AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0436500


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0436500 MtrunA17_Chr6g0464801 44.828 87 24 1 61 147 10 72 1.06e-13 62.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 29 sgRNAs with CRISPR-Local

Find 122 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTATCAGCACTTTGATAATT+AGG 0.202851 3_2:-90086771 Msa0436500:CDS
GTACTAAGATCTGATCTTCT+TGG 0.327969 3_2:+90086739 None:intergenic
GTAACATTTGCTACTTCATT+TGG 0.363423 3_2:+90087550 None:intergenic
GGAACTTTCTTCATATGTCT+AGG 0.392353 3_2:-90087466 Msa0436500:CDS
GAACTTTCTTCATATGTCTA+GGG 0.429731 3_2:-90087465 Msa0436500:CDS
TCAAGATTCTCTTCTGCATC+AGG 0.434480 3_2:+90087433 None:intergenic
AGAGATGGAGGAAGAAGATC+AGG 0.445879 3_2:-90086640 Msa0436500:CDS
GATGCAGAAGAGAATCTTGA+TGG 0.462814 3_2:-90087430 Msa0436500:CDS
CTTAGTATTGGAAGAGGTCC+AGG 0.467546 3_2:-90086616 Msa0436500:CDS
AGAAGATCAGATATTAGTAC+TGG 0.483519 3_2:-90086664 Msa0436500:CDS
AGAAGATCAGGTCTTAGTAT+TGG 0.485294 3_2:-90086628 Msa0436500:CDS
AGAAGATCAGATATTAGTAC+TGG 0.492577 3_2:-90086700 Msa0436500:CDS
ATTAGTACTGGAAGAGATGG+AGG 0.499838 3_2:-90086652 Msa0436500:CDS
AGAAGATCAGATCTTAGTAC+TGG 0.511957 3_2:-90086736 Msa0436500:CDS
AGAAATGCTGAATTAATCCC+TGG 0.519269 3_2:+90086598 None:intergenic
GATATTAGTACTGGAAGAGA+TGG 0.526359 3_2:-90086655 Msa0436500:CDS
TTTGGAGTAAAGAACATGGA+TGG 0.540921 3_2:+90087497 None:intergenic
TCAGATCTTAGTACTGGAAG+AGG 0.548826 3_2:-90086730 Msa0436500:CDS
TCAGATATTAGTACTGGAAG+AGG 0.551309 3_2:-90086694 Msa0436500:CDS
AGAAGAGTCAAGAAGAACAA+TGG 0.568313 3_2:-90087584 Msa0436500:CDS
GAATGTTCAACGAGTGATGA+TGG 0.575026 3_2:-90087388 Msa0436500:CDS
GACATATGAAGAAAGTTCCA+AGG 0.581756 3_2:+90087470 None:intergenic
TCAGGTCTTAGTATTGGAAG+AGG 0.585484 3_2:-90086622 Msa0436500:CDS
TAGCAAATGTTACAAATGAG+AGG 0.594342 3_2:-90087540 Msa0436500:CDS
GATATTAGTACTGGAAGAGG+TGG 0.598287 3_2:-90086691 Msa0436500:CDS
GATCTTAGTACTGGAAGAGG+TGG 0.621063 3_2:-90086727 Msa0436500:CDS
TTAGTATTGGAAGAGGTCCA+GGG 0.652209 3_2:-90086615 Msa0436500:CDS
ACTTTGATAATTAGGAGTGG+CGG 0.657081 3_2:-90086763 Msa0436500:CDS
AGCACTTTGATAATTAGGAG+TGG 0.663797 3_2:-90086766 Msa0436500:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGTAAAAAAAATGATTAATT+TGG - chr3_2:90086968-90086987 Msa0436500:intron 10.0%
!! AGTAAAAAAAATGATTAATT+TGG - chr3_2:90086968-90086987 Msa0436500:intron 10.0%
!!! TGTTCAAAATAGTTTTTTTA+GGG + chr3_2:90087070-90087089 None:intergenic 15.0%
!!! TTGTTCAAAATAGTTTTTTT+AGG + chr3_2:90087071-90087090 None:intergenic 15.0%
!!! TGTTCAAAATAGTTTTTTTA+GGG + chr3_2:90087070-90087089 None:intergenic 15.0%
!!! TTGTTCAAAATAGTTTTTTT+AGG + chr3_2:90087071-90087090 None:intergenic 15.0%
!!! AATTTTTGGAGTAAAGAACA+TGG + chr3_2:90086699-90086718 None:intergenic 25.0%
! AATACTAAGTGTTAGTATGT+TGG - chr3_2:90087103-90087122 Msa0436500:intron 25.0%
!! TTCAGATTAAGTTGTTAATG+AGG - chr3_2:90087161-90087180 Msa0436500:intron 25.0%
!!! GTTGTTAATGAGGTTTTTTT+TGG - chr3_2:90087171-90087190 Msa0436500:intron 25.0%
!! TTGTATCGTTCCAATTTTAT+CGG - chr3_2:90087248-90087267 Msa0436500:intron 25.0%
! AGGTTAAACACAAATCATTT+AGG - chr3_2:90087298-90087317 Msa0436500:intron 25.0%
!! GAAAATCCAAAATCGAATTT+TGG - chr3_2:90087320-90087339 Msa0436500:intron 25.0%
!! ATATTCTAGAGAAAGATTGT+TGG + chr3_2:90087348-90087367 None:intergenic 25.0%
!! TTATCAGCACTTTGATAATT+AGG - chr3_2:90087418-90087437 Msa0436500:CDS 25.0%
!!! AATTTTTGGAGTAAAGAACA+TGG + chr3_2:90086699-90086718 None:intergenic 25.0%
! AATACTAAGTGTTAGTATGT+TGG - chr3_2:90087103-90087122 Msa0436500:intron 25.0%
!! TTCAGATTAAGTTGTTAATG+AGG - chr3_2:90087161-90087180 Msa0436500:intron 25.0%
!!! GTTGTTAATGAGGTTTTTTT+TGG - chr3_2:90087171-90087190 Msa0436500:intron 25.0%
!! TTGTATCGTTCCAATTTTAT+CGG - chr3_2:90087248-90087267 Msa0436500:intron 25.0%
! AGGTTAAACACAAATCATTT+AGG - chr3_2:90087298-90087317 Msa0436500:intron 25.0%
!! GAAAATCCAAAATCGAATTT+TGG - chr3_2:90087320-90087339 Msa0436500:intron 25.0%
!! ATATTCTAGAGAAAGATTGT+TGG + chr3_2:90087348-90087367 None:intergenic 25.0%
!! TTATCAGCACTTTGATAATT+AGG - chr3_2:90087418-90087437 Msa0436500:CDS 25.0%
! GTAACATTTGCTACTTCATT+TGG + chr3_2:90086642-90086661 None:intergenic 30.0%
TAGCAAATGTTACAAATGAG+AGG - chr3_2:90086649-90086668 Msa0436500:CDS 30.0%
TGGATGGTAAAGACAAAAAT+TGG + chr3_2:90086679-90086698 None:intergenic 30.0%
TCTTTACTCCAAAAATTCCT+TGG - chr3_2:90086702-90086721 Msa0436500:CDS 30.0%
! AGAAAGTTCCAAGGAATTTT+TGG + chr3_2:90086713-90086732 None:intergenic 30.0%
GAACTTTCTTCATATGTCTA+GGG - chr3_2:90086724-90086743 Msa0436500:CDS 30.0%
ACAACTTAATCTGAATGACT+TGG + chr3_2:90087156-90087175 None:intergenic 30.0%
!!! GGTTTTTTTTGGACAATTCA+TGG - chr3_2:90087182-90087201 Msa0436500:intron 30.0%
! TTGGAACCAAAATTCGATTT+TGG + chr3_2:90087329-90087348 None:intergenic 30.0%
AGAAGATCAGATATTAGTAC+TGG - chr3_2:90087489-90087508 Msa0436500:CDS 30.0%
AGAAGATCAGATATTAGTAC+TGG - chr3_2:90087489-90087508 Msa0436500:CDS 30.0%
! GTAACATTTGCTACTTCATT+TGG + chr3_2:90086642-90086661 None:intergenic 30.0%
TAGCAAATGTTACAAATGAG+AGG - chr3_2:90086649-90086668 Msa0436500:CDS 30.0%
TGGATGGTAAAGACAAAAAT+TGG + chr3_2:90086679-90086698 None:intergenic 30.0%
TCTTTACTCCAAAAATTCCT+TGG - chr3_2:90086702-90086721 Msa0436500:CDS 30.0%
! AGAAAGTTCCAAGGAATTTT+TGG + chr3_2:90086713-90086732 None:intergenic 30.0%
GAACTTTCTTCATATGTCTA+GGG - chr3_2:90086724-90086743 Msa0436500:CDS 30.0%
ACAACTTAATCTGAATGACT+TGG + chr3_2:90087156-90087175 None:intergenic 30.0%
!!! GGTTTTTTTTGGACAATTCA+TGG - chr3_2:90087182-90087201 Msa0436500:intron 30.0%
! TTGGAACCAAAATTCGATTT+TGG + chr3_2:90087329-90087348 None:intergenic 30.0%
AGAAGATCAGATATTAGTAC+TGG - chr3_2:90087489-90087508 Msa0436500:CDS 30.0%
AGAAGATCAGATATTAGTAC+TGG - chr3_2:90087489-90087508 Msa0436500:CDS 30.0%
AGAAGAGTCAAGAAGAACAA+TGG - chr3_2:90086605-90086624 Msa0436500:CDS 35.0%
! TTTGGAGTAAAGAACATGGA+TGG + chr3_2:90086695-90086714 None:intergenic 35.0%
GACATATGAAGAAAGTTCCA+AGG + chr3_2:90086722-90086741 None:intergenic 35.0%
GGAACTTTCTTCATATGTCT+AGG - chr3_2:90086723-90086742 Msa0436500:CDS 35.0%
! GTGTTAGTATGTTGGTGAAT+AGG - chr3_2:90087111-90087130 Msa0436500:intron 35.0%
!! CTGAATGACTTGGTTCTATA+AGG + chr3_2:90087146-90087165 None:intergenic 35.0%
! AGCACTTTGATAATTAGGAG+TGG - chr3_2:90087423-90087442 Msa0436500:CDS 35.0%
! ACTTTGATAATTAGGAGTGG+CGG - chr3_2:90087426-90087445 Msa0436500:CDS 35.0%
GTACTAAGATCTGATCTTCT+TGG + chr3_2:90087453-90087472 None:intergenic 35.0%
AGAAGATCAGATCTTAGTAC+TGG - chr3_2:90087453-90087472 Msa0436500:CDS 35.0%
! TCAGATATTAGTACTGGAAG+AGG - chr3_2:90087495-90087514 Msa0436500:CDS 35.0%
! GATATTAGTACTGGAAGAGA+TGG - chr3_2:90087534-90087553 Msa0436500:CDS 35.0%
AGAAGATCAGGTCTTAGTAT+TGG - chr3_2:90087561-90087580 Msa0436500:CDS 35.0%
AGAAATGCTGAATTAATCCC+TGG + chr3_2:90087594-90087613 None:intergenic 35.0%
AGAAGAGTCAAGAAGAACAA+TGG - chr3_2:90086605-90086624 Msa0436500:CDS 35.0%
! TTTGGAGTAAAGAACATGGA+TGG + chr3_2:90086695-90086714 None:intergenic 35.0%
GACATATGAAGAAAGTTCCA+AGG + chr3_2:90086722-90086741 None:intergenic 35.0%
GGAACTTTCTTCATATGTCT+AGG - chr3_2:90086723-90086742 Msa0436500:CDS 35.0%
! GTGTTAGTATGTTGGTGAAT+AGG - chr3_2:90087111-90087130 Msa0436500:intron 35.0%
!! CTGAATGACTTGGTTCTATA+AGG + chr3_2:90087146-90087165 None:intergenic 35.0%
! AGCACTTTGATAATTAGGAG+TGG - chr3_2:90087423-90087442 Msa0436500:CDS 35.0%
! ACTTTGATAATTAGGAGTGG+CGG - chr3_2:90087426-90087445 Msa0436500:CDS 35.0%
GTACTAAGATCTGATCTTCT+TGG + chr3_2:90087453-90087472 None:intergenic 35.0%
AGAAGATCAGATCTTAGTAC+TGG - chr3_2:90087453-90087472 Msa0436500:CDS 35.0%
! TCAGATATTAGTACTGGAAG+AGG - chr3_2:90087495-90087514 Msa0436500:CDS 35.0%
! GATATTAGTACTGGAAGAGA+TGG - chr3_2:90087534-90087553 Msa0436500:CDS 35.0%
AGAAGATCAGGTCTTAGTAT+TGG - chr3_2:90087561-90087580 Msa0436500:CDS 35.0%
AGAAATGCTGAATTAATCCC+TGG + chr3_2:90087594-90087613 None:intergenic 35.0%
TCAAGATTCTCTTCTGCATC+AGG + chr3_2:90086759-90086778 None:intergenic 40.0%
GATGCAGAAGAGAATCTTGA+TGG - chr3_2:90086759-90086778 Msa0436500:CDS 40.0%
GAATGTTCAACGAGTGATGA+TGG - chr3_2:90086801-90086820 Msa0436500:intron 40.0%
TCATTAACAACTGTCCCTTC+GGG + chr3_2:90087279-90087298 None:intergenic 40.0%
CTCATTAACAACTGTCCCTT+CGG + chr3_2:90087280-90087299 None:intergenic 40.0%
! TCAGATCTTAGTACTGGAAG+AGG - chr3_2:90087459-90087478 Msa0436500:CDS 40.0%
! GATATTAGTACTGGAAGAGG+TGG - chr3_2:90087498-90087517 Msa0436500:CDS 40.0%
! ATTAGTACTGGAAGAGATGG+AGG - chr3_2:90087537-90087556 Msa0436500:CDS 40.0%
! TCAGGTCTTAGTATTGGAAG+AGG - chr3_2:90087567-90087586 Msa0436500:CDS 40.0%
! TTAGTATTGGAAGAGGTCCA+GGG - chr3_2:90087574-90087593 Msa0436500:CDS 40.0%
TCAAGATTCTCTTCTGCATC+AGG + chr3_2:90086759-90086778 None:intergenic 40.0%
GATGCAGAAGAGAATCTTGA+TGG - chr3_2:90086759-90086778 Msa0436500:CDS 40.0%
GAATGTTCAACGAGTGATGA+TGG - chr3_2:90086801-90086820 Msa0436500:intron 40.0%
TCATTAACAACTGTCCCTTC+GGG + chr3_2:90087279-90087298 None:intergenic 40.0%
CTCATTAACAACTGTCCCTT+CGG + chr3_2:90087280-90087299 None:intergenic 40.0%
! TCAGATCTTAGTACTGGAAG+AGG - chr3_2:90087459-90087478 Msa0436500:CDS 40.0%
! GATATTAGTACTGGAAGAGG+TGG - chr3_2:90087498-90087517 Msa0436500:CDS 40.0%
! ATTAGTACTGGAAGAGATGG+AGG - chr3_2:90087537-90087556 Msa0436500:CDS 40.0%
! TCAGGTCTTAGTATTGGAAG+AGG - chr3_2:90087567-90087586 Msa0436500:CDS 40.0%
! TTAGTATTGGAAGAGGTCCA+GGG - chr3_2:90087574-90087593 Msa0436500:CDS 40.0%
TCGGGGACATCCGATAAAAT+TGG + chr3_2:90087261-90087280 None:intergenic 45.0%
! ATTTTATCGGATGTCCCCGA+AGG - chr3_2:90087261-90087280 Msa0436500:intron 45.0%
! TTTTATCGGATGTCCCCGAA+GGG - chr3_2:90087262-90087281 Msa0436500:intron 45.0%
CATTAACAACTGTCCCTTCG+GGG + chr3_2:90087278-90087297 None:intergenic 45.0%
CGAAGGGACAGTTGTTAATG+AGG - chr3_2:90087278-90087297 Msa0436500:intron 45.0%
! GATCTTAGTACTGGAAGAGG+TGG - chr3_2:90087462-90087481 Msa0436500:CDS 45.0%
AGAGATGGAGGAAGAAGATC+AGG - chr3_2:90087549-90087568 Msa0436500:CDS 45.0%
! CTTAGTATTGGAAGAGGTCC+AGG - chr3_2:90087573-90087592 Msa0436500:CDS 45.0%
TCGGGGACATCCGATAAAAT+TGG + chr3_2:90087261-90087280 None:intergenic 45.0%
! ATTTTATCGGATGTCCCCGA+AGG - chr3_2:90087261-90087280 Msa0436500:intron 45.0%
! TTTTATCGGATGTCCCCGAA+GGG - chr3_2:90087262-90087281 Msa0436500:intron 45.0%
CATTAACAACTGTCCCTTCG+GGG + chr3_2:90087278-90087297 None:intergenic 45.0%
CGAAGGGACAGTTGTTAATG+AGG - chr3_2:90087278-90087297 Msa0436500:intron 45.0%
! GATCTTAGTACTGGAAGAGG+TGG - chr3_2:90087462-90087481 Msa0436500:CDS 45.0%
AGAGATGGAGGAAGAAGATC+AGG - chr3_2:90087549-90087568 Msa0436500:CDS 45.0%
! CTTAGTATTGGAAGAGGTCC+AGG - chr3_2:90087573-90087592 Msa0436500:CDS 45.0%
!!! TTTTTTTTGTTTTTTTTTTT+TGG - chr3_2:90086902-90086921 Msa0436500:intron 5.0%
!!! TTTTTTTGTTTTTTTTTTTT+GGG - chr3_2:90086903-90086922 Msa0436500:intron 5.0%
!!! TTTTTTTTGTTTTTTTTTTT+TGG - chr3_2:90086902-90086921 Msa0436500:intron 5.0%
!!! TTTTTTTGTTTTTTTTTTTT+GGG - chr3_2:90086903-90086922 Msa0436500:intron 5.0%
ATTAGCATGACCCCTGCGCA+AGG + chr3_2:90087223-90087242 None:intergenic 55.0%
ATTAGCATGACCCCTGCGCA+AGG + chr3_2:90087223-90087242 None:intergenic 55.0%
TGTGCGTGTCATCCTTGCGC+AGG - chr3_2:90087208-90087227 Msa0436500:intron 60.0%
GTGCGTGTCATCCTTGCGCA+GGG - chr3_2:90087209-90087228 Msa0436500:intron 60.0%
TGCGTGTCATCCTTGCGCAG+GGG - chr3_2:90087210-90087229 Msa0436500:intron 60.0%
TGTGCGTGTCATCCTTGCGC+AGG - chr3_2:90087208-90087227 Msa0436500:intron 60.0%
GTGCGTGTCATCCTTGCGCA+GGG - chr3_2:90087209-90087228 Msa0436500:intron 60.0%
TGCGTGTCATCCTTGCGCAG+GGG - chr3_2:90087210-90087229 Msa0436500:intron 60.0%
Chromosome Type Strat End Strand Name
chr3_2 gene 90086594 90087617 90086594 ID=Msa0436500;Name=Msa0436500
chr3_2 mRNA 90086594 90087617 90086594 ID=Msa0436500-mRNA-1;Parent=Msa0436500;Name=Msa0436500-mRNA-1;_AED=0.03;_eAED=0.03;_QI=0|1|0|1|1|1|2|0|147
chr3_2 exon 90087378 90087617 90087378 ID=Msa0436500-mRNA-1:exon:26773;Parent=Msa0436500-mRNA-1
chr3_2 exon 90086594 90086797 90086594 ID=Msa0436500-mRNA-1:exon:26772;Parent=Msa0436500-mRNA-1
chr3_2 CDS 90087378 90087617 90087378 ID=Msa0436500-mRNA-1:cds;Parent=Msa0436500-mRNA-1
chr3_2 CDS 90086594 90086797 90086594 ID=Msa0436500-mRNA-1:cds;Parent=Msa0436500-mRNA-1
Gene Sequence

>Msa0436500

ATGGGACACAAAGAAGAGTCAAGAAGAACAATGGAAGAAATATCACCAAATGAAGTAGCAAATGTTACAAATGAGAGGAGTGCCAATTTTTGTCTTTACCATCCATGTTCTTTACTCCAAAAATTCCTTGGAACTTTCTTCATATGTCTAGGGTTTCAAATTCCTGATGCAGAAGAGAATCTTGATGGCAAAGTTCTTGCATGTGAAGAATGTTCAACGAGTGATGATGGTCAAAGTTTTCAACTTATCAGCACTTTGATAATTAGGAGTGGCGGACCAAGAAGATCAGATCTTAGTACTGGAAGAGGTGGACGAAGAAGATCAGATATTAGTACTGGAAGAGGTGGACAAAGAAGATCAGATATTAGTACTGGAAGAGATGGAGGAAGAAGATCAGGTCTTAGTATTGGAAGAGGTCCAGGGATTAATTCAGCATTTCTCTAA

Protein sequence

>Msa0436500

MGHKEESRRTMEEISPNEVANVTNERSANFCLYHPCSLLQKFLGTFFICLGFQIPDAEENLDGKVLACEECSTSDDGQSFQLISTLIIRSGGPRRSDLSTGRGGRRRSDISTGRGGQRRSDISTGRDGGRRSGLSIGRGPGINSAFL*