AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene96699

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 45 sgRNAs with CRISPR-Local

Find 55 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TACCCGGCGCCGGAGACTTA+TGG 0.351875 1.1:+76361583 MS.gene96699:CDS
CCACCTCGTCAGCAAAATTC+AGG 0.380629 1.1:+76361733 MS.gene96699:CDS
ACAAGGTTACCCTCCACAAC+AGG 0.383576 1.1:+76361639 MS.gene96699:CDS
GAATAGAGGATGGACCTTGC+TGG 0.394206 1.1:-76361430 None:intergenic
TCAAGGCTATCCTCCACAAC+AGG 0.403285 1.1:+76361672 MS.gene96699:CDS
CAGCAAAATTCAGGCGGTGC+TGG 0.441154 1.1:+76361742 MS.gene96699:CDS
TTTCCATAAGTCTCCGGCGC+CGG 0.444590 1.1:-76361586 None:intergenic
TTCCATAAGTCTCCGGCGCC+GGG 0.453331 1.1:-76361585 None:intergenic
AATAGAGGATGGACCTTGCT+GGG 0.456352 1.1:-76361429 None:intergenic
CGCCGACGGGCGGTTGCTGT+TGG 0.456584 1.1:-76361400 None:intergenic
CATGGAATTAATAGGTTACC+CGG 0.471275 1.1:+76361567 MS.gene96699:intron
GTGCTGGTTGCATGGAAGGC+TGG 0.477733 1.1:+76361758 MS.gene96699:CDS
GGCGGTGCTGGTTGCATGGA+AGG 0.485634 1.1:+76361754 MS.gene96699:CDS
TAACCTTGTGGAGGATATCC+TGG 0.496681 1.1:-76361625 None:intergenic
TTCAGGCGGTGCTGGTTGCA+TGG 0.511069 1.1:+76361750 MS.gene96699:CDS
TGCTGGGGAGGAACGCCGAC+GGG 0.513380 1.1:-76361413 None:intergenic
TGCGGTGGGTAGCCCTGTTG+TGG 0.549001 1.1:-76361685 None:intergenic
GAGGATGGACCTTGCTGGGG+AGG 0.552104 1.1:-76361425 None:intergenic
TTGCTGGGGAGGAACGCCGA+CGG 0.554888 1.1:-76361414 None:intergenic
TGTGGAGGATATCCTGGTGG+AGG 0.557895 1.1:-76361619 None:intergenic
TGAGGTGGATAGCCCTGTTG+TGG 0.565061 1.1:-76361652 None:intergenic
ATTAATAGGTTACCCGGCGC+CGG 0.567543 1.1:+76361573 MS.gene96699:intron
GTCGGCGTTCCTCCCCAGCA+AGG 0.585619 1.1:+76361416 MS.gene96699:CDS
TGGGGAGGAACGCCGACGGG+CGG 0.586625 1.1:-76361410 None:intergenic
GGTGGATAGCCCTGTTGTGG+AGG 0.592582 1.1:-76361649 None:intergenic
TACTGAGGAGCATATTGCGG+TGG 0.605867 1.1:-76361700 None:intergenic
AACCAACAGCAACCGCCCGT+CGG 0.612199 1.1:+76361398 MS.gene96699:CDS
GTGGAGGATATCCTGGTGGA+GGG 0.625281 1.1:-76361618 None:intergenic
AAAGATGCTTACCCTCCACC+AGG 0.636903 1.1:+76361607 MS.gene96699:CDS
CAACAGGGCTATCCACCTCA+AGG 0.638659 1.1:+76361655 MS.gene96699:CDS
GGTGGTGGCTGAGCGTACTG+AGG 0.643562 1.1:-76361715 None:intergenic
ACTGAGGAGCATATTGCGGT+GGG 0.646934 1.1:-76361699 None:intergenic
TGTTGTGGAGGGTAACCTTG+TGG 0.649835 1.1:-76361637 None:intergenic
ATAGAGGATGGACCTTGCTG+GGG 0.654237 1.1:-76361428 None:intergenic
GTGGATAGCCCTGTTGTGGA+GGG 0.654497 1.1:-76361648 None:intergenic
CAAGGTTACCCTCCACAACA+GGG 0.654753 1.1:+76361640 MS.gene96699:CDS
CCACCAGGATATCCTCCACA+AGG 0.654889 1.1:+76361622 MS.gene96699:CDS
CAAGGCTATCCTCCACAACA+GGG 0.660569 1.1:+76361673 MS.gene96699:CDS
GGTGGGTAGCCCTGTTGTGG+AGG 0.665741 1.1:-76361682 None:intergenic
GCGTACTGAGGAGCATATTG+CGG 0.667195 1.1:-76361703 None:intergenic
TGTTGTGGAGGATAGCCTTG+AGG 0.680004 1.1:-76361670 None:intergenic
TGTGGAGGATAGCCTTGAGG+TGG 0.684209 1.1:-76361667 None:intergenic
CCTCGTCAGCAAAATTCAGG+CGG 0.710460 1.1:+76361736 MS.gene96699:CDS
CCTTGTGGAGGATATCCTGG+TGG 0.714352 1.1:-76361622 None:intergenic
TGTGGAGGGTAACCTTGTGG+AGG 0.722140 1.1:-76361634 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAGATGATAAATTAACATGC+AGG - chr1.1:76361495-76361514 None:intergenic 25.0%
! AGTGATTTCATGGAATTAAT+AGG + chr1.1:76361559-76361578 MS.gene96699:intron 25.0%
! GTGTATAATATATATGCATG+CGG - chr1.1:76361460-76361479 None:intergenic 25.0%
! GTTTCAATTAAGTGATTTCA+TGG + chr1.1:76361549-76361568 MS.gene96699:intron 25.0%
CATGGAATTAATAGGTTACC+CGG + chr1.1:76361567-76361586 MS.gene96699:intron 35.0%
ATGCATGCGGTTAAGAATAG+AGG - chr1.1:76361447-76361466 None:intergenic 40.0%
ATGCGGTTAAGAATAGAGGA+TGG - chr1.1:76361443-76361462 None:intergenic 40.0%
! GCATCTTTTCCATAAGTCTC+CGG - chr1.1:76361595-76361614 None:intergenic 40.0%
AATAGAGGATGGACCTTGCT+GGG - chr1.1:76361432-76361451 None:intergenic 45.0%
TAACCTTGTGGAGGATATCC+TGG - chr1.1:76361628-76361647 None:intergenic 45.0%
AAAGATGCTTACCCTCCACC+AGG + chr1.1:76361607-76361626 MS.gene96699:CDS 50.0%
ACAAGGTTACCCTCCACAAC+AGG + chr1.1:76361639-76361658 MS.gene96699:CDS 50.0%
ATAGAGGATGGACCTTGCTG+GGG - chr1.1:76361431-76361450 None:intergenic 50.0%
ATTAATAGGTTACCCGGCGC+CGG + chr1.1:76361573-76361592 MS.gene96699:intron 50.0%
CAAGGCTATCCTCCACAACA+GGG + chr1.1:76361673-76361692 MS.gene96699:CDS 50.0%
CAAGGTTACCCTCCACAACA+GGG + chr1.1:76361640-76361659 MS.gene96699:CDS 50.0%
CCACCTCGTCAGCAAAATTC+AGG + chr1.1:76361733-76361752 MS.gene96699:CDS 50.0%
CCTCGTCAGCAAAATTCAGG+CGG + chr1.1:76361736-76361755 MS.gene96699:CDS 50.0%
GAATAGAGGATGGACCTTGC+TGG - chr1.1:76361433-76361452 None:intergenic 50.0%
TCAAGGCTATCCTCCACAAC+AGG + chr1.1:76361672-76361691 MS.gene96699:CDS 50.0%
TGTTGTGGAGGGTAACCTTG+TGG - chr1.1:76361640-76361659 None:intergenic 50.0%
! ACTGAGGAGCATATTGCGGT+GGG - chr1.1:76361702-76361721 None:intergenic 50.0%
! CCTGAATTTTGCTGACGAGG+TGG - chr1.1:76361736-76361755 None:intergenic 50.0%
! GAATTTTGCTGACGAGGTGG+TGG - chr1.1:76361733-76361752 None:intergenic 50.0%
! GCGTACTGAGGAGCATATTG+CGG - chr1.1:76361706-76361725 None:intergenic 50.0%
! TACTGAGGAGCATATTGCGG+TGG - chr1.1:76361703-76361722 None:intergenic 50.0%
! TGTTGTGGAGGATAGCCTTG+AGG - chr1.1:76361673-76361692 None:intergenic 50.0%
CAACAGGGCTATCCACCTCA+AGG + chr1.1:76361655-76361674 MS.gene96699:CDS 55.0%
CAGCAAAATTCAGGCGGTGC+TGG + chr1.1:76361742-76361761 MS.gene96699:CDS 55.0%
CCACCAGGATATCCTCCACA+AGG + chr1.1:76361622-76361641 MS.gene96699:CDS 55.0%
CCTTGTGGAGGATATCCTGG+TGG - chr1.1:76361625-76361644 None:intergenic 55.0%
GTGGAGGATATCCTGGTGGA+GGG - chr1.1:76361621-76361640 None:intergenic 55.0%
GTGGATAGCCCTGTTGTGGA+GGG - chr1.1:76361651-76361670 None:intergenic 55.0%
TGAGGTGGATAGCCCTGTTG+TGG - chr1.1:76361655-76361674 None:intergenic 55.0%
TGTGGAGGATATCCTGGTGG+AGG - chr1.1:76361622-76361641 None:intergenic 55.0%
TGTGGAGGGTAACCTTGTGG+AGG - chr1.1:76361637-76361656 None:intergenic 55.0%
TTTCCATAAGTCTCCGGCGC+CGG - chr1.1:76361589-76361608 None:intergenic 55.0%
! CCGCCTGAATTTTGCTGACG+AGG - chr1.1:76361739-76361758 None:intergenic 55.0%
! TGTGGAGGATAGCCTTGAGG+TGG - chr1.1:76361670-76361689 None:intergenic 55.0%
AACCAACAGCAACCGCCCGT+CGG + chr1.1:76361398-76361417 MS.gene96699:CDS 60.0%
GGTGGATAGCCCTGTTGTGG+AGG - chr1.1:76361652-76361671 None:intergenic 60.0%
TTCCATAAGTCTCCGGCGCC+GGG - chr1.1:76361588-76361607 None:intergenic 60.0%
!! GTGCTGGTTGCATGGAAGGC+TGG + chr1.1:76361758-76361777 MS.gene96699:CDS 60.0%
!! TTCAGGCGGTGCTGGTTGCA+TGG + chr1.1:76361750-76361769 MS.gene96699:CDS 60.0%
GAGGATGGACCTTGCTGGGG+AGG - chr1.1:76361428-76361447 None:intergenic 65.0%
GGTGGGTAGCCCTGTTGTGG+AGG - chr1.1:76361685-76361704 None:intergenic 65.0%
TGCGGTGGGTAGCCCTGTTG+TGG - chr1.1:76361688-76361707 None:intergenic 65.0%
TTGCTGGGGAGGAACGCCGA+CGG - chr1.1:76361417-76361436 None:intergenic 65.0%
! GGTGGTGGCTGAGCGTACTG+AGG - chr1.1:76361718-76361737 None:intergenic 65.0%
! TACCCGGCGCCGGAGACTTA+TGG + chr1.1:76361583-76361602 MS.gene96699:CDS 65.0%
!! GGCGGTGCTGGTTGCATGGA+AGG + chr1.1:76361754-76361773 MS.gene96699:CDS 65.0%
GTCGGCGTTCCTCCCCAGCA+AGG + chr1.1:76361416-76361435 MS.gene96699:CDS 70.0%
TGCTGGGGAGGAACGCCGAC+GGG - chr1.1:76361416-76361435 None:intergenic 70.0%
CGCCGACGGGCGGTTGCTGT+TGG - chr1.1:76361403-76361422 None:intergenic 75.0%
TGGGGAGGAACGCCGACGGG+CGG - chr1.1:76361413-76361432 None:intergenic 75.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 76361386 76361783 76361386 ID=MS.gene96699
chr1.1 mRNA 76361386 76361783 76361386 ID=MS.gene96699.t1;Parent=MS.gene96699
chr1.1 exon 76361386 76361437 76361386 ID=MS.gene96699.t1.exon1;Parent=MS.gene96699.t1
chr1.1 CDS 76361386 76361437 76361386 ID=cds.MS.gene96699.t1;Parent=MS.gene96699.t1
chr1.1 exon 76361581 76361783 76361581 ID=MS.gene96699.t1.exon2;Parent=MS.gene96699.t1
chr1.1 CDS 76361581 76361783 76361581 ID=cds.MS.gene96699.t1;Parent=MS.gene96699.t1
Gene Sequence

>MS.gene96699

ATGAGTTACTACAACCAACAGCAACCGCCCGTCGGCGTTCCTCCCCAGCAAGGTCCATCCTCTATTCTTAACCGCATGCATATATATTATACACTTCAATTCAACTCCTGCATGTTAATTTATCATCTTGATTCTCGATCTTTCTTTTTTCTTTTCAATCTTTGTTTCAATTAAGTGATTTCATGGAATTAATAGGTTACCCGGCGCCGGAGACTTATGGAAAAGATGCTTACCCTCCACCAGGATATCCTCCACAAGGTTACCCTCCACAACAGGGCTATCCACCTCAAGGCTATCCTCCACAACAGGGCTACCCACCGCAATATGCTCCTCAGTACGCTCAGCCACCACCTCGTCAGCAAAATTCAGGCGGTGCTGGTTGCATGGAAGGCTGGTAA
Protein sequence

>MS.gene96699.t1

MSYYNQQQPPVGVPPQQGYPAPETYGKDAYPPPGYPPQGYPPQQGYPPQGYPPQQGYPPQYAPQYAQPPPRQQNSGGAGCMEGW