AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0220660

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0220660 MtrunA17_Chr2g0324311 97.143 70 1 1 1 69 1 70 5.83e-42 130
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0220660 AT4G28290.1 50.847 59 28 1 12 69 22 80 2.51e-12 56.6
Msa0220660 AT4G28290.2 50.847 59 28 1 12 69 22 80 2.51e-12 56.6
Msa0220660 AT5G42110.1 44.444 54 30 0 16 69 9 62 7.28e-11 52.4

Find 46 sgRNAs with CRISPR-Local

Find 115 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGAGAGAGACAGAGGAAATT+TGG 0.190544 2_1:+69077186 None:intergenic
AAATTAAAAGTATAAGATTT+TGG 0.218403 2_1:-69076543 Msa0220660:three_prime_UTR
GAAATTTGGTTGCGGAAGTT+TGG 0.279865 2_1:+69077200 None:intergenic
AAATTTGGTTGCGGAAGTTT+GGG 0.297294 2_1:+69077201 None:intergenic
CGCTGTCTCCGTTTCTTCTT+CGG 0.298620 2_1:-69077007 Msa0220660:CDS
GGAAGCGGCGGCGACGGAGG+CGG 0.308504 2_1:+69077035 None:intergenic
TGAGAGAAACAAATGAAGAT+TGG 0.330432 2_1:+69077091 None:intergenic
AAAACAAAACATATACAAAT+AGG 0.343427 2_1:-69077324 Msa0220660:five_prime_UTR
AAGAAGAAGATTTCACTTGT+TGG 0.358736 2_1:-69076671 Msa0220660:three_prime_UTR
GAGAGAAACAAATGAAGATT+GGG 0.372997 2_1:+69077092 None:intergenic
TATATATAGGAGAGAATTGT+AGG 0.402874 2_1:+69077239 None:intergenic
CGGCGACGGAGGCGGCGAAG+AGG 0.418581 2_1:+69077043 None:intergenic
GGAGACAGCGGTGGCGGAAG+CGG 0.428305 2_1:+69077020 None:intergenic
GGTGGCGGAAGCGGCGGCGA+CGG 0.429714 2_1:+69077029 None:intergenic
GAAGTTTGGGGAGGGTTTGA+CGG 0.430577 2_1:+69077214 None:intergenic
GGGTTTGACGGCATATATAT+AGG 0.431512 2_1:+69077226 None:intergenic
GGCAAATAACTCAAATCATC+AGG 0.435276 2_1:-69076986 Msa0220660:intron
GAAGAAGAAGAGAGAGAAAG+AGG 0.446300 2_1:+69077150 None:intergenic
TCATAGATGAAAGAGGGGTT+TGG 0.481099 2_1:-69076753 Msa0220660:exon
GGCGGAAGCGGCGGCGACGG+AGG 0.483294 2_1:+69077032 None:intergenic
ACCGCCACAATGAAGAAATC+CGG 0.492103 2_1:-69077066 Msa0220660:exon
AAATTTGCGCCGAGATTCGA+TGG 0.499729 2_1:-69076806 Msa0220660:CDS
GACGGAGGCGGCGAAGAGGC+CGG 0.501966 2_1:+69077047 None:intergenic
GACAGCGGTGGCGGAAGCGG+CGG 0.505444 2_1:+69077023 None:intergenic
AGAAACGGAGACAGCGGTGG+CGG 0.505992 2_1:+69077014 None:intergenic
TGATACGCGAAATTATTACT+TGG 0.513903 2_1:-69076601 Msa0220660:three_prime_UTR
GTTATTTGCCGAAGAAGAAA+CGG 0.515047 2_1:+69076999 None:intergenic
AAACGCAAACCATCGAATCT+CGG 0.521279 2_1:+69076797 None:intergenic
TGGTTGCGGAAGTTTGGGGA+GGG 0.545314 2_1:+69077206 None:intergenic
AGACAGAGGAAATTTGGTTG+CGG 0.546519 2_1:+69077192 None:intergenic
AACTGCTCATAGATGAAAGA+GGG 0.547718 2_1:-69076759 Msa0220660:exon
ACAAGACGAAGAAACATATG+AGG 0.552549 2_1:+69076717 None:intergenic
TGAGAGATCTTCGTCGTCGA+CGG 0.553746 2_1:-69076831 Msa0220660:CDS
GTAGGTTAAATTAATTTATG+CGG 0.561826 2_1:+69077257 None:intergenic
ATTTGTAGAGAGTGAATATG+TGG 0.567779 2_1:+69077126 None:intergenic
GAGGCCGGATTTCTTCATTG+TGG 0.578217 2_1:+69077062 None:intergenic
GTCTTGTTGAACTTCTTGTG+TGG 0.583419 2_1:-69076701 Msa0220660:three_prime_UTR
TTGGTTGCGGAAGTTTGGGG+AGG 0.585468 2_1:+69077205 None:intergenic
GCCGGATTTCTTCATTGTGG+CGG 0.585971 2_1:+69077065 None:intergenic
TAACTGCTCATAGATGAAAG+AGG 0.603127 2_1:-69076760 Msa0220660:exon
AATTTGGTTGCGGAAGTTTG+GGG 0.614651 2_1:+69077202 None:intergenic
AGAAGAAACGGAGACAGCGG+TGG 0.633424 2_1:+69077011 None:intergenic
GACGGTACGGTTGAAAGAAG+AGG 0.642636 2_1:-69076860 Msa0220660:CDS
CGAAGAAGAAACGGAGACAG+CGG 0.672061 2_1:+69077008 None:intergenic
ACTGCTCATAGATGAAAGAG+GGG 0.694445 2_1:-69076758 Msa0220660:exon
ACGACGAAGATCTCTCATCA+CGG 0.735576 2_1:+69076837 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAATTAAAAGTATAAGATTT+TGG - chr2_1:69077340-69077359 Msa0220660:five_prime_UTR 10.0%
!!! AAATTAAAAGTATAAGATTT+TGG - chr2_1:69077340-69077359 Msa0220660:five_prime_UTR 10.0%
!!! TTTGTTTTAACTTAACTTTT+TGG + chr2_1:69076542-69076561 None:intergenic 15.0%
!! AAAACAAAACATATACAAAT+AGG - chr2_1:69076559-69076578 Msa0220660:three_prime_UTR 15.0%
!!! TTTGTTTTAACTTAACTTTT+TGG + chr2_1:69076542-69076561 None:intergenic 15.0%
!! AAAACAAAACATATACAAAT+AGG - chr2_1:69076559-69076578 Msa0220660:three_prime_UTR 15.0%
!! GTAGGTTAAATTAATTTATG+CGG + chr2_1:69076629-69076648 None:intergenic 20.0%
!!! TGAATAAATTTTCAGATCTT+GGG + chr2_1:69076952-69076971 None:intergenic 20.0%
!!! TTGAATAAATTTTCAGATCT+TGG + chr2_1:69076953-69076972 None:intergenic 20.0%
!!! TTCTTTTTTGTAATCCTTAA+TGG - chr2_1:69077310-69077329 Msa0220660:five_prime_UTR 20.0%
!!! TCTTTTTTGTAATCCTTAAT+GGG - chr2_1:69077311-69077330 Msa0220660:five_prime_UTR 20.0%
!!! TTAATTTTCATTACCCATTA+AGG + chr2_1:69077327-69077346 None:intergenic 20.0%
!! GTAGGTTAAATTAATTTATG+CGG + chr2_1:69076629-69076648 None:intergenic 20.0%
!!! TGAATAAATTTTCAGATCTT+GGG + chr2_1:69076952-69076971 None:intergenic 20.0%
!!! TTGAATAAATTTTCAGATCT+TGG + chr2_1:69076953-69076972 None:intergenic 20.0%
!!! TTCTTTTTTGTAATCCTTAA+TGG - chr2_1:69077310-69077329 Msa0220660:five_prime_UTR 20.0%
!!! TCTTTTTTGTAATCCTTAAT+GGG - chr2_1:69077311-69077330 Msa0220660:five_prime_UTR 20.0%
!!! TTAATTTTCATTACCCATTA+AGG + chr2_1:69077327-69077346 None:intergenic 20.0%
! CACAAAAGAATGAGAAAAAA+AGG - chr2_1:69076588-69076607 Msa0220660:three_prime_UTR 25.0%
! TATATATAGGAGAGAATTGT+AGG + chr2_1:69076647-69076666 None:intergenic 25.0%
!! TGTGAATTTGTGTTTTGTAT+AGG - chr2_1:69077001-69077020 Msa0220660:CDS 25.0%
!! AATTTGTGTTTTGTATAGGA+CGG - chr2_1:69077005-69077024 Msa0220660:CDS 25.0%
! CACAAAAGAATGAGAAAAAA+AGG - chr2_1:69076588-69076607 Msa0220660:three_prime_UTR 25.0%
! TATATATAGGAGAGAATTGT+AGG + chr2_1:69076647-69076666 None:intergenic 25.0%
!! TGTGAATTTGTGTTTTGTAT+AGG - chr2_1:69077001-69077020 Msa0220660:CDS 25.0%
!! AATTTGTGTTTTGTATAGGA+CGG - chr2_1:69077005-69077024 Msa0220660:CDS 25.0%
ATTTGTAGAGAGTGAATATG+TGG + chr2_1:69076760-69076779 None:intergenic 30.0%
GAGAGAAACAAATGAAGATT+GGG + chr2_1:69076794-69076813 None:intergenic 30.0%
TGAGAGAAACAAATGAAGAT+TGG + chr2_1:69076795-69076814 None:intergenic 30.0%
AAGAAGAAGATTTCACTTGT+TGG - chr2_1:69077212-69077231 Msa0220660:five_prime_UTR 30.0%
TGATACGCGAAATTATTACT+TGG - chr2_1:69077282-69077301 Msa0220660:five_prime_UTR 30.0%
ATTTGTAGAGAGTGAATATG+TGG + chr2_1:69076760-69076779 None:intergenic 30.0%
GAGAGAAACAAATGAAGATT+GGG + chr2_1:69076794-69076813 None:intergenic 30.0%
TGAGAGAAACAAATGAAGAT+TGG + chr2_1:69076795-69076814 None:intergenic 30.0%
AAGAAGAAGATTTCACTTGT+TGG - chr2_1:69077212-69077231 Msa0220660:five_prime_UTR 30.0%
TGATACGCGAAATTATTACT+TGG - chr2_1:69077282-69077301 Msa0220660:five_prime_UTR 30.0%
AAATTTGGTTGCGGAAGTTT+GGG + chr2_1:69076685-69076704 None:intergenic 35.0%
GTTATTTGCCGAAGAAGAAA+CGG + chr2_1:69076887-69076906 None:intergenic 35.0%
GGCAAATAACTCAAATCATC+AGG - chr2_1:69076897-69076916 Msa0220660:intron 35.0%
TAACTGCTCATAGATGAAAG+AGG - chr2_1:69077123-69077142 Msa0220660:five_prime_UTR 35.0%
AACTGCTCATAGATGAAAGA+GGG - chr2_1:69077124-69077143 Msa0220660:five_prime_UTR 35.0%
ACAAGACGAAGAAACATATG+AGG + chr2_1:69077169-69077188 None:intergenic 35.0%
AAATTTGGTTGCGGAAGTTT+GGG + chr2_1:69076685-69076704 None:intergenic 35.0%
GTTATTTGCCGAAGAAGAAA+CGG + chr2_1:69076887-69076906 None:intergenic 35.0%
GGCAAATAACTCAAATCATC+AGG - chr2_1:69076897-69076916 Msa0220660:intron 35.0%
TAACTGCTCATAGATGAAAG+AGG - chr2_1:69077123-69077142 Msa0220660:five_prime_UTR 35.0%
AACTGCTCATAGATGAAAGA+GGG - chr2_1:69077124-69077143 Msa0220660:five_prime_UTR 35.0%
ACAAGACGAAGAAACATATG+AGG + chr2_1:69077169-69077188 None:intergenic 35.0%
GGGTTTGACGGCATATATAT+AGG + chr2_1:69076660-69076679 None:intergenic 40.0%
AATTTGGTTGCGGAAGTTTG+GGG + chr2_1:69076684-69076703 None:intergenic 40.0%
GAAATTTGGTTGCGGAAGTT+TGG + chr2_1:69076686-69076705 None:intergenic 40.0%
AGACAGAGGAAATTTGGTTG+CGG + chr2_1:69076694-69076713 None:intergenic 40.0%
AGAGAGAGACAGAGGAAATT+TGG + chr2_1:69076700-69076719 None:intergenic 40.0%
GAAGAAGAAGAGAGAGAAAG+AGG + chr2_1:69076736-69076755 None:intergenic 40.0%
! GTGTTTTGTATAGGACGGTA+CGG - chr2_1:69077010-69077029 Msa0220660:CDS 40.0%
AAACGCAAACCATCGAATCT+CGG + chr2_1:69077089-69077108 None:intergenic 40.0%
ACTGCTCATAGATGAAAGAG+GGG - chr2_1:69077125-69077144 Msa0220660:five_prime_UTR 40.0%
TCATAGATGAAAGAGGGGTT+TGG - chr2_1:69077130-69077149 Msa0220660:five_prime_UTR 40.0%
! GTCTTGTTGAACTTCTTGTG+TGG - chr2_1:69077182-69077201 Msa0220660:five_prime_UTR 40.0%
GGGTTTGACGGCATATATAT+AGG + chr2_1:69076660-69076679 None:intergenic 40.0%
AATTTGGTTGCGGAAGTTTG+GGG + chr2_1:69076684-69076703 None:intergenic 40.0%
GAAATTTGGTTGCGGAAGTT+TGG + chr2_1:69076686-69076705 None:intergenic 40.0%
AGACAGAGGAAATTTGGTTG+CGG + chr2_1:69076694-69076713 None:intergenic 40.0%
AGAGAGAGACAGAGGAAATT+TGG + chr2_1:69076700-69076719 None:intergenic 40.0%
GAAGAAGAAGAGAGAGAAAG+AGG + chr2_1:69076736-69076755 None:intergenic 40.0%
! GTGTTTTGTATAGGACGGTA+CGG - chr2_1:69077010-69077029 Msa0220660:CDS 40.0%
AAACGCAAACCATCGAATCT+CGG + chr2_1:69077089-69077108 None:intergenic 40.0%
ACTGCTCATAGATGAAAGAG+GGG - chr2_1:69077125-69077144 Msa0220660:five_prime_UTR 40.0%
TCATAGATGAAAGAGGGGTT+TGG - chr2_1:69077130-69077149 Msa0220660:five_prime_UTR 40.0%
! GTCTTGTTGAACTTCTTGTG+TGG - chr2_1:69077182-69077201 Msa0220660:five_prime_UTR 40.0%
ACCGCCACAATGAAGAAATC+CGG - chr2_1:69076817-69076836 Msa0220660:CDS 45.0%
ACGACGAAGATCTCTCATCA+CGG + chr2_1:69077049-69077068 None:intergenic 45.0%
AAATTTGCGCCGAGATTCGA+TGG - chr2_1:69077077-69077096 Msa0220660:exon 45.0%
ACCGCCACAATGAAGAAATC+CGG - chr2_1:69076817-69076836 Msa0220660:CDS 45.0%
ACGACGAAGATCTCTCATCA+CGG + chr2_1:69077049-69077068 None:intergenic 45.0%
AAATTTGCGCCGAGATTCGA+TGG - chr2_1:69077077-69077096 Msa0220660:exon 45.0%
!!! TAATTTTTGTTTATATTTTT+TGG - chr2_1:69077369-69077388 Msa0220660:five_prime_UTR 5.0%
GAAGTTTGGGGAGGGTTTGA+CGG + chr2_1:69076672-69076691 None:intergenic 50.0%
AGAGAGAGAGAGAGAGACAG+AGG + chr2_1:69076708-69076727 None:intergenic 50.0%
GCCGGATTTCTTCATTGTGG+CGG + chr2_1:69076821-69076840 None:intergenic 50.0%
GAGGCCGGATTTCTTCATTG+TGG + chr2_1:69076824-69076843 None:intergenic 50.0%
CGAAGAAGAAACGGAGACAG+CGG + chr2_1:69076878-69076897 None:intergenic 50.0%
CGCTGTCTCCGTTTCTTCTT+CGG - chr2_1:69076876-69076895 Msa0220660:intron 50.0%
GACGGTACGGTTGAAAGAAG+AGG - chr2_1:69077023-69077042 Msa0220660:CDS 50.0%
TGAGAGATCTTCGTCGTCGA+CGG - chr2_1:69077052-69077071 Msa0220660:CDS 50.0%
GAAGTTTGGGGAGGGTTTGA+CGG + chr2_1:69076672-69076691 None:intergenic 50.0%
AGAGAGAGAGAGAGAGACAG+AGG + chr2_1:69076708-69076727 None:intergenic 50.0%
GCCGGATTTCTTCATTGTGG+CGG + chr2_1:69076821-69076840 None:intergenic 50.0%
GAGGCCGGATTTCTTCATTG+TGG + chr2_1:69076824-69076843 None:intergenic 50.0%
CGAAGAAGAAACGGAGACAG+CGG + chr2_1:69076878-69076897 None:intergenic 50.0%
CGCTGTCTCCGTTTCTTCTT+CGG - chr2_1:69076876-69076895 Msa0220660:intron 50.0%
GACGGTACGGTTGAAAGAAG+AGG - chr2_1:69077023-69077042 Msa0220660:CDS 50.0%
TGAGAGATCTTCGTCGTCGA+CGG - chr2_1:69077052-69077071 Msa0220660:CDS 50.0%
TGGTTGCGGAAGTTTGGGGA+GGG + chr2_1:69076680-69076699 None:intergenic 55.0%
TTGGTTGCGGAAGTTTGGGG+AGG + chr2_1:69076681-69076700 None:intergenic 55.0%
AGAAGAAACGGAGACAGCGG+TGG + chr2_1:69076875-69076894 None:intergenic 55.0%
TGGTTGCGGAAGTTTGGGGA+GGG + chr2_1:69076680-69076699 None:intergenic 55.0%
TTGGTTGCGGAAGTTTGGGG+AGG + chr2_1:69076681-69076700 None:intergenic 55.0%
AGAAGAAACGGAGACAGCGG+TGG + chr2_1:69076875-69076894 None:intergenic 55.0%
AGAAACGGAGACAGCGGTGG+CGG + chr2_1:69076872-69076891 None:intergenic 60.0%
AGAAACGGAGACAGCGGTGG+CGG + chr2_1:69076872-69076891 None:intergenic 60.0%
!! GGAGACAGCGGTGGCGGAAG+CGG + chr2_1:69076866-69076885 None:intergenic 70.0%
!! GGAGACAGCGGTGGCGGAAG+CGG + chr2_1:69076866-69076885 None:intergenic 70.0%
GACGGAGGCGGCGAAGAGGC+CGG + chr2_1:69076839-69076858 None:intergenic 75.0%
!! GACAGCGGTGGCGGAAGCGG+CGG + chr2_1:69076863-69076882 None:intergenic 75.0%
GACGGAGGCGGCGAAGAGGC+CGG + chr2_1:69076839-69076858 None:intergenic 75.0%
!! GACAGCGGTGGCGGAAGCGG+CGG + chr2_1:69076863-69076882 None:intergenic 75.0%
! CGGCGACGGAGGCGGCGAAG+AGG + chr2_1:69076843-69076862 None:intergenic 80.0%
! GGAAGCGGCGGCGACGGAGG+CGG + chr2_1:69076851-69076870 None:intergenic 80.0%
!!! GGTGGCGGAAGCGGCGGCGA+CGG + chr2_1:69076857-69076876 None:intergenic 80.0%
! CGGCGACGGAGGCGGCGAAG+AGG + chr2_1:69076843-69076862 None:intergenic 80.0%
! GGAAGCGGCGGCGACGGAGG+CGG + chr2_1:69076851-69076870 None:intergenic 80.0%
!!! GGTGGCGGAAGCGGCGGCGA+CGG + chr2_1:69076857-69076876 None:intergenic 80.0%
! GGCGGAAGCGGCGGCGACGG+AGG + chr2_1:69076854-69076873 None:intergenic 85.0%
! GGCGGAAGCGGCGGCGACGG+AGG + chr2_1:69076854-69076873 None:intergenic 85.0%
Chromosome Type Strat End Strand Name
chr2_1 gene 69076516 69077389 69076516 ID=Msa0220660;Name=Msa0220660
chr2_1 mRNA 69076516 69077389 69076516 ID=Msa0220660-mRNA-1;Parent=Msa0220660;Name=Msa0220660-mRNA-1;_AED=0.00;_eAED=0.00;_QI=310|1|1|1|1|1|2|250|69
chr2_1 exon 69076516 69076882 69076516 ID=Msa0220660-mRNA-1:exon:19519;Parent=Msa0220660-mRNA-1
chr2_1 exon 69076987 69077389 69076987 ID=Msa0220660-mRNA-1:exon:19518;Parent=Msa0220660-mRNA-1
chr2_1 five_prime_UTR 69077080 69077389 69077080 ID=Msa0220660-mRNA-1:five_prime_utr;Parent=Msa0220660-mRNA-1
chr2_1 CDS 69076987 69077079 69076987 ID=Msa0220660-mRNA-1:cds;Parent=Msa0220660-mRNA-1
chr2_1 CDS 69076766 69076882 69076766 ID=Msa0220660-mRNA-1:cds;Parent=Msa0220660-mRNA-1
chr2_1 three_prime_UTR 69076516 69076765 69076516 ID=Msa0220660-mRNA-1:three_prime_utr;Parent=Msa0220660-mRNA-1
Gene Sequence

>Msa0220660

ATGAAGAAATCCGGCCTCTTCGCCGCCTCCGTCGCCGCCGCTTCCGCCACCGCTGTCTCCGTTTCTTCTTCGGCAAATAACTCAAATCATCAGGACGGTACGGTTGAAAGAAGAGGCCGTGATGAGAGATCTTCGTCGTCGACGGAGAAATTTGCGCCGAGATTCGATGGTTTGCGTTTCATAGAAACGCTGATAACTGCTCATAGATGA
Protein sequence

>Msa0220660

MKKSGLFAASVAAASATAVSVSSSANNSNHQDGTVERRGRDERSSSSTEKFAPRFDGLRFIETLITAHR*