AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0833480

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0833480 MtrunA17_Chr7g0276661 73.718 156 25 2 9 149 13 167 7.05e-78 228
Msa0833480 MtrunA17_Chr1g0175881 53.285 137 46 4 2 138 6 124 8.72e-41 133
Msa0833480 MtrunA17_Chr2g0281511 37.273 110 68 1 40 148 10 119 1.13e-28 102
Msa0833480 MtrunA17_Chr2g0309121 39.655 116 65 3 34 148 7 118 2.16e-27 99.0
Msa0833480 MtrunA17_Chr8g0356961 33.333 99 63 1 54 149 77 175 1.90e-16 72.0
Msa0833480 MtrunA17_Chr0c01g0489371 35.955 89 54 1 54 139 226 314 1.94e-15 71.6
Msa0833480 MtrunA17_Chr5g0434641 33.708 89 56 1 54 139 210 298 1.63e-13 66.2
Msa0833480 MtrunA17_Chr3g0081891 37.097 62 39 0 41 102 11 72 7.45e-13 60.5
Msa0833480 MtrunA17_Chr6g0485871 34.940 83 53 1 55 136 216 298 7.93e-12 61.6
Msa0833480 MtrunA17_Chr8g0372431 29.167 96 67 1 54 148 6 101 8.51e-12 58.2
Msa0833480 MtrunA17_Chr5g0430421 73.684 38 8 2 18 55 1 36 2.75e-11 55.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 31 sgRNAs with CRISPR-Local

Find 43 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCATCAACTATTCGAATTT+TGG 0.090848 5_4:-6637139 None:intergenic
TACAGGTAATGGGTGAAAAT+TGG 0.209416 5_4:-6636851 None:intergenic
CCATCGACTTCTTCTTCATT+TGG 0.245009 5_4:-6636883 None:intergenic
GTGGATGGTTTGAGTTTGTT+AGG 0.256057 5_4:+6637229 Msa0833480:CDS
TACTTTGAATTGCAATCTTC+CGG 0.260223 5_4:-6637101 None:intergenic
GGCTGTTGGACGGAGTGTTC+TGG 0.356206 5_4:+6636981 Msa0833480:CDS
CGAATAGTTGATGATGAAAC+TGG 0.373610 5_4:+6637147 Msa0833480:CDS
GAATGTGAAGTTCGTGATAA+AGG 0.381874 5_4:+6637180 Msa0833480:CDS
ACTTTGAATTGCAATCTTCC+GGG 0.386700 5_4:-6637100 None:intergenic
AAGTTCGTGATAAAGGAAAT+TGG 0.388847 5_4:+6637187 Msa0833480:CDS
ACAGGTAATGGGTGAAAATT+GGG 0.407202 5_4:-6636850 None:intergenic
ATTAGTTCTGCTACGGCTGT+TGG 0.467637 5_4:+6636967 Msa0833480:CDS
TGGATGGTTTGAGTTTGTTA+GGG 0.477462 5_4:+6637230 Msa0833480:CDS
AAATGTCTTCTTCTAGTAGC+AGG 0.479507 5_4:+6636720 None:intergenic
CTGCAGCCATGTAATTGATC+CGG 0.509939 5_4:+6636810 Msa0833480:intron
TTTGAAATTGTGCAGATACT+GGG 0.510532 5_4:-6636906 None:intergenic
ATGGAGAAATACGTTGGTAG+TGG 0.538951 5_4:+6637210 Msa0833480:CDS
CCATGTAATTGATCCGGAGT+TGG 0.545499 5_4:+6636816 Msa0833480:CDS
GGCATCAATTCGTCCAACTC+CGG 0.549037 5_4:-6636829 None:intergenic
CCAACTCCGGATCAATTACA+TGG 0.550497 5_4:-6636816 None:intergenic
AGAAATACGTTGGTAGTGGA+TGG 0.551017 5_4:+6637214 Msa0833480:CDS
TCGTGATAAAGGAAATTGGA+TGG 0.565929 5_4:+6637191 Msa0833480:CDS
TGAATGTGTAGCATATTCCC+CGG 0.571619 5_4:+6637082 Msa0833480:intron
GCATAGTATTAGTTCTGCTA+CGG 0.580120 5_4:+6636960 Msa0833480:CDS
AGGGCAAAAGAACTCAAAGA+AGG 0.584629 5_4:+6637249 Msa0833480:CDS
GATACAAATAATTTGTGTGG+AGG 0.593345 5_4:-6637300 None:intergenic
GTTCTGCTACGGCTGTTGGA+CGG 0.598239 5_4:+6636971 Msa0833480:CDS
CTTTGAATTGCAATCTTCCG+GGG 0.600541 5_4:-6637099 None:intergenic
AATTGGATGGAGAAATACGT+TGG 0.604235 5_4:+6637204 Msa0833480:CDS
ACTGATACAAATAATTTGTG+TGG 0.607437 5_4:-6637303 None:intergenic
CCAAATGAAGAAGAAGTCGA+TGG 0.658231 5_4:+6636883 Msa0833480:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTGTTTTTTTAATCTTC+TGG + chr5_4:6636764-6636783 Msa0833480:intron 15.0%
!! CAATTTCAAAAATTTCAAAA+CGG + chr5_4:6636919-6636938 Msa0833480:CDS 15.0%
!!! AGTTTTAATTTTATTTTTGC+TGG + chr5_4:6637006-6637025 Msa0833480:intron 15.0%
!! ATCATCAACTATTCGAATTT+TGG - chr5_4:6637142-6637161 None:intergenic 25.0%
!! ACTGATACAAATAATTTGTG+TGG - chr5_4:6637306-6637325 None:intergenic 25.0%
! TTTGAAATTGTGCAGATACT+GGG - chr5_4:6636909-6636928 None:intergenic 30.0%
!!! TTTTGAAATTGTGCAGATAC+TGG - chr5_4:6636910-6636929 None:intergenic 30.0%
! AAAACGGTGATCATACTTTT+TGG + chr5_4:6636935-6636954 Msa0833480:CDS 30.0%
TACTTTGAATTGCAATCTTC+CGG - chr5_4:6637104-6637123 None:intergenic 30.0%
AAGTTCGTGATAAAGGAAAT+TGG + chr5_4:6637187-6637206 Msa0833480:CDS 30.0%
! GATACAAATAATTTGTGTGG+AGG - chr5_4:6637303-6637322 None:intergenic 30.0%
!! ACAGGTAATGGGTGAAAATT+GGG - chr5_4:6636853-6636872 None:intergenic 35.0%
!! TACAGGTAATGGGTGAAAAT+TGG - chr5_4:6636854-6636873 None:intergenic 35.0%
! GATTTTCGTCTACAGGTAAT+GGG - chr5_4:6636864-6636883 None:intergenic 35.0%
! TCATTTGGATTTTCGTCTAC+AGG - chr5_4:6636871-6636890 None:intergenic 35.0%
!! GCATAGTATTAGTTCTGCTA+CGG + chr5_4:6636960-6636979 Msa0833480:CDS 35.0%
ACTTTGAATTGCAATCTTCC+GGG - chr5_4:6637103-6637122 None:intergenic 35.0%
!! CGAATAGTTGATGATGAAAC+TGG + chr5_4:6637147-6637166 Msa0833480:CDS 35.0%
GAATGTGAAGTTCGTGATAA+AGG + chr5_4:6637180-6637199 Msa0833480:CDS 35.0%
TCGTGATAAAGGAAATTGGA+TGG + chr5_4:6637191-6637210 Msa0833480:CDS 35.0%
AATTGGATGGAGAAATACGT+TGG + chr5_4:6637204-6637223 Msa0833480:CDS 35.0%
!! TGGATGGTTTGAGTTTGTTA+GGG + chr5_4:6637230-6637249 Msa0833480:CDS 35.0%
! GGATTTTCGTCTACAGGTAA+TGG - chr5_4:6636865-6636884 None:intergenic 40.0%
!! CCATCGACTTCTTCTTCATT+TGG - chr5_4:6636886-6636905 None:intergenic 40.0%
CCAAATGAAGAAGAAGTCGA+TGG + chr5_4:6636883-6636902 Msa0833480:CDS 40.0%
TTTGCTGGATTATTTGCGCA+TGG + chr5_4:6637021-6637040 Msa0833480:intron 40.0%
TTGCTGGATTATTTGCGCAT+GGG + chr5_4:6637022-6637041 Msa0833480:intron 40.0%
TGAATGTGTAGCATATTCCC+CGG + chr5_4:6637082-6637101 Msa0833480:intron 40.0%
CTTTGAATTGCAATCTTCCG+GGG - chr5_4:6637102-6637121 None:intergenic 40.0%
! ATGGAGAAATACGTTGGTAG+TGG + chr5_4:6637210-6637229 Msa0833480:CDS 40.0%
!! AGAAATACGTTGGTAGTGGA+TGG + chr5_4:6637214-6637233 Msa0833480:CDS 40.0%
! GTGGATGGTTTGAGTTTGTT+AGG + chr5_4:6637229-6637248 Msa0833480:CDS 40.0%
AGGGCAAAAGAACTCAAAGA+AGG + chr5_4:6637249-6637268 Msa0833480:CDS 40.0%
CTGCAGCCATGTAATTGATC+CGG + chr5_4:6636810-6636829 Msa0833480:intron 45.0%
CCAACTCCGGATCAATTACA+TGG - chr5_4:6636819-6636838 None:intergenic 45.0%
CCATGTAATTGATCCGGAGT+TGG + chr5_4:6636816-6636835 Msa0833480:CDS 45.0%
!! ATTAGTTCTGCTACGGCTGT+TGG + chr5_4:6636967-6636986 Msa0833480:CDS 45.0%
GGCATCAATTCGTCCAACTC+CGG - chr5_4:6636832-6636851 None:intergenic 50.0%
CTGGATTATTTGCGCATGGG+TGG + chr5_4:6637025-6637044 Msa0833480:intron 50.0%
GATTATTTGCGCATGGGTGG+TGG + chr5_4:6637028-6637047 Msa0833480:intron 50.0%
GTTCTGCTACGGCTGTTGGA+CGG + chr5_4:6636971-6636990 Msa0833480:CDS 55.0%
! GGCTGTTGGACGGAGTGTTC+TGG + chr5_4:6636981-6637000 Msa0833480:CDS 60.0%
! GCGCATGGGTGGTGGCTTTG+TGG + chr5_4:6637036-6637055 Msa0833480:intron 65.0%
Chromosome Type Strat End Strand Name
chr5_4 gene 6636722 6637335 6636722 ID=Msa0833480;Name=Msa0833480
chr5_4 mRNA 6636722 6637335 6636722 ID=Msa0833480-mRNA-1;Parent=Msa0833480;Name=Msa0833480-mRNA-1;_AED=0.13;_eAED=0.13;_QI=0|0|0|0.66|1|1|3|0|149
chr5_4 exon 6636722 6636741 6636722 ID=Msa0833480-mRNA-1:exon:2899;Parent=Msa0833480-mRNA-1
chr5_4 exon 6636816 6637002 6636816 ID=Msa0833480-mRNA-1:exon:2900;Parent=Msa0833480-mRNA-1
chr5_4 exon 6637093 6637335 6637093 ID=Msa0833480-mRNA-1:exon:2901;Parent=Msa0833480-mRNA-1
chr5_4 CDS 6636722 6636741 6636722 ID=Msa0833480-mRNA-1:cds;Parent=Msa0833480-mRNA-1
chr5_4 CDS 6636816 6637002 6636816 ID=Msa0833480-mRNA-1:cds;Parent=Msa0833480-mRNA-1
chr5_4 CDS 6637093 6637335 6637093 ID=Msa0833480-mRNA-1:cds;Parent=Msa0833480-mRNA-1
Gene Sequence

>Msa0833480

ATGTCTTCTTCTAGTAGCAGCCATGTAATTGATCCGGAGTTGGACGAATTGATGCCCAATTTTCACCCATTACCTGTAGACGAAAATCCAAATGAAGAAGAAGTCGATGGCCCAGTATCTGCACAATTTCAAAAATTTCAAAACGGTGATCATACTTTTTGGATGCATAGTATTAGTTCTGCTACGGCTGTTGGACGGAGTGTTCTGCATATTCCCCGGAAGATTGCAATTCAAAGTATGTATGTGAATCAATCCAAAATTCGAATAGTTGATGATGAAACTGGAGAAGAATATGAATGTGAAGTTCGTGATAAAGGAAATTGGATGGAGAAATACGTTGGTAGTGGATGGTTTGAGTTTGTTAGGGCAAAAGAACTCAAAGAAGGAGATTCGTTGTTCTTCACTATTGATAATCCTCCACACAAATTATTTGTATCAGTGATTAGATAG
Protein sequence

>Msa0833480

MSSSSSSHVIDPELDELMPNFHPLPVDENPNEEEVDGPVSAQFQKFQNGDHTFWMHSISSATAVGRSVLHIPRKIAIQSMYVNQSKIRIVDDETGEEYECEVRDKGNWMEKYVGSGWFEFVRAKELKEGDSLFFTIDNPPHKLFVSVIR*