AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1368250


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 77 sgRNAs with CRISPR-Local

Find 81 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCTGCCTCCCGTAGGAGTC+TGG 0.214220 tig0018631:-3744 Msa1368250:intron
GAAGAAACAATGACGGTATC+TGG 0.223499 tig0018631:+3857 None:intergenic
CGCTTTACGCCCAATCATTC+CGG 0.287091 tig0018631:-3942 Msa1368250:CDS
CAATGCCGCGTGGAGGTAAA+AGG 0.308793 tig0018631:+3805 None:intergenic
TCCTTTCGCTCCTCAGCTTA+CGG 0.318574 tig0018631:-3600 Msa1368250:CDS
ATCAGACGCGAGCCCCTCCT+TGG 0.323688 tig0018631:-3632 Msa1368250:CDS
CTCTGTCTTACCGCGGCTGC+TGG 0.335301 tig0018631:-3905 Msa1368250:CDS
CCTTTCGCTCCTCAGCTTAC+GGG 0.341229 tig0018631:-3599 Msa1368250:CDS
CAAGCGTTATCCGGAATGAT+TGG 0.365557 tig0018631:+3932 None:intergenic
CAGCTGTTGTTCCCCTCCCA+AGG 0.401225 tig0018631:-3559 Msa1368250:CDS
CAGAGGATGCAAGCGTTATC+CGG 0.442617 tig0018631:+3923 None:intergenic
GGTTGAGCCCTGGGATTTGA+CGG 0.443812 tig0018631:-3989 None:intergenic
CTTGGGAGGGGAACAACAGC+TGG 0.448224 tig0018631:+3560 None:intergenic
CTCGCGTCTGATTAGCTAGT+TGG 0.450357 tig0018631:+3643 None:intergenic
GTTGTTCCCCTCCCAAGGGC+AGG 0.453286 tig0018631:-3554 Msa1368250:CDS
TCAGACGCGAGCCCCTCCTT+GGG 0.455699 tig0018631:-3631 Msa1368250:CDS
GCTGCCTCCCGTAGGAGTCT+GGG 0.465822 tig0018631:-3743 Msa1368250:intron
TAAGTTCGCCGTCAAATCCC+AGG 0.467544 tig0018631:+3981 None:intergenic
TAAGAACCTGCCCTTGGGAG+GGG 0.474163 tig0018631:+3548 None:intergenic
CTCCTACGGGAGGCAGCAGT+GGG 0.476121 tig0018631:+3749 None:intergenic
AGGGGAACAACAGCTGGAAA+CGG 0.479232 tig0018631:+3566 None:intergenic
TTTACACATGCAAGTCGAAC+GGG 0.480570 tig0018631:+3488 None:intergenic
CCACGCGGCATTGCTCCGTC+AGG 0.484232 tig0018631:-3795 Msa1368250:CDS
ACTCCTACGGGAGGCAGCAG+TGG 0.491996 tig0018631:+3748 None:intergenic
AAGAAACAATGACGGTATCT+GGG 0.492143 tig0018631:+3858 None:intergenic
AACGCGTAAGAACCTGCCCT+TGG 0.497667 tig0018631:+3542 None:intergenic
AGGAGGAATCCGCCCAAGGA+GGG 0.502243 tig0018631:+3619 None:intergenic
TGGTGTTTCCAGTGGCGGAC+GGG 0.506464 tig0018631:+3514 None:intergenic
AAGCGTTATCCGGAATGATT+GGG 0.511219 tig0018631:+3933 None:intergenic
CATGCAAGTCGAACGGGAAG+TGG 0.511388 tig0018631:+3494 None:intergenic
GTTACTCACCCGTCCGCCAC+TGG 0.515654 tig0018631:-3522 Msa1368250:CDS
GTGGTGTTTCCAGTGGCGGA+CGG 0.521309 tig0018631:+3513 None:intergenic
ACGCGTAAGAACCTGCCCTT+GGG 0.530469 tig0018631:+3543 None:intergenic
AGCTGTTGTTCCCCTCCCAA+GGG 0.533909 tig0018631:-3558 Msa1368250:CDS
CGCAATGGGCGAAAGCCTGA+CGG 0.536266 tig0018631:+3780 None:intergenic
CCAAGGCGGTGATCAGTAGC+TGG 0.540351 tig0018631:+3681 None:intergenic
TAACTCTGTGCCAGCAGCCG+CGG 0.544469 tig0018631:+3895 None:intergenic
CGTAAGAACCTGCCCTTGGG+AGG 0.550231 tig0018631:+3546 None:intergenic
CCCGTAAGCTGAGGAGCGAA+AGG 0.554829 tig0018631:+3599 None:intergenic
GAGAGGATGATCAGCCACAC+TGG 0.556699 tig0018631:+3707 None:intergenic
GTAAGAACCTGCCCTTGGGA+GGG 0.557080 tig0018631:+3547 None:intergenic
GCGTGGAGGTAAAAGGCCTA+CGG 0.560249 tig0018631:+3812 None:intergenic
GGAGGAATCCGCCCAAGGAG+GGG 0.562553 tig0018631:+3620 None:intergenic
AAGTTCGCCGTCAAATCCCA+GGG 0.564420 tig0018631:+3982 None:intergenic
CGTGGAGGTAAAAGGCCTAC+GGG 0.570032 tig0018631:+3813 None:intergenic
GACGCGAGCCCCTCCTTGGG+CGG 0.572606 tig0018631:-3628 Msa1368250:CDS
CTTTCGCTCCTCAGCTTACG+GGG 0.577687 tig0018631:-3598 Msa1368250:CDS
CCAGCTACTGATCACCGCCT+TGG 0.578071 tig0018631:-3681 Msa1368250:CDS
CGTCAGGCTTTCGCCCATTG+CGG 0.587223 tig0018631:-3779 Msa1368250:CDS
GGGCGTAAAGCGTCTGTAGG+TGG 0.587281 tig0018631:+3953 None:intergenic
AGTGTGGCTGATCATCCTCT+CGG 0.593369 tig0018631:-3705 Msa1368250:CDS
CGAAAGGAGGAATCCGCCCA+AGG 0.596152 tig0018631:+3615 None:intergenic
CTTTACACATGCAAGTCGAA+CGG 0.597034 tig0018631:+3487 None:intergenic
TCCTGGCTCAGGATGAACGC+TGG 0.603603 tig0018631:+3457 None:intergenic
AGAGGATGATCAGCCACACT+GGG 0.612353 tig0018631:+3708 None:intergenic
TGCTAATACCCCGTAAGCTG+AGG 0.615470 tig0018631:+3590 None:intergenic
GGTATCTGGGGAATAAGCAT+CGG 0.620214 tig0018631:+3871 None:intergenic
ACGGGAAGTGGTGTTTCCAG+TGG 0.620953 tig0018631:+3506 None:intergenic
AAGGAGGAATCCGCCCAAGG+AGG 0.622334 tig0018631:+3618 None:intergenic
GGAAGTGGTGTTTCCAGTGG+CGG 0.627120 tig0018631:+3509 None:intergenic
TCCTGGAGAAGAAACAATGA+CGG 0.628601 tig0018631:+3850 None:intergenic
GCCACACTGGGACTGAGACA+AGG 0.629204 tig0018631:+3720 None:intergenic
ATTGGGCGTAAAGCGTCTGT+AGG 0.632255 tig0018631:+3950 None:intergenic
GACGGAGCAATGCCGCGTGG+AGG 0.640730 tig0018631:+3798 None:intergenic
GTCTGATTAGCTAGTTGGTG+AGG 0.641304 tig0018631:+3648 None:intergenic
CAGCAGCCGCGGTAAGACAG+AGG 0.650015 tig0018631:+3906 None:intergenic
TGGCTCAGGATGAACGCTGG+CGG 0.650788 tig0018631:+3460 None:intergenic
AAAAGAAGTTCATGACCCGT+AGG 0.653857 tig0018631:-3828 Msa1368250:CDS
GTAAGCTGAGGAGCGAAAGG+AGG 0.654589 tig0018631:+3602 None:intergenic
GCCTTGTCTCAGTCCCAGTG+TGG 0.654955 tig0018631:-3721 Msa1368250:CDS
AGAAACAATGACGGTATCTG+GGG 0.658343 tig0018631:+3859 None:intergenic
TGATCAGTAGCTGGTCCGAG+AGG 0.705254 tig0018631:+3690 None:intergenic
CCTGACGGAGCAATGCCGCG+TGG 0.711882 tig0018631:+3795 None:intergenic
GGTGAGGTAATAGCTTACCA+AGG 0.724474 tig0018631:+3664 None:intergenic
GAGGTAATAGCTTACCAAGG+CGG 0.748896 tig0018631:+3667 None:intergenic
TTGCATCCTCTGTCTTACCG+CGG 0.760348 tig0018631:-3912 Msa1368250:CDS
TCCTACGGGAGGCAGCAGTG+GGG 0.779333 tig0018631:+3750 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAGAAACAATGACGGTATCT+GGG + tig0018631:3592-3611 None:intergenic 35.0%
AAGCGTTATCCGGAATGATT+GGG + tig0018631:3517-3536 None:intergenic 40.0%
AGAAACAATGACGGTATCTG+GGG + tig0018631:3591-3610 None:intergenic 40.0%
GAAGAAACAATGACGGTATC+TGG + tig0018631:3593-3612 None:intergenic 40.0%
TCCTGGAGAAGAAACAATGA+CGG + tig0018631:3600-3619 None:intergenic 40.0%
AAAAGAAGTTCATGACCCGT+AGG - tig0018631:3619-3638 Msa1368250:CDS 40.0%
TTTACACATGCAAGTCGAAC+GGG + tig0018631:3962-3981 None:intergenic 40.0%
CTTTACACATGCAAGTCGAA+CGG + tig0018631:3963-3982 None:intergenic 40.0%
CAAGCGTTATCCGGAATGAT+TGG + tig0018631:3518-3537 None:intergenic 45.0%
GGTATCTGGGGAATAAGCAT+CGG + tig0018631:3579-3598 None:intergenic 45.0%
! ACCGTCATTGTTTCTTCTCC+AGG - tig0018631:3596-3615 Msa1368250:CDS 45.0%
! GGGTCATGAACTTCTTTTCC+TGG + tig0018631:3617-3636 None:intergenic 45.0%
! AGTGGGGAATTTTCCGCAAT+GGG + tig0018631:3684-3703 None:intergenic 45.0%
GAGGTAATAGCTTACCAAGG+CGG + tig0018631:3783-3802 None:intergenic 45.0%
GGTGAGGTAATAGCTTACCA+AGG + tig0018631:3786-3805 None:intergenic 45.0%
! GTCTGATTAGCTAGTTGGTG+AGG + tig0018631:3802-3821 None:intergenic 45.0%
! ATTGGGCGTAAAGCGTCTGT+AGG + tig0018631:3500-3519 None:intergenic 50.0%
CGCTTTACGCCCAATCATTC+CGG - tig0018631:3505-3524 Msa1368250:CDS 50.0%
CAGAGGATGCAAGCGTTATC+CGG + tig0018631:3527-3546 None:intergenic 50.0%
TTGCATCCTCTGTCTTACCG+CGG - tig0018631:3535-3554 Msa1368250:CDS 50.0%
! CAGTGGGGAATTTTCCGCAA+TGG + tig0018631:3685-3704 None:intergenic 50.0%
AGAGGATGATCAGCCACACT+GGG + tig0018631:3742-3761 None:intergenic 50.0%
AGTGTGGCTGATCATCCTCT+CGG - tig0018631:3742-3761 Msa1368250:intron 50.0%
! CTCGCGTCTGATTAGCTAGT+TGG + tig0018631:3807-3826 None:intergenic 50.0%
TCCTTTCGCTCCTCAGCTTA+CGG - tig0018631:3847-3866 Msa1368250:intron 50.0%
TGCTAATACCCCGTAAGCTG+AGG + tig0018631:3860-3879 None:intergenic 50.0%
AGGGGAACAACAGCTGGAAA+CGG + tig0018631:3884-3903 None:intergenic 50.0%
CGTGGAGGTAAAAGGCCTAC+GGG + tig0018631:3637-3656 None:intergenic 55.0%
GCGTGGAGGTAAAAGGCCTA+CGG + tig0018631:3638-3657 None:intergenic 55.0%
! GTAGGCCTTTTACCTCCACG+CGG - tig0018631:3637-3656 Msa1368250:CDS 55.0%
CAATGCCGCGTGGAGGTAAA+AGG + tig0018631:3645-3664 None:intergenic 55.0%
AGACAAGGCCCAGACTCCTA+CGG + tig0018631:3715-3734 None:intergenic 55.0%
GAGAGGATGATCAGCCACAC+TGG + tig0018631:3743-3762 None:intergenic 55.0%
TGATCAGTAGCTGGTCCGAG+AGG + tig0018631:3760-3779 None:intergenic 55.0%
GTAAGCTGAGGAGCGAAAGG+AGG + tig0018631:3848-3867 None:intergenic 55.0%
CCTTTCGCTCCTCAGCTTAC+GGG - tig0018631:3848-3867 Msa1368250:intron 55.0%
CTTTCGCTCCTCAGCTTACG+GGG - tig0018631:3849-3868 Msa1368250:intron 55.0%
AGCTGTTGTTCCCCTCCCAA+GGG - tig0018631:3889-3908 Msa1368250:CDS 55.0%
TAAGAACCTGCCCTTGGGAG+GGG + tig0018631:3902-3921 None:intergenic 55.0%
GTAAGAACCTGCCCTTGGGA+GGG + tig0018631:3903-3922 None:intergenic 55.0%
ACGCGTAAGAACCTGCCCTT+GGG + tig0018631:3907-3926 None:intergenic 55.0%
AACGCGTAAGAACCTGCCCT+TGG + tig0018631:3908-3927 None:intergenic 55.0%
GGAAGTGGTGTTTCCAGTGG+CGG + tig0018631:3941-3960 None:intergenic 55.0%
ACGGGAAGTGGTGTTTCCAG+TGG + tig0018631:3944-3963 None:intergenic 55.0%
CATGCAAGTCGAACGGGAAG+TGG + tig0018631:3956-3975 None:intergenic 55.0%
! GGGCGTAAAGCGTCTGTAGG+TGG + tig0018631:3497-3516 None:intergenic 60.0%
TAACTCTGTGCCAGCAGCCG+CGG + tig0018631:3555-3574 None:intergenic 60.0%
CGCAATGGGCGAAAGCCTGA+CGG + tig0018631:3670-3689 None:intergenic 60.0%
CGTCAGGCTTTCGCCCATTG+CGG - tig0018631:3668-3687 Msa1368250:CDS 60.0%
GACAAGGCCCAGACTCCTAC+GGG + tig0018631:3714-3733 None:intergenic 60.0%
GCCTTGTCTCAGTCCCAGTG+TGG - tig0018631:3726-3745 Msa1368250:CDS 60.0%
GCCACACTGGGACTGAGACA+AGG + tig0018631:3730-3749 None:intergenic 60.0%
CCAAGGCGGTGATCAGTAGC+TGG + tig0018631:3769-3788 None:intergenic 60.0%
CCAGCTACTGATCACCGCCT+TGG - tig0018631:3766-3785 Msa1368250:CDS 60.0%
AGGAGGAATCCGCCCAAGGA+GGG + tig0018631:3831-3850 None:intergenic 60.0%
AAGGAGGAATCCGCCCAAGG+AGG + tig0018631:3832-3851 None:intergenic 60.0%
CGAAAGGAGGAATCCGCCCA+AGG + tig0018631:3835-3854 None:intergenic 60.0%
CCCGTAAGCTGAGGAGCGAA+AGG + tig0018631:3851-3870 None:intergenic 60.0%
CTTGGGAGGGGAACAACAGC+TGG + tig0018631:3890-3909 None:intergenic 60.0%
CAGCTGTTGTTCCCCTCCCA+AGG - tig0018631:3888-3907 Msa1368250:CDS 60.0%
CGTAAGAACCTGCCCTTGGG+AGG + tig0018631:3904-3923 None:intergenic 60.0%
!! TGGTGTTTCCAGTGGCGGAC+GGG + tig0018631:3936-3955 None:intergenic 60.0%
! GTGGTGTTTCCAGTGGCGGA+CGG + tig0018631:3937-3956 None:intergenic 60.0%
CAGCAGCCGCGGTAAGACAG+AGG + tig0018631:3544-3563 None:intergenic 65.0%
CTCTGTCTTACCGCGGCTGC+TGG - tig0018631:3542-3561 Msa1368250:CDS 65.0%
TCCTACGGGAGGCAGCAGTG+GGG + tig0018631:3700-3719 None:intergenic 65.0%
CTCCTACGGGAGGCAGCAGT+GGG + tig0018631:3701-3720 None:intergenic 65.0%
ACTCCTACGGGAGGCAGCAG+TGG + tig0018631:3702-3721 None:intergenic 65.0%
TGCTGCCTCCCGTAGGAGTC+TGG - tig0018631:3703-3722 Msa1368250:CDS 65.0%
GCTGCCTCCCGTAGGAGTCT+GGG - tig0018631:3704-3723 Msa1368250:CDS 65.0%
AAGGCCCAGACTCCTACGGG+AGG + tig0018631:3711-3730 None:intergenic 65.0%
ATCAGACGCGAGCCCCTCCT+TGG - tig0018631:3815-3834 Msa1368250:CDS 65.0%
TCAGACGCGAGCCCCTCCTT+GGG - tig0018631:3816-3835 Msa1368250:CDS 65.0%
GGAGGAATCCGCCCAAGGAG+GGG + tig0018631:3830-3849 None:intergenic 65.0%
GTTGTTCCCCTCCCAAGGGC+AGG - tig0018631:3893-3912 Msa1368250:CDS 65.0%
GTTACTCACCCGTCCGCCAC+TGG - tig0018631:3925-3944 Msa1368250:CDS 65.0%
GACGGAGCAATGCCGCGTGG+AGG + tig0018631:3652-3671 None:intergenic 70.0%
CCTGACGGAGCAATGCCGCG+TGG + tig0018631:3655-3674 None:intergenic 70.0%
CCACGCGGCATTGCTCCGTC+AGG - tig0018631:3652-3671 Msa1368250:CDS 70.0%
TCCCCACTGCTGCCTCCCGT+AGG - tig0018631:3696-3715 Msa1368250:CDS 70.0%
GACGCGAGCCCCTCCTTGGG+CGG - tig0018631:3819-3838 Msa1368250:CDS 75.0%
Chromosome Type Strat End Strand Name
tig0018631 gene 3467 4002 3467 ID=Msa1368250;Name=Msa1368250
tig0018631 mRNA 3467 4002 3467 ID=Msa1368250-mRNA-1;Parent=Msa1368250;Name=Msa1368250-mRNA-1;_AED=0.42;_eAED=0.44;_QI=0|0|0|1|0|0|3|0|173
tig0018631 exon 3865 4002 3865 ID=Msa1368250-mRNA-1:exon:398;Parent=Msa1368250-mRNA-1
tig0018631 exon 3756 3851 3756 ID=Msa1368250-mRNA-1:exon:397;Parent=Msa1368250-mRNA-1
tig0018631 exon 3467 3751 3467 ID=Msa1368250-mRNA-1:exon:396;Parent=Msa1368250-mRNA-1
tig0018631 CDS 3865 4002 3865 ID=Msa1368250-mRNA-1:cds;Parent=Msa1368250-mRNA-1
tig0018631 CDS 3756 3851 3756 ID=Msa1368250-mRNA-1:cds;Parent=Msa1368250-mRNA-1
tig0018631 CDS 3467 3751 3467 ID=Msa1368250-mRNA-1:cds;Parent=Msa1368250-mRNA-1
Gene Sequence

>Msa1368250

CTGGGATTTGACGGCGAACTTAAAAAGCCACCTACAGACGCTTTACGCCCAATCATTCCGGATAACGCTTGCATCCTCTGTCTTACCGCGGCTGCTGGCACAGAGTTAGCCGATGCTTATTCCCCAGATACCGTCATTGAAAAGAAGTTCATGACCCGTAGGCCTTTTACCTCCACGCGGCATTGCTCCGTCAGGCTTTCGCCCATTGCGGAAAATTCCCCACTGCTGCCTCCCGAGTCTGGGCCTTGTCTCAGTCCCAGTGTGGCTGATCATCCTCTCGGACCAGCTACTGATCACCGCCTTGGTAAGCTATTACCTCACCAACTAGCTAATCAGACGCGAGCCCCTCCTTGGGCGGATTCCTCCTTTCGCTCCTCAGCTTACGGGGTATTAGCAGCCGTTTCCAGCTGTTGTTCCCCTCCCAAGGGCAGGTTCTTACGCGTTACTCACCCGTCCGCCACTGGAAACACCACTTCCCGTTCGACTTGCATGTGTAAAGCATGCCGCCAGCGTTCATCC

Protein sequence

>Msa1368250

LGFDGELKKPPTDALRPIIPDNACILCLTAAAGTELADAYSPDTVIEKKFMTRRPFTSTRHCSVRLSPIAENSPLLPPESGPCLSPSVADHPLGPATDHRLGKLLPHQLANQTRAPPWADSSFRSSAYGVLAAVSSCCSPPKGRFLRVTHPSATGNTTSRSTCMCKACRQRSS