 1.22e-12 61.2
Msa0709850 MtrunA17_Chr7g0241761 46.032 63 34 0 3 65 35 97 2.25e-12 60.5
Msa0709850 MtrunA17_Chr3g0104071 43.284 67 38 0 3 69 43 109 3.06e-12 60.1
Msa0709850 MtrunA17_Chr1g0210471 34.286 70 46 0 3 72 24 93 1.38e-11 57.8
Msa0709850 MtrunA17_Chr1g0194071 53.571 56 25 1 2 56 10 65 2.82e-11 54.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0709850 AT1G75250.2 49.398 83 38 1 3 81 12 94 2.92e-23 85.5
Msa0709850 AT4G39250.1 48.780 82 40 1 3 84 14 93 3.86e-23 85.1
Msa0709850 AT1G75250.1 57.812 64 27 0 3 66 12 75 4.79e-23 85.5
Msa0709850 AT1G19510.1 59.016 61 25 0 6 66 15 75 1.03e-21 81.6
Msa0709850 AT2G21650.1 45.122 82 44 1 3 84 14 94 4.41e-19 74.7
Msa0709850 AT5G05790.2 50.000 64 32 0 3 66 31 94 2.51e-16 71.2
Msa0709850 AT5G05790.1 50.000 64 32 0 3 66 31 94 2.51e-16 71.2
Msa0709850 AT2G18328.1 51.667 60 29 0 7 66 15 74 5.23e-16 66.2
Msa0709850 AT5G08520.1 40.244 82 49 0 3 84 12 93 7.19e-15 67.8
Msa0709850 AT3G11280.2 44.444 63 35 0 3 65 33 95 1.73e-14 66.2
Msa0709850 AT3G11280.1 44.444 63 35 0 3 65 33 95 1.73e-14 66.2
Msa0709850 AT4G36570.1 61.364 44 17 0 3 46 12 55 9.44e-14 60.1
Msa0709850 AT2G38090.1 46.032 63 34 0 3 65 29 91 1.24e-13 64.3
Msa0709850 AT5G58900.1 46.032 63 34 0 3 65 34 96 1.52e-13 63.9
Msa0709850 AT1G49010.1 38.667 75 43 1 3 74 8 82 1.19e-12 61.6
Msa0709850 AT5G01200.1 39.506 81 48 1 3 82 30 110 3.38e-11 57.4
Msa0709850 AT5G04760.1 39.683 63 37 1 3 65 6 67 7.94e-11 55.8

Find 24 sgRNAs with CRISPR-Local

Find 25 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCAACAATGGAAGGCAATT+TGG 0.250643 5_1:+955249 Msa0709850:CDS
TGCCACCGATTTGGATCTTC+TGG 0.260812 5_1:-955090 None:intergenic
AAATCCCACTGCCAACTTAC+AGG 0.308746 5_1:+955208 Msa0709850:CDS
GCCACATGTTGCCACCGATT+TGG 0.310871 5_1:-955099 None:intergenic
TTCGAATGAGATCTTCCTTT+AGG 0.339675 5_1:-955173 None:intergenic
GAGGATGCACTTGCAGTATA+TGG 0.363746 5_1:+955066 Msa0709850:CDS
GACAAATTAGCAGCATGGGT+TGG 0.508959 5_1:+955019 None:intergenic
AATCCCACTGCCAACTTACA+GGG 0.517510 5_1:+955209 Msa0709850:CDS
CCAACTTACAGGGGAGGTGC+TGG 0.534339 5_1:+955219 Msa0709850:CDS
CTCCCCTGTAAGTTGGCAGT+GGG 0.537457 5_1:-955212 None:intergenic
CCAGCACCTCCCCTGTAAGT+TGG 0.540006 5_1:-955219 None:intergenic
CAACATGTGGCTAATGCTGT+TGG 0.541304 5_1:+955111 Msa0709850:CDS
GGCAATTTGGCAATGAGCAA+AGG 0.543201 5_1:+955262 Msa0709850:CDS
CCTCCCCTGTAAGTTGGCAG+TGG 0.556127 5_1:-955213 None:intergenic
ATGGTCCAGAAGATCCAAAT+CGG 0.560223 5_1:+955085 Msa0709850:CDS
CATGTGGCTAATGCTGTTGG+TGG 0.579036 5_1:+955114 Msa0709850:CDS
TCCAAATCGGTGGCAACATG+TGG 0.582584 5_1:+955098 Msa0709850:CDS
AATGCATTACGAGATCCTAA+AGG 0.590523 5_1:+955158 Msa0709850:CDS
GCTGGTATCAATATCAACAA+TGG 0.592424 5_1:+955237 Msa0709850:CDS
GTATCAATATCAACAATGGA+AGG 0.611037 5_1:+955241 Msa0709850:CDS
TGGTGGAAAATCCATACAAG+AGG 0.660309 5_1:+955131 Msa0709850:CDS
ATCCCACTGCCAACTTACAG+GGG 0.669431 5_1:+955210 Msa0709850:CDS
CCACTGCCAACTTACAGGGG+AGG 0.671704 5_1:+955213 Msa0709850:CDS
GTCCAGAAGATCCAAATCGG+TGG 0.678303 5_1:+955088 Msa0709850:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
GTATCAATATCAACAATGGA+AGG + chr5_1:955241-955260 Msa0709850:CDS 30.0%
! ATGCATTTTCACCTCTTGTA+TGG - chr5_1:955145-955164 None:intergenic 35.0%
AATGCATTACGAGATCCTAA+AGG + chr5_1:955158-955177 Msa0709850:CDS 35.0%
TTCGAATGAGATCTTCCTTT+AGG - chr5_1:955176-955195 None:intergenic 35.0%
GCTGGTATCAATATCAACAA+TGG + chr5_1:955237-955256 Msa0709850:CDS 35.0%
ATCAACAATGGAAGGCAATT+TGG + chr5_1:955249-955268 Msa0709850:CDS 35.0%
! AGAAGAGAACAGACGTTTTG+AGG + chr5_1:955047-955066 Msa0709850:CDS 40.0%
ATGGTCCAGAAGATCCAAAT+CGG + chr5_1:955085-955104 Msa0709850:CDS 40.0%
TGGTGGAAAATCCATACAAG+AGG + chr5_1:955131-955150 Msa0709850:CDS 40.0%
GAGGATGCACTTGCAGTATA+TGG + chr5_1:955066-955085 Msa0709850:CDS 45.0%
CAACATGTGGCTAATGCTGT+TGG + chr5_1:955111-955130 Msa0709850:CDS 45.0%
AAATCCCACTGCCAACTTAC+AGG + chr5_1:955208-955227 Msa0709850:CDS 45.0%
AATCCCACTGCCAACTTACA+GGG + chr5_1:955209-955228 Msa0709850:CDS 45.0%
GGCAATTTGGCAATGAGCAA+AGG + chr5_1:955262-955281 Msa0709850:CDS 45.0%
GTCCAGAAGATCCAAATCGG+TGG + chr5_1:955088-955107 Msa0709850:CDS 50.0%
!! TGCCACCGATTTGGATCTTC+TGG - chr5_1:955093-955112 None:intergenic 50.0%
TCCAAATCGGTGGCAACATG+TGG + chr5_1:955098-955117 Msa0709850:CDS 50.0%
CATGTGGCTAATGCTGTTGG+TGG + chr5_1:955114-955133 Msa0709850:CDS 50.0%
ATCCCACTGCCAACTTACAG+GGG + chr5_1:955210-955229 Msa0709850:CDS 50.0%
! GCCACATGTTGCCACCGATT+TGG - chr5_1:955102-955121 None:intergenic 55.0%
! CTCCCCTGTAAGTTGGCAGT+GGG - chr5_1:955215-955234 None:intergenic 55.0%
! CCTCCCCTGTAAGTTGGCAG+TGG - chr5_1:955216-955235 None:intergenic 60.0%
CCACTGCCAACTTACAGGGG+AGG + chr5_1:955213-955232 Msa0709850:CDS 60.0%
CCAGCACCTCCCCTGTAAGT+TGG - chr5_1:955222-955241 None:intergenic 60.0%
! CCAACTTACAGGGGAGGTGC+TGG + chr5_1:955219-955238 Msa0709850:CDS 60.0%
Chromosome Type Strat End Strand Name
chr5_1 gene 955033 955287 955033 ID=Msa0709850;Name=Msa0709850
chr5_1 mRNA 955033 955287 955033 ID=Msa0709850-mRNA-1;Parent=Msa0709850;Name=Msa0709850-mRNA-1;_AED=0.02;_eAED=0.02;_QI=0|-1|0|1|-1|1|1|0|84
chr5_1 exon 955033 955287 955033 ID=Msa0709850-mRNA-1:exon:444;Parent=Msa0709850-mRNA-1
chr5_1 CDS 955033 955287 955033 ID=Msa0709850-mRNA-1:cds;Parent=Msa0709850-mRNA-1
Gene Sequence

>Msa0709850

ATGGGTTGGACAAGAGAAGAGAACAGACGTTTTGAGGATGCACTTGCAGTATATGGTCCAGAAGATCCAAATCGGTGGCAACATGTGGCTAATGCTGTTGGTGGAAAATCCATACAAGAGGTGAAAATGCATTACGAGATCCTAAAGGAAGATCTCATTCGAATTGAGCATGATCAAATCCCACTGCCAACTTACAGGGGAGGTGCTGGTATCAATATCAACAATGGAAGGCAATTTGGCAATGAGCAAAGGTAA
Protein sequence

>Msa0709850

MGWTREENRRFEDALAVYGPEDPNRWQHVANAVGGKSIQEVKMHYEILKEDLIRIEHDQIPLPTYRGGAGININNGRQFGNEQR*