AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0274950

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0274950 MtrunA17_Chr2g0286491 95.890 146 6 0 1 146 1 146 1.91e-73 216
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 37 sgRNAs with CRISPR-Local

Find 43 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAATTTCTGGTGACAAATTT+TGG 0.075161 2_3:+6807727 None:intergenic
ATATGGTGCAAATGCATAAA+AGG 0.180376 2_3:+6807590 None:intergenic
GGCAAAAGTGGAGCAATTTC+TGG 0.273208 2_3:+6807714 None:intergenic
GTGGGGAGTGTTGGAAGTTC+AGG 0.295068 2_3:+6807801 None:intergenic
TTTGGAGGGCTTGGATTAGA+AGG 0.302628 2_3:+6807639 None:intergenic
TCATCAGGGTTTGGAGGGCT+TGG 0.359011 2_3:+6807630 None:intergenic
AGTGTTGGAAGTTCAGGAAT+AGG 0.412702 2_3:+6807807 None:intergenic
CCTGGAGCAATCACATCATC+AGG 0.417148 2_3:+6807615 None:intergenic
TGGAAAGGAGAGATTGAAGA+TGG 0.421105 2_3:+6807747 None:intergenic
GCAATCACATCATCAGGGTT+TGG 0.456047 2_3:+6807621 None:intergenic
CCACCAGGAGAAGGCAAAAG+TGG 0.462978 2_3:+6807702 None:intergenic
TGCAGTGCTAATGATCATCA+TGG 0.495669 2_3:-6807874 Msa0274950:CDS
GGTGCTTTACCAACTCCTAC+AGG 0.501175 2_3:-6807681 Msa0274950:CDS
TGCACCATATGGATCAATAC+AGG 0.502932 2_3:-6807577 Msa0274950:CDS
TTTGTTGCTGATGAAGTAGT+GGG 0.510994 2_3:+6807783 None:intergenic
GCTTGGATTAGAAGGAATAG+TGG 0.512010 2_3:+6807647 None:intergenic
AGTTACACTTCTATGACCAT+TGG 0.512749 2_3:+6807548 None:intergenic
TATGGTGCAAATGCATAAAA+GGG 0.522319 2_3:+6807591 None:intergenic
GATGAAGTAGTGGGGAGTGT+TGG 0.541029 2_3:+6807792 None:intergenic
TCACATCATCAGGGTTTGGA+GGG 0.550618 2_3:+6807625 None:intergenic
CCTGATGATGTGATTGCTCC+AGG 0.558442 2_3:-6807615 Msa0274950:CDS
GGAGAGATTGAAGATGGAGA+AGG 0.558979 2_3:+6807753 None:intergenic
GTAGCCTGTATTGATCCATA+TGG 0.563050 2_3:+6807573 None:intergenic
ATCACATCATCAGGGTTTGG+AGG 0.576892 2_3:+6807624 None:intergenic
TCAATACAGGCTACTTCCAA+TGG 0.585113 2_3:-6807564 Msa0274950:CDS
ATGTCAGAGCCTGTAGGAGT+TGG 0.587495 2_3:+6807672 None:intergenic
CTTGGATTAGAAGGAATAGT+GGG 0.589460 2_3:+6807648 None:intergenic
GGTAAAGCACCACCAGGAGA+AGG 0.590434 2_3:+6807693 None:intergenic
TTGTTGCTGATGAAGTAGTG+GGG 0.591429 2_3:+6807784 None:intergenic
TAAACCTGCAAAAGCAGTAG+TGG 0.596613 2_3:+6807515 None:intergenic
GCAAATGCATAAAAGGGACC+TGG 0.600170 2_3:+6807597 None:intergenic
TGTGAATATGATGAAAGGAT+AGG 0.606732 2_3:+6807837 None:intergenic
TATGATGAAAGGATAGGCGA+AGG 0.614531 2_3:+6807843 None:intergenic
GTGATTGTGAATATGATGAA+AGG 0.630882 2_3:+6807832 None:intergenic
GGAGTTGGTAAAGCACCACC+AGG 0.652199 2_3:+6807687 None:intergenic
GTGGGAATGTCAGAGCCTGT+AGG 0.652375 2_3:+6807666 None:intergenic
CTGGAGCAATCACATCATCA+GGG 0.679344 2_3:+6807616 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
TGTGAATATGATGAAAGGAT+AGG + chr2_3:6807542-6807561 None:intergenic 30.0%
GTGATTGTGAATATGATGAA+AGG + chr2_3:6807547-6807566 None:intergenic 30.0%
!!! CAATTTCTGGTGACAAATTT+TGG + chr2_3:6807652-6807671 None:intergenic 30.0%
TATGGTGCAAATGCATAAAA+GGG + chr2_3:6807788-6807807 None:intergenic 30.0%
ATATGGTGCAAATGCATAAA+AGG + chr2_3:6807789-6807808 None:intergenic 30.0%
! TTTTATGCATTTGCACCATA+TGG - chr2_3:6807788-6807807 Msa0274950:CDS 30.0%
TTTGTTGCTGATGAAGTAGT+GGG + chr2_3:6807596-6807615 None:intergenic 35.0%
! TTTTGTTGCTGATGAAGTAG+TGG + chr2_3:6807597-6807616 None:intergenic 35.0%
!! TCTGGTGACAAATTTTGGAA+AGG + chr2_3:6807647-6807666 None:intergenic 35.0%
! CTTGGATTAGAAGGAATAGT+GGG + chr2_3:6807731-6807750 None:intergenic 35.0%
AGTTACACTTCTATGACCAT+TGG + chr2_3:6807831-6807850 None:intergenic 35.0%
TGCAGTGCTAATGATCATCA+TGG - chr2_3:6807502-6807521 Msa0274950:CDS 40.0%
TATGATGAAAGGATAGGCGA+AGG + chr2_3:6807536-6807555 None:intergenic 40.0%
! AGTGTTGGAAGTTCAGGAAT+AGG + chr2_3:6807572-6807591 None:intergenic 40.0%
TTGTTGCTGATGAAGTAGTG+GGG + chr2_3:6807595-6807614 None:intergenic 40.0%
TGGAAAGGAGAGATTGAAGA+TGG + chr2_3:6807632-6807651 None:intergenic 40.0%
! GCTTGGATTAGAAGGAATAG+TGG + chr2_3:6807732-6807751 None:intergenic 40.0%
TGCACCATATGGATCAATAC+AGG - chr2_3:6807799-6807818 Msa0274950:CDS 40.0%
! GTAGCCTGTATTGATCCATA+TGG + chr2_3:6807806-6807825 None:intergenic 40.0%
TCAATACAGGCTACTTCCAA+TGG - chr2_3:6807812-6807831 Msa0274950:CDS 40.0%
TAAACCTGCAAAAGCAGTAG+TGG + chr2_3:6807864-6807883 None:intergenic 40.0%
GGAGAGATTGAAGATGGAGA+AGG + chr2_3:6807626-6807645 None:intergenic 45.0%
GGCAAAAGTGGAGCAATTTC+TGG + chr2_3:6807665-6807684 None:intergenic 45.0%
! TTTGGAGGGCTTGGATTAGA+AGG + chr2_3:6807740-6807759 None:intergenic 45.0%
TCACATCATCAGGGTTTGGA+GGG + chr2_3:6807754-6807773 None:intergenic 45.0%
ATCACATCATCAGGGTTTGG+AGG + chr2_3:6807755-6807774 None:intergenic 45.0%
GCAATCACATCATCAGGGTT+TGG + chr2_3:6807758-6807777 None:intergenic 45.0%
CTGGAGCAATCACATCATCA+GGG + chr2_3:6807763-6807782 None:intergenic 45.0%
GCAAATGCATAAAAGGGACC+TGG + chr2_3:6807782-6807801 None:intergenic 45.0%
!! ATAGCCACTACTGCTTTTGC+AGG - chr2_3:6807857-6807876 Msa0274950:CDS 45.0%
! GATGAAGTAGTGGGGAGTGT+TGG + chr2_3:6807587-6807606 None:intergenic 50.0%
GGTGCTTTACCAACTCCTAC+AGG - chr2_3:6807695-6807714 Msa0274950:CDS 50.0%
ATGTCAGAGCCTGTAGGAGT+TGG + chr2_3:6807707-6807726 None:intergenic 50.0%
CCTGGAGCAATCACATCATC+AGG + chr2_3:6807764-6807783 None:intergenic 50.0%
! CCTGATGATGTGATTGCTCC+AGG - chr2_3:6807761-6807780 Msa0274950:CDS 50.0%
!! GTGGGGAGTGTTGGAAGTTC+AGG + chr2_3:6807578-6807597 None:intergenic 55.0%
!! GCTCCACTTTTGCCTTCTCC+TGG - chr2_3:6807671-6807690 Msa0274950:CDS 55.0%
CCACCAGGAGAAGGCAAAAG+TGG + chr2_3:6807677-6807696 None:intergenic 55.0%
!! CCACTTTTGCCTTCTCCTGG+TGG - chr2_3:6807674-6807693 Msa0274950:CDS 55.0%
! GGTAAAGCACCACCAGGAGA+AGG + chr2_3:6807686-6807705 None:intergenic 55.0%
!! GGAGTTGGTAAAGCACCACC+AGG + chr2_3:6807692-6807711 None:intergenic 55.0%
GTGGGAATGTCAGAGCCTGT+AGG + chr2_3:6807713-6807732 None:intergenic 55.0%
TCATCAGGGTTTGGAGGGCT+TGG + chr2_3:6807749-6807768 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr2_3 gene 6807479 6807919 6807479 ID=Msa0274950;Name=Msa0274950
chr2_3 mRNA 6807479 6807919 6807479 ID=Msa0274950-mRNA-1;Parent=Msa0274950;Name=Msa0274950-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|146
chr2_3 exon 6807479 6807919 6807479 ID=Msa0274950-mRNA-1:exon:3234;Parent=Msa0274950-mRNA-1
chr2_3 CDS 6807479 6807919 6807479 ID=Msa0274950-mRNA-1:cds;Parent=Msa0274950-mRNA-1
Gene Sequence

>Msa0274950

ATGGCATCATCATTCACAGTTTATGCAGTGCTAATGATCATCATGGTTTTCATGCCTTCGCCTATCCTTTCATCATATTCACAATCACAACCTATTCCTGAACTTCCAACACTCCCCACTACTTCATCAGCAACAAAAACAGATCCTTCTCCATCTTCAATCTCTCCTTTCCAAAATTTGTCACCAGAAATTGCTCCACTTTTGCCTTCTCCTGGTGGTGCTTTACCAACTCCTACAGGCTCTGACATTCCCACTATTCCTTCTAATCCAAGCCCTCCAAACCCTGATGATGTGATTGCTCCAGGTCCCTTTTATGCATTTGCACCATATGGATCAATACAGGCTACTTCCAATGGTCATAGAAGTGTAACTTTTGACATAGCCACTACTGCTTTTGCAGGTTTAGCAGCATTATCTTCTCTGCAGTATATGAGAGTATGA
Protein sequence

>Msa0274950

MASSFTVYAVLMIIMVFMPSPILSSYSQSQPIPELPTLPTTSSATKTDPSPSSISPFQNLSPEIAPLLPSPGGALPTPTGSDIPTIPSNPSPPNPDDVIAPGPFYAFAPYGSIQATSNGHRSVTFDIATTAFAGLAALSSLQYMRV*