AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0394900

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0394900 MtrunA17_Chr3g0092621 81.944 72 13 0 34 105 80 151 8.14e-38 125
Msa0394900 MtrunA17_Chr4g0055931 71.233 73 21 0 33 105 90 162 2.74e-35 122
Msa0394900 MtrunA17_Chr2g0331031 68.493 73 23 0 33 105 104 176 4.12e-34 120
Msa0394900 MtrunA17_Chr6g0488471 72.857 70 19 0 33 102 92 161 2.35e-33 117
Msa0394900 MtrunA17_Chr5g0415191 84.286 70 11 0 37 106 101 170 3.76e-32 114
Msa0394900 MtrunA17_Chr4g0059701 92.857 70 5 0 37 106 83 152 1.11e-31 112
Msa0394900 MtrunA17_Chr8g0389241 61.628 86 27 2 17 102 89 168 1.80e-31 111
Msa0394900 MtrunA17_Chr4g0062741 69.118 68 21 0 37 104 137 204 9.58e-30 107
Msa0394900 MtrunA17_Chr1g0162081 67.647 68 22 0 37 104 121 188 1.28e-28 104
Msa0394900 MtrunA17_Chr3g0104071 63.889 72 26 0 33 104 142 213 1.50e-28 105
Msa0394900 MtrunA17_Chr1g0210471 63.889 72 26 0 33 104 119 190 3.36e-28 102
Msa0394900 MtrunA17_Chr5g0429521 63.889 72 26 0 33 104 127 198 1.42e-27 102
Msa0394900 MtrunA17_Chr7g0241761 63.380 71 26 0 33 103 135 205 5.47e-27 100
Msa0394900 MtrunA17_Chr6g0452791 73.333 60 16 0 38 97 80 139 1.55e-26 96.3
Msa0394900 MtrunA17_Chr5g0436501 59.211 76 29 1 33 106 120 195 1.96e-24 93.2
Msa0394900 MtrunA17_Chr3g0135671 60.870 69 24 1 37 102 90 158 6.42e-24 91.3
Msa0394900 MtrunA17_Chr5g0409841 50.000 66 31 1 40 103 94 159 1.90e-18 77.0
Msa0394900 MtrunA17_Chr5g0440741 49.254 67 31 1 40 103 102 168 1.62e-17 75.1
Msa0394900 MtrunA17_Chr5g0440731 47.143 70 34 1 37 103 104 173 2.28e-17 75.1
Msa0394900 MtrunA17_Chr5g0409831 60.417 48 19 0 38 85 77 124 3.97e-16 70.9
Msa0394900 MtrunA17_Chr8g0365011 47.436 78 27 2 40 103 94 171 6.56e-16 70.9
Msa0394900 MtrunA17_Chr8g0364731 55.932 59 24 1 47 103 10 68 2.38e-14 65.1
Msa0394900 MtrunA17_Chr1g0192061 41.860 86 44 3 24 106 49 131 1.84e-13 62.8
Msa0394900 MtrunA17_Chr3g0113121 45.833 72 32 2 40 104 97 168 4.08e-12 59.7
Msa0394900 MtrunA17_Chr5g0432921 47.761 67 32 2 40 104 115 180 4.32e-12 59.7
Msa0394900 MtrunA17_Chr5g0432941 41.463 82 45 2 25 104 100 180 6.59e-12 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0394900 AT5G47390.1 72.603 73 20 0 33 105 91 163 1.56e-35 124
Msa0394900 AT1G49010.1 70.588 68 20 0 37 104 133 200 2.57e-30 109
Msa0394900 AT1G70000.1 81.429 70 13 0 37 106 97 166 6.85e-30 107
Msa0394900 AT1G70000.2 81.429 70 13 0 37 106 97 166 6.85e-30 107
Msa0394900 AT5G04760.1 63.014 73 27 0 32 104 93 165 2.24e-28 102
Msa0394900 AT3G16350.1 69.863 73 22 0 33 105 132 204 3.09e-28 105
Msa0394900 AT2G38090.1 66.176 68 23 0 37 104 140 207 3.63e-28 103
Msa0394900 AT5G08520.1 66.176 68 23 0 37 104 117 184 4.48e-28 103
Msa0394900 AT5G56840.1 65.217 69 23 1 37 104 90 158 4.94e-28 102
Msa0394900 AT5G58900.1 63.889 72 26 0 33 104 136 207 8.40e-28 102
Msa0394900 AT5G61620.1 65.278 72 23 2 33 103 103 173 2.11e-27 102
Msa0394900 AT1G74840.2 82.857 70 12 0 37 106 95 164 2.47e-27 100
Msa0394900 AT1G19000.2 81.429 70 13 0 37 106 101 170 2.48e-27 101
Msa0394900 AT1G19000.1 81.429 70 13 0 37 106 101 170 2.48e-27 101
Msa0394900 AT1G74840.1 82.857 70 12 0 37 106 95 164 2.81e-27 100
Msa0394900 AT5G01200.1 59.722 72 29 0 33 104 141 212 4.64e-25 95.1
Msa0394900 AT5G05790.2 60.294 68 27 0 37 104 130 197 4.07e-24 92.8
Msa0394900 AT5G05790.1 60.294 68 27 0 37 104 130 197 4.07e-24 92.8
Msa0394900 AT3G11280.2 60.294 68 27 0 37 104 126 193 5.16e-24 92.4
Msa0394900 AT3G11280.1 60.294 68 27 0 37 104 126 193 5.16e-24 92.4
Msa0394900 AT5G23650.1 56.716 67 29 0 37 103 119 185 5.63e-21 85.5
Msa0394900 AT4G09450.1 54.412 68 31 0 36 103 89 156 2.41e-20 81.6
Msa0394900 AT3G10580.2 55.224 67 28 1 37 103 94 158 4.92e-20 82.0
Msa0394900 AT3G10580.1 55.224 67 28 1 37 103 94 158 7.18e-20 82.0
Msa0394900 AT3G10590.1 39.252 107 62 2 2 106 73 178 9.62e-17 72.4

Find 15 sgRNAs with CRISPR-Local

Find 44 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATGCTCATAAGTACTTTCT+CGG 0.360679 3_2:+10138648 Msa0394900:CDS
TTGGTTGGATTGGAGAAAGT+GGG 0.463944 3_2:+10138558 Msa0394900:CDS
AGAAAGTGGGAAAAGGTGAT+TGG 0.482958 3_2:+10138571 Msa0394900:CDS
TTTGGTTGGATTGGAGAAAG+TGG 0.531455 3_2:+10138557 Msa0394900:CDS
GGATTGGAGAAAGTGGGAAA+AGG 0.562648 3_2:+10138564 Msa0394900:CDS
TTGTGCTCTTCCTCAGTCCA+CGG 0.578432 3_2:-10138528 None:intergenic
TATCAAAGAGACTAGATCTA+CGG 0.606389 3_2:-10138695 None:intergenic
GTGATTGGAGAGGAATCTCA+AGG 0.619264 3_2:+10138586 Msa0394900:CDS
GTGGGAAAAGGTGATTGGAG+AGG 0.624127 3_2:+10138576 Msa0394900:CDS
TGAATGGATCAGGGATTCCG+TGG 0.626840 3_2:+10138511 Msa0394900:intron
GCATGACTTGCAACATGCGT+AGG 0.635692 3_2:-10138630 None:intergenic
CTTTGATATCACCACCGACA+CGG 0.638033 3_2:+10138710 Msa0394900:CDS
GACGGCGATTGAGATTACTT+CGG 0.641222 3_2:-10138671 None:intergenic
ATCAGGGATTCCGTGGACTG+AGG 0.660333 3_2:+10138518 Msa0394900:intron
AGAGACTAGATCTACGGCGA+CGG 0.684123 3_2:-10138689 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTTCAATCAATTCAAACAA+AGG - chr3_2:10138461-10138480 None:intergenic 20.0%
!!! TGTTATTGATTTTCTTTGAA+TGG + chr3_2:10138495-10138514 Msa0394900:intron 20.0%
! AATATCTACTTAAAATCCTG+AGG - chr3_2:10138310-10138329 None:intergenic 25.0%
!! TCTCACATTTAAATGGTTTT+TGG + chr3_2:10138366-10138385 Msa0394900:intron 25.0%
!!! ACTCAGCAACAAACATTTTT+TGG - chr3_2:10138042-10138061 None:intergenic 30.0%
CAAATTCACAAAAAACACAC+AGG - chr3_2:10138096-10138115 None:intergenic 30.0%
!!! GTTTTTTGTGAATTTGCTTC+TGG + chr3_2:10138100-10138119 Msa0394900:CDS 30.0%
AATGCAGCACAATTCAAAAT+TGG - chr3_2:10138162-10138181 None:intergenic 30.0%
ACATGTGCACAAACTTTAAT+TGG + chr3_2:10138225-10138244 Msa0394900:intron 30.0%
ATAACTACATCTTATGCAAG+AGG + chr3_2:10138249-10138268 Msa0394900:intron 30.0%
CTACATGTCTCACATTTAAA+TGG + chr3_2:10138359-10138378 Msa0394900:intron 30.0%
! TGATTTTCTTTGAATGGATC+AGG + chr3_2:10138501-10138520 Msa0394900:intron 30.0%
! GATTTTCTTTGAATGGATCA+GGG + chr3_2:10138502-10138521 Msa0394900:intron 30.0%
TATCAAAGAGACTAGATCTA+CGG - chr3_2:10138698-10138717 None:intergenic 30.0%
ACAAAAAACACACAGGATAG+GGG - chr3_2:10138089-10138108 None:intergenic 35.0%
CACAAAAAACACACAGGATA+GGG - chr3_2:10138090-10138109 None:intergenic 35.0%
TCACAAAAAACACACAGGAT+AGG - chr3_2:10138091-10138110 None:intergenic 35.0%
!! GAATTTGCTTCTGGTTTGTA+AGG + chr3_2:10138109-10138128 Msa0394900:intron 35.0%
!! TAGCAGGTTTGTTACTTACA+AGG + chr3_2:10138132-10138151 Msa0394900:intron 35.0%
TTGTGCTGCATTATTCATCT+AGG + chr3_2:10138170-10138189 Msa0394900:intron 35.0%
TGTGCTGCATTATTCATCTA+GGG + chr3_2:10138171-10138190 Msa0394900:intron 35.0%
TCACTTGGATTGAGCATTAA+AGG + chr3_2:10138277-10138296 Msa0394900:intron 35.0%
CATTAAAGGTTGTTTACCTC+AGG + chr3_2:10138291-10138310 Msa0394900:intron 35.0%
!!! CAAGATGTTTTTGGTTGGAT+TGG + chr3_2:10138548-10138567 Msa0394900:CDS 35.0%
CATGCTCATAAGTACTTTCT+CGG + chr3_2:10138648-10138667 Msa0394900:CDS 35.0%
CAAAAAACACACAGGATAGG+GGG - chr3_2:10138088-10138107 None:intergenic 40.0%
GTGCTGCATTATTCATCTAG+GGG + chr3_2:10138172-10138191 Msa0394900:intron 40.0%
ATGCAAGAGGAACTTTCACT+TGG + chr3_2:10138262-10138281 Msa0394900:intron 40.0%
CATTCTCTCTGAGCAAACAA+TGG + chr3_2:10138336-10138355 Msa0394900:intron 40.0%
!! GGAAGAGCACAAGATGTTTT+TGG + chr3_2:10138539-10138558 Msa0394900:CDS 40.0%
!!! GAGCACAAGATGTTTTTGGT+TGG + chr3_2:10138543-10138562 Msa0394900:CDS 40.0%
! TTTGGTTGGATTGGAGAAAG+TGG + chr3_2:10138557-10138576 Msa0394900:CDS 40.0%
! TTGGTTGGATTGGAGAAAGT+GGG + chr3_2:10138558-10138577 Msa0394900:CDS 40.0%
AGAAAGTGGGAAAAGGTGAT+TGG + chr3_2:10138571-10138590 Msa0394900:CDS 40.0%
!! CTTCTGGTTTGTAAGGTAGC+AGG + chr3_2:10138116-10138135 Msa0394900:intron 45.0%
GGATTGGAGAAAGTGGGAAA+AGG + chr3_2:10138564-10138583 Msa0394900:CDS 45.0%
GTGATTGGAGAGGAATCTCA+AGG + chr3_2:10138586-10138605 Msa0394900:CDS 45.0%
GACGGCGATTGAGATTACTT+CGG - chr3_2:10138674-10138693 None:intergenic 45.0%
TGAATGGATCAGGGATTCCG+TGG + chr3_2:10138511-10138530 Msa0394900:intron 50.0%
TTGTGCTCTTCCTCAGTCCA+CGG - chr3_2:10138531-10138550 None:intergenic 50.0%
GTGGGAAAAGGTGATTGGAG+AGG + chr3_2:10138576-10138595 Msa0394900:CDS 50.0%
! GCATGACTTGCAACATGCGT+AGG - chr3_2:10138633-10138652 None:intergenic 50.0%
AGAGACTAGATCTACGGCGA+CGG - chr3_2:10138692-10138711 None:intergenic 50.0%
! ATCAGGGATTCCGTGGACTG+AGG + chr3_2:10138518-10138537 Msa0394900:intron 55.0%
Chromosome Type Strat End Strand Name
chr3_2 gene 10138013 10138731 10138013 ID=Msa0394900;Name=Msa0394900
chr3_2 mRNA 10138013 10138731 10138013 ID=Msa0394900-mRNA-1;Parent=Msa0394900;Name=Msa0394900-mRNA-1;_AED=0.08;_eAED=0.08;_QI=0|0|0|1|1|1|2|0|106
chr3_2 exon 10138013 10138121 10138013 ID=Msa0394900-mRNA-1:exon:2629;Parent=Msa0394900-mRNA-1
chr3_2 exon 10138523 10138731 10138523 ID=Msa0394900-mRNA-1:exon:2630;Parent=Msa0394900-mRNA-1
chr3_2 CDS 10138013 10138121 10138013 ID=Msa0394900-mRNA-1:cds;Parent=Msa0394900-mRNA-1
chr3_2 CDS 10138523 10138731 10138523 ID=Msa0394900-mRNA-1:cds;Parent=Msa0394900-mRNA-1
Gene Sequence

>Msa0394900

GCAATGTCTATCATGAAGATTCAATACCAAAAAATGTTTGTTGCTGAGTTTTTGAGAGCTGTTTTTTGTGTGCCCCCTATCCTGTGTGTTTTTTGTGAATTTGCTTCTGGGATTCCGTGGACTGAGGAAGAGCACAAGATGTTTTTGGTTGGATTGGAGAAAGTGGGAAAAGGTGATTGGAGAGGAATCTCAAGGAACTATGTGAAAACAAGAACGCCTACGCATGTTGCAAGTCATGCTCATAAGTACTTTCTCGGCCGAAGTAATCTCAATCGCCGTCGCCGTAGATCTAGTCTCTTTGATATCACCACCGACACG
Protein sequence

>Msa0394900

AMSIMKIQYQKMFVAEFLRAVFCVPPILCVFCEFASGIPWTEEEHKMFLVGLEKVGKGDWRGISRNYVKTRTPTHVASHAHKYFLGRSNLNRRRRRSSLFDITTDT