AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0804240

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0804240 MtrunA17_Chr5g0411901 95.349 86 4 0 1 86 277 362 3.29e-53 169
Msa0804240 MtrunA17_Chr5g0411881 91.860 86 7 0 1 86 277 362 6.48e-52 166
Msa0804240 MtrunA17_Chr5g0411911 87.209 86 11 0 1 86 278 363 1.46e-48 157
Msa0804240 MtrunA17_Chr5g0411931 87.059 85 11 0 1 85 276 360 5.84e-46 150
Msa0804240 MtrunA17_Chr4g0064291 84.706 85 13 0 1 85 276 360 3.17e-45 148
Msa0804240 MtrunA17_Chr5g0411801 78.824 85 18 0 1 85 308 392 1.26e-42 142
Msa0804240 MtrunA17_Chr5g0411821 81.176 85 16 0 1 85 276 360 2.05e-42 142
Msa0804240 MtrunA17_Chr5g0411811 81.176 85 16 0 1 85 276 360 3.16e-42 140
Msa0804240 MtrunA17_Chr5g0411871 72.941 85 23 0 1 85 291 375 1.18e-40 137
Msa0804240 MtrunA17_Chr5g0411841 76.471 85 20 0 1 85 276 360 1.45e-39 134
Msa0804240 MtrunA17_Chr5g0411791 82.353 85 15 0 1 85 250 334 7.26e-38 129
Msa0804240 MtrunA17_Chr5g0411861 81.538 65 12 0 22 86 1 65 3.35e-35 114
Msa0804240 MtrunA17_Chr8g0367151 81.176 85 16 0 1 85 276 360 9.95e-35 121
Msa0804240 MtrunA17_Chr5g0411941 65.060 83 29 0 1 83 276 358 5.50e-32 114
Msa0804240 MtrunA17_Chr8g0383721 65.432 81 28 0 2 82 276 356 6.89e-32 113
Msa0804240 MtrunA17_Chr2g0279791 60.870 69 27 0 15 83 338 406 4.29e-22 87.8
Msa0804240 MtrunA17_Chr1g0157021 56.250 80 35 0 1 80 276 355 1.23e-19 80.9
Msa0804240 MtrunA17_Chr1g0208031 42.308 78 45 0 1 78 274 351 1.75e-18 77.8
Msa0804240 MtrunA17_Chr2g0279801 61.538 52 20 0 32 83 163 214 4.83e-16 69.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0804240 AT4G37980.1 70.930 86 25 0 1 86 272 357 2.96e-39 133
Msa0804240 AT4G37990.1 72.093 86 24 0 1 86 272 357 7.54e-38 129
Msa0804240 AT4G39330.1 65.385 78 27 0 7 84 282 359 3.10e-32 115
Msa0804240 AT4G37970.1 62.195 82 31 0 1 82 277 358 7.07e-32 114
Msa0804240 AT2G21730.1 60.256 78 31 0 7 84 278 355 3.85e-29 107
Msa0804240 AT2G21890.1 56.627 83 36 0 2 84 272 354 3.66e-28 104
Msa0804240 AT1G72680.1 58.462 65 27 0 19 83 291 355 1.29e-21 86.7
Msa0804240 AT4G34230.1 48.718 78 40 0 1 78 273 350 1.22e-20 84.0
Msa0804240 AT4G34230.2 47.436 78 41 0 1 78 273 350 9.24e-20 81.6
Msa0804240 AT3G19450.1 40.741 81 48 0 1 81 274 354 2.65e-16 72.0

Find 16 sgRNAs with CRISPR-Local

Find 17 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTAGTAGCTGGAAGTTTAAT+TGG 0.186001 5_3:+19853820 Msa0804240:CDS
TATCGATTCGTGATTGATAT+TGG 0.245698 5_3:+19853970 Msa0804240:CDS
TCCTGCAATGTTTAAGGGCT+TGG 0.287864 5_3:-19854006 None:intergenic
AAGTTTAATTGGAGGGATAA+AGG 0.373525 5_3:+19853831 Msa0804240:CDS
ATAGGAATAACCTCAATATC+AGG 0.384692 5_3:-19853898 None:intergenic
GTAGGGAGAAAGTTAGTAGC+TGG 0.438913 5_3:+19853808 Msa0804240:intron
GCTGTGTTGACATAATCAAT+AGG 0.471251 5_3:-19853916 None:intergenic
CCTCCAAGTAAAGAAAATAC+AGG 0.487127 5_3:-19853673 None:intergenic
CAATGTAAAGCCTGATATTG+AGG 0.489359 5_3:+19853888 Msa0804240:CDS
TAGCTGGAAGTTTAATTGGA+GGG 0.528518 5_3:+19853824 Msa0804240:CDS
GAAAATACAGGAAGCTCTAG+AGG 0.546279 5_3:-19853661 None:intergenic
GTAGCTGGAAGTTTAATTGG+AGG 0.559892 5_3:+19853823 Msa0804240:CDS
GGAAAGCTTGTAATGGTTGG+TGG 0.563386 5_3:+19853628 None:intergenic
GCTTGTAATGGTTGGTGGAG+TGG 0.601696 5_3:+19853633 None:intergenic
AATGGAAAGCTTGTAATGGT+TGG 0.618001 5_3:+19853625 None:intergenic
TGATTATGTCAACACAGCAG+TGG 0.636651 5_3:+19853921 Msa0804240:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAAATTTCACATTATTTGT+AGG + chr5_3:19853790-19853809 Msa0804240:intron 15.0%
!! TAAATTTCACATTATTTGTA+GGG + chr5_3:19853791-19853810 Msa0804240:intron 15.0%
!!! TCAAGAAATGATTGATTTTG+CGG + chr5_3:19853858-19853877 Msa0804240:CDS 25.0%
! CTTCCTGTATTTTCTTTACT+TGG + chr5_3:19853670-19853689 Msa0804240:CDS 30.0%
TTAGTAGCTGGAAGTTTAAT+TGG + chr5_3:19853820-19853839 Msa0804240:CDS 30.0%
AAGTTTAATTGGAGGGATAA+AGG + chr5_3:19853831-19853850 Msa0804240:CDS 30.0%
ATAGGAATAACCTCAATATC+AGG - chr5_3:19853901-19853920 None:intergenic 30.0%
!! TATCGATTCGTGATTGATAT+TGG + chr5_3:19853970-19853989 Msa0804240:CDS 30.0%
CCTCCAAGTAAAGAAAATAC+AGG - chr5_3:19853676-19853695 None:intergenic 35.0%
! CCTGTATTTTCTTTACTTGG+AGG + chr5_3:19853673-19853692 Msa0804240:CDS 35.0%
TAGCTGGAAGTTTAATTGGA+GGG + chr5_3:19853824-19853843 Msa0804240:CDS 35.0%
CAATGTAAAGCCTGATATTG+AGG + chr5_3:19853888-19853907 Msa0804240:CDS 35.0%
! GCTGTGTTGACATAATCAAT+AGG - chr5_3:19853919-19853938 None:intergenic 35.0%
! GAAAATACAGGAAGCTCTAG+AGG - chr5_3:19853664-19853683 None:intergenic 40.0%
GTAGCTGGAAGTTTAATTGG+AGG + chr5_3:19853823-19853842 Msa0804240:CDS 40.0%
TGATTATGTCAACACAGCAG+TGG + chr5_3:19853921-19853940 Msa0804240:CDS 40.0%
GTAGGGAGAAAGTTAGTAGC+TGG + chr5_3:19853808-19853827 Msa0804240:intron 45.0%
Chromosome Type Strat End Strand Name
chr5_3 gene 19853640 19854017 19853640 ID=Msa0804240;Name=Msa0804240
chr5_3 mRNA 19853640 19854017 19853640 ID=Msa0804240-mRNA-1;Parent=Msa0804240;Name=Msa0804240-mRNA-1;_AED=0.47;_eAED=0.48;_QI=0|0|0|1|1|1|2|0|86
chr5_3 exon 19853640 19853694 19853640 ID=Msa0804240-mRNA-1:exon:8125;Parent=Msa0804240-mRNA-1
chr5_3 exon 19853812 19854017 19853812 ID=Msa0804240-mRNA-1:exon:8126;Parent=Msa0804240-mRNA-1
chr5_3 CDS 19853640 19853694 19853640 ID=Msa0804240-mRNA-1:cds;Parent=Msa0804240-mRNA-1
chr5_3 CDS 19853812 19854017 19853812 ID=Msa0804240-mRNA-1:cds;Parent=Msa0804240-mRNA-1
Gene Sequence

>Msa0804240

ATGGTTGGTGGAGTGGCAAAGCCTCTAGAGCTTCCTGTATTTTCTTTACTTGGAGGGAGAAAGTTAGTAGCTGGAAGTTTAATTGGAGGGATAAAGGAGACTCAAGAAATGATTGATTTTGCGGCAAAACACAATGTAAAGCCTGATATTGAGGTTATTCCTATTGATTATGTCAACACAGCAGTGGAGCGTCTCGAGAAAGCAGACGTGAAATATCGATTCGTGATTGATATTGGAAATACGCTGAAACCAAGCCCTTAA
Protein sequence

>Msa0804240

MVGGVAKPLELPVFSLLGGRKLVAGSLIGGIKETQEMIDFAAKHNVKPDIEVIPIDYVNTAVERLEKADVKYRFVIDIGNTLKPSP*